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PubMed2003

Pattern identification and classification in gene expression data using an autoassociative neural network model.

The application of DNA microarray technology for analysis of gene expression creates enormous opportunities to accelerate the pace in understanding living systems and identification of target genes and pathways for drug development and therapeutic intervention. Parallel monitoring of the expression profiles of thousands of genes seems particularly promising for a deeper understanding of cancer biology and the identification of molecular signatures supporting the histological classification schemes of neoplastic specimens. However, the increasing volume of data generated by microarray experiments poses the challenge of developing equally efficient methods and analysis procedures to extract, interpret, and upgrade the information content of these databases. Herein, a computational procedure for pattern identification, feature extraction, and classification of gene expression data through the analysis of an autoassociative neural network model is described. The identified patterns and features contain critical information about gene-phenotype relationships observed during changes in cell physiology. They represent a rational and dimensionally reduced base for understanding the basic biology of the onset of diseases, defining targets of therapeutic intervention, and developing diagnostic tools for the identification and classification of pathological states. The proposed method has been tested on two different microarray datasets-Golub's analysis of acute human leukemia [Golub et al. (1999) Science 286:531-537], and the human colon adenocarcinoma study presented by Alon et al. [1999; Proc Natl Acad Sci USA 97:10101-10106]. The analysis of the neural network internal structure allows the identification of specific phenotype markers and the extraction of peculiar associations among genes and physiological states. At the same time, the neural network outputs provide assignment to multiple classes, such as different pathological conditions or tissue samples, for previously unseen instances.

Adenocarcinoma↗
PubMed2005

Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?

Taxon sampling may be critically important for phylogenetic accuracy because adding taxa can help to subdivide misleading long branches. Although the idea that added taxa can break up long branches was exemplified by a study of "incomplete" fossil taxa, the issue of taxon completeness (i.e., proportion of missing data) has been largely ignored in most subsequent discussions of taxon sampling and long-branch attraction. In this article, I use simulations to test the ability of incomplete taxa to subdivide long branches and improve phylogenetic accuracy in situations of potential long-branch attraction. The results show that for most methods and conditions examined, adding taxa that are only 50% complete may provide similar benefits to adding the same number of complete taxa (suggesting that the advantages of increased taxon sampling may be obtained with less data than previously considered). For parsimony, taxa that are less complete (5% to 25% complete) may often have limited ability to rescue analyses from long-branch attraction. In contrast, highly incomplete taxa can be surprisingly beneficial when using model-based methods. The results also suggest the importance of model-based methods in phylogenetic analyses that combine molecular and fossil data.

Classification↗
PubMed2005

Genetic characterization of the lobster pathogen Aerococcus viridans var. homari by 16S rRNA gene sequence and RAPD.

A combination of 16S rRNA sequencing and random amplified polymorphic DNA (RAPD) analysis was used to evaluate the genetic diversity within Aerococcus viridans var. homari, the causative agent of gaffkemia in lobsters. A collection of 7 A. viridans var. homari strains and 2 avirulent A. viridans-like cocci isolated from homarid lobsters harvested from different regions on the Atlantic Coast of North America were analyzed. The isolates are separated geographically and temporally between the years 1947 and 2000. Sequencing of 16S rRNA genes confirmed the inclusion of all 9 isolates in the monophyletic A. viridans clade (99.8 to 100% similarity). RAPD analysis revealed that the 9 A. viridans var. homari isolates could be separated into 2 distinct subtypes. Subtype 1 included the 7 pathogenic lobster isolates and constituted a homogeneous group regardless of their geographical, temporal or virulence differences. Subtype 2 contained the 2 avirulent A. viridans-like cocci that had distinct RAPD patterns and clustered separately with the non-marine A. viridans. RAPD analysis represented a useful method for determining molecular subtyping for the intraspecific classification and epidemiological investigations of A. viridans var. homari.

Animals↗
PubMed1998

Risk factors for high-grade cervical intraepithelial neoplasia in patients with mild cytological dyskaryosis: human papillomavirus testing versus multivariate tree analysis of demographic data.

The objective of this study was to compare the use of molecular hybridization by hybrid capture methodology for human papillomavirus (HPV) with the use of demographic and lifestyle variables as intermediate triage in patients with cytological mild dyskaryosis. The study was designed as a prospective study using regression tree analysis of demographic data in consecutive patients who were subjected to colposcopic evaluation at the colposcopy clinic at the First Department of Obstetrics and Gynaecology, University of Milan (Milan, Italy). A total of 177 women were subjected to colposcopy because of a single routine Pap smear showing mild dyskaryosis. A structured interview, sampling for HPV testing for the detection of viral DNA by hybrid capture methodology, and colposcopic evaluation with cervical biopsies were performed for each subject. The accuracies of molecular hybridization for HPV and of the classification model based on the demographic and lifestyle variables in predicting patients with histologically high-grade cervical intraepithelial lesions were measured. The classification model based on the demographic and lifestyle variables showed comparable results with molecular hybridization for HPV (specificity, 0.75 versus 0.73; sensitivity, 0.61 versus 0.67, respectively). The use of demographic and lifestyle variables appears to be a simple and economic possibility for triaging patients with mild dyskaryotic smears in a screening program.

Adult↗
PubMed2006

Evaluation of recA gene as a phylogenetic marker in the classification of dairy propionibacteria.

The aim of this study was to investigate the validity of recA gene as a molecular marker for the reliable discrimination and classification of dairy propionibacteria and the closely related species. Regions of the recA gene, varying in size between 613 and 677 nucleotides, were sequenced for Propionibacterium acidipropionici, P. cyclohexanicum, P. freudenreichii, P. jensenii, P. microaerophilum and P. thoenii using degenerate consensus primers constructed by aligning recA sequences of some actinobacteria. The 16S rRNA encoding genes for the type and reference strains of the species P. acidipropionici, P. jensenii and P. thoenii were also sequenced to remove ambiguous positions present in the current database reports, such to improve the classification scheme of reference. As found for other bacterial species, recA sequences permitted a better distinction among the dairy propionibacteria considered than 16S rRNA gene. However, the topology of phylogenetic trees constructed on the recA gene regions sequenced and their putative translations appeared rather different and less statistically valid than the 16S rRNA gene tree. In addition, the possibility of designing PCR-based identification and detection tests on the new recA sequences was demonstrated by assessing specific amplification protocols for P. cyclohexanicum and P. microaerophilum.

DNA, Bacterial↗
PubMed1996

Molecular biology and evolution of resistance of toxicants.

To the prevailing biochemical/physiological classification of mechanisms of organismal resistance to toxicants, an additional molecular dimension is proposed. Predictions are developed regarding the relative prevalence of different classes of mutations and are found to compare favorably with reports from the literature. In particular, point mutations in target loci were the dominant form of resistance for both lab and field selection. Amplifications of target loci were less common than structural mutations, and more common for lab-selected than for field-selected strains. Amplification was the most common mechanism of up-regulation of metabolizing enzymes. In comparison, only one mutation involving cis-regulation and several involving trans-acting regulation were found. Mutations involving gene disruption and down-regulation were uncommon, but were found in appropriate cases, i.e., when toxicants stimulated rather than inhibited target function and when metabolizing enzymes converted toxicants into more toxic metabolites. Additional phenomena of likely but uncertain importance are genetic "succession," recombinational limitation, and negative cross-resistance. More work on these phenomena and on quantification of fitness costs of resistance is recommended.

Animal Population Groups↗
PubMed2006

Protein classification using ontology classification.

MOTIVATION: The classification of proteins expressed by an organism is an important step in understanding the molecular biology of that organism. Traditionally, this classification has been performed by human experts. Human knowledge can recognise the functional properties that are sufficient to place an individual gene product into a particular protein family group. Automation of this task usually fails to meet the 'gold standard' of the human annotator because of the difficult recognition stage. The growing number of genomes, the rapid changes in knowledge and the central role of classification in the annotation process, however, motivates the need to automate this process. RESULTS: We capture human understanding of how to recognise members of the protein phosphatases family by domain architecture as an ontology. By describing protein instances in terms of the domains they contain, it is possible to use description logic reasoners and our ontology to assign those proteins to a protein family class. We have tested our system on classifying the protein phosphatases of the human and Aspergillus fumigatus genomes and found that our knowledge-based, automatic classification matches, and sometimes surpasses, that of the human annotators. We have made the classification process fast and reproducible and, where appropriate knowledge is available, the method can potentially be generalised for use with any protein family. AVAILABILITY: All components described in this paper are freely available. OWL ontology http://www.bioinf.man.ac.uk/phosphabase myGrid http://www.mygrid.org.uk Instance Store http://instancestore.man.ac.uk.

Algorithms↗
PubMed2005

Distinct allelic variants of TSC1 and TSC2 in epilepsy-associated cortical malformations without balloon cells.

Epilepsy-associated malformations of cortical development (MCDs) comprise a variety of dysplastic and neoplastic lesions of yet undetermined molecular pathology. Histopathologic similarities between MCDs and dysplastic brain lesions in the autosomal inherited neurocutaneous phacomatosis tuberous sclerosis (TSC), which affects the TSC1 and/or TSC2 genes, suggest common pathogenetic mechanisms. Previous studies revealed different alterations of TSC1 and TSC2 in epilepsy-associated malformations and glio-neuronal tumors despite histopathologic similarities. In order to examine current clinico-pathologic classification systems of cortical malformations on the molecular level, we carried out a mutational analysis of TSC1 and TSC2 in a series of surgical specimens obtained from patients with FCD without Taylor type balloon cells (FCDIIa; n = 20), architectural dysplasias (FCDI; n = 15), nodular cortical heterotopias (NCH; n = 4), and heterotopic white matter neurons (WMNH; n = 19). In FCDIIa, abundant genomic polymorphisms were detected in TSC2 (intron 4) but no allelic variants observed in exon 17 of TSC1. This allelic distribution pattern is in contrast to findings in FCDI and WMNH but also to those previously reported in FCDIIb (Taylor's balloon cell type). The latter revealed increased frequencies of specific alleles only in TSC1. The determination of characteristic molecular genetic alterations in specific epilepsy-associated malformations will support a comprehensive clinico-pathologic classification system and help to identify molecular pathways with potential pathogenetic relevance. Our work is supported by DFG (SFB TR3 [AJB], DFG Bl 421/1-1 [IB]), BONFOR, and Deutsche Krebshilfe.

Alleles↗
PubMed2006

Phylogenetic relationships and historical biogeography of neotropical parrots (Psittaciformes: Psittacidae: Arini) inferred from mitochondrial and nuclear DNA sequences.

Previous hypotheses of phylogenetic relationships among Neotropical parrots were based on limited taxon sampling and lacked support for most internal nodes. In this study we increased the number of taxa (29 species belonging to 25 of the 30 genera) and gene sequences (6388 base pairs of RAG-1, cyt b, NADH2, ATPase 6, ATPase 8, COIII, 12S rDNA, and 16S rDNA) to obtain a stronger molecular phylogenetic hypothesis for this group of birds. Analyses of the combined gene sequences using maximum likelihood and Bayesian methods resulted in a well-supported phylogeny and indicated that amazons and allies are a sister clade to macaws, conures, and relatives, and these two clades are in turn a sister group to parrotlets. Key morphological and behavioral characters used in previous classifications were mapped on the molecular tree and were phylogenetically uninformative. We estimated divergence times of taxa using the molecular tree and Bayesian and penalized likelihood methods that allow for rate variation in DNA substitutions among sites and taxa. Our estimates suggest that the Neotropical parrots shared a common ancestor with Australian parrots 59 Mya (million of years ago; 95% credibility interval (CrI) 66, 51 Mya), well before Australia separated from Antarctica and South America, implying that ancestral parrots were widespread in Gondwanaland. Thus, the divergence of Australian and Neotropical parrots could be attributed to vicariance. The three major clades of Neotropical parrots originated about 50 Mya (95% CrI 57, 41 Mya), coinciding with periods of higher sea level when both Antarctica and South America were fragmented with transcontinental seaways, and likely isolated the ancestors of modern Neotropical parrots in different regions in these continents. The correspondence between major paleoenvironmental changes in South America and the diversification of genera in the clade of amazons and allies between 46 and 16 Mya suggests they diversified exclusively in South America. Conversely, ancestors of parrotlets and of macaws, conures, and allies may have been isolated in Antarctica and/or the southern cone of South America, and only dispersed out of these southern regions when climate cooled and Antarctica became ice-encrusted about 35 Mya. The subsequent radiation of macaws and their allies in South America beginning about 28 Mya (95% CrI 22, 35 Mya) coincides with the uplift of the Andes and the subsequent formation of dry, open grassland habitats that would have facilitated ecological speciation via niche expansion from forested habitats.

Animals↗
PubMed2002

The World Health Organization classification of malignant lymphoma: incidence and clinical prognosis in HTLV-1-endemic area of Fukuoka.

New insights into the pathogenesis of lymphoid malignancies have been gained through novel genetic, molecular and immunological techniques. A new classification system for lymphoid malignancies, known as the new World Health Organization (WHO) classification, has been proposed recently based on these findings. The relative incidence of the subtypes of malignant lymphoma is known to differ according to geographic location. Adult T-cell leukemia/lymphoma (ATLL) is a human malignancy associated with human T-cell leukemia virus type 1 (HTLV-1), and the Kyushu islands are an HTLV-1 endemic area. To clarify the relationship between the histological classification and prognosis of lymphoid malignancies, we reclassified previous cases in our department and summarized our previous reports using the WHO classification. Of 933 cases of lymphoid malignancies, 471 (50%) were B-cell lymphoma, 396 (42%) T/natural killer (NK)-cell lymphoma and 41 (4%) Hodgkin lymphoma (HL). Analysis of clinical outcome showed favorable prognosis for HL, intermediate for B-cell lymphoma and poor prognosis for T-cell lymphoma. Among B-cell lymphomas, the commonest type was diffuse large B-cell lymphoma (n = 281; 60%). Marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT) was diagnosed in 82 cases (17%), follicular lymphoma in 52 (11%) and mantle cell lymphoma in 24 (5%). Other less common lymphomas were Burkitt lymphoma (n = 9; 2%) and lymphoblastic lymphoma (n = 5; 1%). Using overall survival rates, the various B-cell lymphoma types could be divided into three broad groups for prognostic purposes: (i) low-risk group comprising follicular lymphoma and MALT; (ii) intermediate-risk group comprising diffuse large B-cell lymphoma and Burkitt lymphoma; and (iii) high-risk group comprising mantle cell lymphoma and lymphoblastic lymphoma. Among the T/NK-cell lymphomas, the commonest type was ATLL (n = 191; 48%), followed by peripheral T-cell lymphoma, unspecified (n = 83; 21%), angioimmunoblastic lymphadenopathy with dysproteinemia (AILD) (n = 38; 10%), anaplastic large cell lymphoma (ALCL) (n = 22; 6%). Less common types were lymphoblastic lymphoma (n = 17; 4%), nasal and nasal-type NK/T-cell lymphoma (n = 17; 4%), mycosis fungoides (MF) (n = 9; 2%) and other rare types. With respect to clinical prognosis, T/NK-cell lymphomas fell into three groups: (i) relative low-risk group comprising ALCL, AILD, MF and lymphoblastic lymphoma; (ii) relative intermediate-risk group comprising NK/T-cell lymphoma and unspecified lymphoma; and (iii) extremely high-risk group comprising ATLL. Among the lymphoblastic lymphomas, B-cell type and T-cell type lymphomas exhibited different clinical outcomes. We conclude that the histological, phenotypic and genotypic classification of the new WHO system should be beneficial for the clinical approach to these tumors.

Endemic Diseases↗
PubMed1999

Molecular mechanism of retention in reversed-phase high-performance liquid chromatography and classification of modern stationary phases by using quantitative structure-retention relationships.

Quantitative structure-retention relationships (QSRRs) were derived for logarithms of retention factors normalised to a hypothetical zero percent organic modifier eluent, log kw, determined on 18 reversed-phase high-performance liquid chromatography (RP-HPLC) columns for 25 carefully designed, structurally diverse test analytes. The study was aimed at elucidating molecular mechanism of retention and at finding an objective manner of quantitative comparison of retention properties and classification of modern stationary phases for RP-HPLC. Three QSRR approaches were employed: (i) relating log kw to logarithms of octanol-water partition coefficient (log P); (ii) describing log kw in terms of linear solvation-energy relationship-based parameters of Abraham; (iii) regressing log kw against simple structural descriptors acquired by calculation chemistry. All the approaches produced statistically significant and physically interpretable QSRRs. By means of QSRRs the stationary phase materials were classified according to the prevailing intermolecular interactions in the separation process. Hydrophobic properties of the columns tested were parametrized. Abilities of individual phases to provide contributions to the overall retention due to non-polar London-type intermolecular interactions were quantified. Measures of hydrogen-bond donor activity and dipolarity of stationary phases are proposed along with two other phase polarity parameters. The parameters proposed quantitatively characterize the RP-HPLC stationary phases and provide a rational explanation for the differences in retention patterns of individual columns observed when applying the conventional empirical testing methods.

Chromatography, High Pressure Liquid↗
PubMed1986

Patterns of reaction of monoclonal antibodies HMFG-1 and -2 with benign breast tissues and breast carcinomas.

The monoclonal antibodies HMFG-1 and HMFG-2 are directed against different epitopes on a large molecule in the human milk fat globule and are also expressed on breast tumors. Here we examine the relative intensity of staining of the two antibodies in formalin fixed paraffin embedded tissue sections from malignant and benign mammary lesions. Most ductal carcinomas and their lymph node metastases stained more strongly with HMFG-2 whereas primary lobular carcinomas are more variable but the majority of their lymph node metastases stained more strongly with HMFG-1. Western blots of gel separated extracts of formalin fixed, paraffin embedded tumor tissue, stained with the antibodies in an ELISA assay, show that the molecular weight of components expressing the antigenic determinants varies. Smaller molecular weight components recognised by HMFG-2 and present in metastatic tumors may be lost during tissue processing. To assess the importance of the molecular weight parameter in tumor classification and prognosis it will be necessary to use frozen tissue.

Antibodies, Monoclonal↗
PubMed2006

New insights into myosin evolution and classification.

Myosins are eukaryotic actin-dependent molecular motors important for a broad range of functions like muscle contraction, vision, hearing, cell motility, and host cell invasion of apicomplexan parasites. Myosin heavy chains consist of distinct head, neck, and tail domains and have previously been categorized into 18 different classes based on phylogenetic analysis of their conserved heads. Here we describe a comprehensive phylogenetic examination of many previously unclassified myosins, with particular emphasis on sequences from apicomplexan and other chromalveolate protists including the model organism Toxoplasma, the malaria parasite Plasmodium, and the ciliate Tetrahymena. Using different phylogenetic inference methods and taking protein domain architectures, specific amino acid polymorphisms, and organismal distribution into account, we demonstrate a hitherto unrecognized common origin for ciliate and apicomplexan class XIV myosins. Our data also suggest common origins for some apicomplexan myosins and class VI, for classes II and XVIII, for classes XII and XV, and for some microsporidian myosins and class V, thereby reconciling evolutionary history and myosin structure in several cases and corroborating the common coevolution of myosin head, neck, and tail domains. Six novel myosin classes are established to accommodate sequences from chordate metazoans (class XIX), insects (class XX), kinetoplastids (class XXI), and apicomplexans and diatom algae (classes XXII, XXIII, and XXIV). These myosin (sub)classes include sequences with protein domains (FYVE, WW, UBA, ATS1-like, and WD40) previously unknown to be associated with myosin motors. Regarding the apicomplexan "myosome," we significantly update class XIV classification, propose a systematic naming convention, and discuss possible functions in these parasites.

Animals↗
PubMed2026

IASLC Update on Classification of Pulmonary Neuroendocrine Neoplasms.

Since the publication of the 2021 WHO classification of thoracic tumors, our knowledge of pulmonary neuroendocrine neoplasms (NENs) has expanded significantly, particularly through the elucidation of molecular pathways and proposals to refine histopathologic classification. This expanded knowledge across all aspects of pulmonary NENs holds promise for more precise stratification of neuroendocrine tumors (NETs) and the potential development of novel, subtype-specific therapeutic strategies for all NENs. Based on our comprehensive review of the current pulmonary NEN landscape, our multidisciplinary expert panel has deliberated on the modification and updating of the 2021 classification, resulting in the proposal of a new pulmonary carcinoid/NET classification presented in this position paper, which incorporates the following three major points: (1) The proposed framework continues the shift from the traditional carcinoid terminology toward broader adoption of the "NET" nomenclature as found in other organ systems while retaining the term "carcinoid" as the primary diagnostic term to ensure clear communication with thoracic clinical providers. (2) Ki-67 has been incorporated as a diagnostic criterion, aligning with practices in other NET classifications. (3) There is formal recognition of the concept of "carcinoid/NET G3," a rare subset of lung carcinoids characterized by increased proliferative activity but with molecular features more aligned with pulmonary NETs than with high-grade neuroendocrine carcinomas. This position paper on the current knowledge of pulmonary NENs, including the proposed carcinoid/NET classification, will aid in accurate tumor categorization and guide treatment strategies.

Carcinoid tumor↗
PubMed2006

A phylogeny for the Cisticolidae (Aves: Passeriformes) based on nuclear and mitochondrial DNA sequence data, and a re-interpretation of an unique nest-building specialization.

Based on some general similarities in feeding adaptations, a large number of Old World passerine birds were in the past lumped in one broad family, the Sylviidae. Recent molecular studies, starting with the DNA-DNA hybridization work by Sibley et al. [Sibley, C.G., Ahlquist, J.E., 1990. Phylogeny and Classification of Birds: A Study in Molecular Evolution, Yale University Press, New Haven, CT], have revealed that this group is in fact a paraphyletic assemblage, mainly in the superfamily Sylvioidea, and within this assemblage a distinct group (the Cisticolidae) can be identified around the genus Cisticola. In this study we try to define natural lineages within it, based on DNA sequence data from 35 ingroup taxa representing 12 putative genera. Both nuclear myoglobin intron II (630 bp in our study) and mitochondrial ND2 (1041 bp) genes were sequenced, and 1671 bp were aligned and subjected to parsimony, maximum likelihood and Bayesian analyses. The results strongly support the monophyly of a cisticolid clade, with the Malagasy warblers Neomixis constituting the deepest branch within the clade. Three major clades receive statistical support, but not all relationships between and within these are well resolved. All species of the genus Bathmocercus belong to the Cisticolidae but in two different clades. The tailorbirds appear also polyphyletic with most species of the genus Orthotomus (but O. cucullatus falling in the outgroup) and the African metopias being in two different clades. Also the genus Apalis is polyphyletic, but all other included genera seem to be confirmed as natural units. Based on these findings we resurrect the genera Scepomycter and Artisornis. Calamonastes is confirmed to be in the Cisticolidae and grouped with Camaroptera. Main basic nest types do not follow the phylogenetic branching, and notably the peculiar "tailorbird" technique of stitching leaves together around the nest is found in different parts of the phylogeny. The basic types of nests seem to be found in particular environments, and the sewing may therefore have evolved in some ancestor of the Cisticolidae and was later lost or modified in some genera or species following the spread of drier habitats from the mid-Miocene.

Animals↗
PubMed2004

Recognition of functional sites in protein structures.

Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.

Algorithms↗
PubMed2006

New insight into diversity in the genus Xenorhabdus, including the description of ten novel species.

We investigated the diversity of a collection of 76 Xenorhabdus strains, isolated from at least 27 species of Steinernema nematodes and collected in 32 countries, using three complementary approaches: 16S rRNA gene sequencing, molecular typing and phenotypic characterization. The 16S rRNA gene sequences of the Xenorhabdus strains were highly conserved (similarity coefficient >95 %), suggesting that the common ancestor of the genus probably emerged between 250 and 500 million years ago. Based on comparisons of the 16S rRNA gene sequences, we identified 13 groups and seven unique sequences. This classification was confirmed by analysis of molecular typing profiles of the strains, leading to the classification of new isolates into the Xenorhabdus species described previously and the description of ten novel Xenorhabdus species: Xenorhabdus cabanillasii sp. nov. (type strain USTX62(T)=CIP 109066(T)=DSM 17905(T)), Xenorhabdus doucetiae sp. nov. (type strain FRM16(T)=CIP 109074(T)=DSM 17909(T)), Xenorhabdus griffiniae sp. nov. (type strain ID10(T)=CIP 109073(T)=DSM 17911(T)), Xenorhabdus hominickii sp. nov. (type strain KE01(T)=CIP 109072(T)=DSM 17903(T)), Xenorhabdus koppenhoeferi sp. nov. (type strain USNJ01(T)=CIP 109199(T)=DSM 18168(T)), Xenorhabdus kozodoii sp. nov. (type strain SaV(T)=CIP 109068(T)=DSM 17907(T)), Xenorhabdus mauleonii sp. nov. (type strain VC01(T)=CIP 109075(T)=DSM 17908(T)), Xenorhabdus miraniensis sp. nov. (type strain Q1(T)=CIP 109069(T)=DSM 17902(T)), Xenorhabdus romanii sp. nov. (type strain PR06-A(T)=CIP 109070(T)=DSM 17910(T)) and Xenorhabdus stockiae sp. nov. (type strain TH01(T)=CIP 109067(T)=DSM 17904(T)). The Xenorhabdus strains studied here had very similar phenotypic patterns, but phenotypic features nonetheless differentiated the following species: X. bovienii, X. cabanillasii, X. hominickii, X. kozodoii, X. nematophila, X. poinarii and X. szentirmaii. Based on phenotypic analysis, we identified two major groups of strains. Phenotypic group G(A) comprised strains able to grow at temperatures of 35-42 degrees C, whereas phenotypic group G(B) comprised strains that grew at temperatures below 35 degrees C, suggesting that some Xenorhabdus species may be adapted to tropical or temperate regions and/or influenced by the growth and development temperature of their nematode host.

Animals↗