Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B. bronchiseptica, B. pertussis, and B. parapertussis reveals extensive diversity in surface structures associated with host interaction

Bordetella avium is a pathogen of poultry and is phylogenetically distinct from Bordetella bronchiseptica, Bordetella pertussis, and Bordetella parapertussis, which are other species in the Bordetella genus that infect mammals. In order to understand the evolutionary relatedness of Bordetella species and further the understanding of pathogenesis, we obtained the complete genome sequence of B. avium strain 197N, a pathogenic strain that has been extensively studied. With 3,732,255 base pairs of DNA and 3,417 predicted coding sequences, it has the smallest genome and gene complement of the sequenced bordetellae. In this study, the presence or absence of previously reported virulence factors from B. avium was confirmed, and the genetic bases for growth characteristics were elucidated. Over 1,100 genes present in B. avium but not in B. bronchiseptica were identified, and most were predicted to encode surface or secreted proteins that are likely to define an organism adapted to the avian rather than the mammalian respiratory tracts. These include genes coding for the synthesis of a polysaccharide capsule, hemagglutinins, a type I secretion system adjacent to two very large genes for secreted proteins, and unique genes for both lipopolysaccharide and fimbrial biogenesis. Three apparently complete prophages are also present. The BvgAS virulence regulatory system appears to have polymorphisms at a poly(C) tract that is involved in phase variation in other bordetellae. A number of putative iron-regulated outer membrane proteins were predicted from the sequence, and this regulation was confirmed experimentally for five of these.     

Deciphering Bartonella Diversity,Recombination, and Host Specificity in a Rodent Community

Host-specificity is an intrinsic feature of many bacterial pathogens, resulting from a long history of co-adaptation between bacteria and their hosts. Alpha-proteobacteria belonging to the genus Bartonella infect the erythrocytes of a wide range of mammal orders, including rodents. In this study, we performed genetic analysis of Bartonella colonizing a rodent community dominated by bank voles (Myodes glareolus) and wood mice (Apodemus sylvaticus) in a French suburban forest to evaluate their diversity, their capacity to recombine and their level of host specificity. Following the analysis of 550 rodents, we detected 63 distinct genotypes related to B. taylorii, B. grahamii, B. doshiae and a new B. rochalimae-like species. Investigating the most highly represented species, we showed that B. taylorii strain diversity was markedly higher than that of B. grahamii, suggesting a possible severe bottleneck for the latter species. The majority of recovered genotypes presented a strong association with either bank voles or wood mice, with the exception of three B. taylorii genotypes which had a broader host range. Despite the physical barriers created by host specificity, we observed lateral gene transfer between Bartonella genotypes associated with wood mice and Bartonella adapted to bank voles, suggesting that those genotypes might co-habit during their life cycle.     

Clonal diversity and host distribution in Bordetella bronchiseptica.

A total of 303 isolates of Bordetella bronchiseptica recovered from 11 host species were characterized by the electrophoretic mobilities of 15 metabolic enzymes, and 21 distinctive multilocus genotypes (electrophoretic types) were distinguished on the basis of allele profiles at the enzyme loci. The population structure of B. bronchiseptica is clonal, and its genetic diversity is limited in comparison with most other pathogenic bacteria, perhaps reflecting a relatively recent origin of the species. Electrophoretic types mark clones which are, in many cases, nonrandomly associated with host species. Clones differing only slightly in overall chromosomal genetic character may have pronounced differences in virulence potential. There was considerable variation among individual clones and clone families in degree of host specificity and among various species of hosts in the diversity of clones causing disease. The diversity of clones infecting dogs was an order of magnitude greater than that of clones infecting pigs. Most bordetellosis in pigs in the United States and Japan was found to be caused by strains of a single multilocus genotype.     

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp

Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.     

Evidence of diversity and recombination in <Emphasis Type="Italic">Arsenophonus</Emphasis> symbionts of the <Emphasis Type="Italic">Bemisia tabaci</Emphasis>species complex

BACKGROUND: Maternally inherited bacterial symbionts infecting arthropods have major implications on host ecology and evolution. Among them, the genus Arsenophonus is particularly characterized by a large host spectrum and a wide range of symbiotic relationships (from mutualism to parasitism), making it a good model to study the evolution of host-symbiont associations. However, few data are available on the diversity and distribution of Arsenophonus within host lineages. Here, we propose a survey on Arsenophonus diversity in whitefly species (Hemiptera), in particular the Bemisia tabaci species complex. This polyphagous insect pest is composed of genetic groups that differ in many ecological aspects. They harbor specific bacterial communities, among them several lineages of Arsenophonus, enabling a study of the evolutionary history of these bacteria at a fine host taxonomic level, in association to host geographical range and ecology. RESULTS: Among 152 individuals, our analysis identified 19 allelic profiles and 6 phylogenetic groups, demonstrating this bacterium's high diversity. These groups, based on Arsenophonus phylogeny, correlated with B. tabaci genetic groups with two exceptions reflecting horizontal transfers. None of three genes analyzed provided evidence of intragenic recombination, but intergenic recombination events were detected. A mutation inducing a STOP codon on one gene in a strain infecting one B. tabaci genetic group was also found. Phylogenetic analyses of the three concatenated loci revealed the existence of two clades of Arsenophonus. One, composed of strains found in other Hemiptera, could be the ancestral clade in whiteflies. The other, which regroups strains found in Hymenoptera and Diptera, may have been acquired more recently by whiteflies through lateral transfers. CONCLUSIONS: This analysis of the genus Arsenophonus revealed a diversity within the B. tabaci species complex which resembles that reported on the larger scale of insect taxonomy. We also provide evidence for recombination events within the Arsenophonus genome and horizontal transmission of strains among insect taxa. This work provides further insight into the evolution of the Arsenophonus genome, the infection dynamics of this bacterium and its influence on its insect host's ecology.     

Pathogenomics of Xanthomonas: understanding bacterium-plant interactions

Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant hosts, including many economically important crops. Pathogenic species and pathovars within species show a high degree of host plant specificity and many exhibit tissue specificity, invading either the vascular system or the mesophyll tissue of the host. In this Review, we discuss the insights that functional and comparative genomic studies are providing into the adaptation of this group of bacteria to exploit the extraordinary diversity of plant hosts and different host tissues.     

Modes of acquisition of Wolbachia: horizontal transfer, hybrid introgression, and codivergence in the Nasonia species complex

Wolbachia are maternally inherited bacteria that infect a large number of insects and are responsible for different reproductive alterations of their hosts. One of the key features of Wolbachia biology is its ability to move within and between host species, which contributes to the impressive diversity and range of infected hosts. Using multiple Wolbachia genes, including five developed for Multi-Locus Sequence Typing (MLST), the diversity and modes of movement of Wolbachia within the wasp genus Nasonia were investigated. Eleven different Wolbachia were found in the four species of Nasonia , including five newly identified infections. Five infections were acquired by horizontal transmission from other insect taxa, three have been acquired by hybridization between two Nasonia species, which resulted in a mitochondrial- Wolbachia sweep from one species to the other, and at least three have codiverged during speciation of their hosts. The results show that a variety of transfer mechanisms of Wolbachia are possible even within a single host genus. Codivergence of Wolbachia and their hosts is uncommon and provides a rare opportunity to investigate long-term Wolbachia evolution within a host lineage. Using synonymous divergence among codiverging infections and host nuclear genes, we estimate Wolbachia mutation rates to be approximately one-third that of the nuclear genome.     

The role of phylogeny and ecology in experimental host specificity: insights from a eugregarine-host system

The degree to which parasites use hosts is fundamental to host-parasite coevolution studies, yet difficult to assess and interpret in an evolutionary manner. Previous assessments of parasitism in eugregarine-host systems suggest high degrees of host specificity to particular host stages and host species; however, rarely have the evolutionary constraints on host specificity been studied experimentally. A series of experimental infections were conducted to determine the extent of host stadium specificity (larval vs. adult stage) and host specificity among 6 tenebrionid host species and 5 eugregarine parasite species. Eugregarines from all host species infected both the larva and adult stages of the host, and each parasite taxa colonized several host species (Tribolium spp. and Palorus subdepressus). Parasite infection patterns were not congruent with host phylogeny, suggesting that host phylogeny is not a significant predictor of host-parasite interactions in this system. However, the 2 host stages produced significantly different numbers of parasite propagules, indicating that ecological factors may be important determinants of host specificity in this host-parasite system. While field infections reflect extant natural infection patterns of parasites, experimental infections can demonstrate potential host-parasite interactions, which aids in identifying factors that may be significant in shaping future host-parasite interactions.     

Increased sampling reveals novel lineages of Entamoeba: consequences of genetic diversity and host specificity for taxonomy and molecular detection

To expand the representation for phylogenetic analysis, ten additional complete Entamoeba small-subunit rRNA gene sequences were obtained from humans, non-human primates, cattle and a tortoise. For some novel sequences no corresponding morphological data were available, and we suggest that these organisms should be referred to as ribosomal lineages (RL) rather than being assigned species names at present. To investigate genetic diversity and host specificity of selected Entamoeba species, a total of 91 new partial small subunit rRNA gene sequences were obtained, including 49 from Entamoeba coli, 18 from Entamoeba polecki, and 17 from Entamoeba hartmanni. We propose a new nomenclature for significant variants within established Entamoeba species. Based on current data we propose that the uninucleated-cyst-producing Entamoeba infecting humans is called Entamoeba polecki and divided into four subtypes (ST1-ST4) and that Entamoeba coli is divided into two subtypes (ST1-ST2). New hosts for several species were detected and, while host specificity and genetic diversity of several species remain to be clarified, it is clear that previous reliance on cultivated material has given us a misleading and incomplete picture of variation within the genus Entamoeba.     

Insight into the routes of Wolbachia invasion: high levels of horizontal transfer in the spider genus Agelenopsis revealed by Wolbachia strain and mitochondrial DNA diversity

The pandemic distribution of Wolbachia (alpha-proteobacteria) across arthropods is largely due to the ability of these maternally inherited endosymbionts to successfully shift hosts across species boundaries. Yet it remains unclear whether Wolbachia has preferential routes of transfer among species. Here, we examined populations of eight species of the North American funnel-web spider genus Agelenopsis to evaluate whether Wolbachia show evidence for host specificity and the relative contribution of horizontal vs. vertical transmission of strains within and among related host species. Wolbachia strains were characterized by multilocus sequence typing (MLST) and Wolbachia surface protein (WSP) sequences, and analysed in relation to host phylogeny, mitochondrial diversity and geographical range. Results indicate that at least three sets of divergent Wolbachia strains invaded the genus Agelenopsis. After each invasion, the Wolbachia strains preferentially shuffled across species of this host genus by horizontal transfer rather than cospeciation. Decoupling of Wolbachia and host mitochondrial haplotype (mitotypes) evolutionary histories within single species reveals an extensive contribution of horizontal transfer also in the rapid dispersal of Wolbachia among conspecific host populations. These findings provide some of the strongest evidence to support the association of related Wolbachia strains with related hosts by means of both vertical and horizontal strain transmission. Similar analyses across a broader range of invertebrate taxa are needed, using sensitive methods for strain typing such as MLST, to determine if this pattern of Wolbachia dispersal is peculiar to Agelenopsis (or spiders), or is in fact a general pattern in arthropods.     

Evolution of host specificity in fleas: is it directional and irreversible?

Evolutionary trends in the evolution of host specificity have been the focus of much discussion but little rigorous empirical testing. On the one hand, specialization is often presumed to lead irreversibly into evolutionary dead ends and little diversification; this would mean that generalists might evolve into specialists, but not vice versa. On the other hand, low host specificity may limit the risk of extinction and provide more immediate fitness benefits to parasites, such that selection may favour evolution toward a generalist strategy. Here, we test for directionality in the evolution of host specificity using a large data set and phylogenetic information on 297 species of fleas parasitic on small mammals. The analyses determined whether host specificity, measured both as the number of host species exploited and their taxonomic diversity, was related to clade rank of the flea species, or the number of branching events between an extant species and the root of the phylogenetic tree (i.e., the total path length from the root of the tree to the species). Based on regression analyses, we found positive relationships between the number of host species used and clade rank across all 297 species, as well as within one (Hystrichopsyllidae) of four large families and one of seven large genera investigated separately; in addition, we found a positive relationship between the taxonomic diversity of host species used and clade rank in another of the seven genera. These results suggest a slight evolutionary trend of decreasing host specificity. Using a much more conservative likelihood ratio test, however, a random walk, or null model, of evolution could not be discarded in favour of the directional trends in all cases mentioned above. Still, these results suggest that host specificity may have tended to decrease in many flea lineages, a process that could have been driven by the benefits of exploiting a wide range of host species.     

Evolution and determinants of host specificity in the genus Lamellodiscus (Monogenea)

The evolution and determinants of host specificity in Lamellodiscus species (Monogenea, Diplectanidae) were investigated. The 20 known Mediterranean species were studied, all parasites of fishes from the family Sparidae (Teleostei). An index of specificity, which takes into account the phylogenetic relationships of their fish host species, was defined. The link between specificity and its potential determinants was investigated in a phylogenetic context using the method of independent contrasts. Host specificity in Lamellodiscus species appeared to be highly constrained by phylogeny, but also linked to host size. Mapping specificity onto the parasite phylogenetic tree suggests that specialist species do not represent an evolutionary dead end, and that specialization is not a derived condition. It is hypothesized that the ability to be generalist or specialist in Lamellodiscus is controlled by intrinsic, phylogenetically-related characteristics, and that specialist species tend to use large hosts, which may be more predictable.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77, 431−443.     

Chromosomal DNA from both flagellate and non-flagellate Bordetella species contains sequences homologous to the Salmonella H1 flagellin gene

Abstract The genus Bordetella contains four species: two are non-motile, the human pathogens B. pertussis and B. parapertussis ; and two are motile, the broad host-range mammalian pathogen B. bronchiseptica , and the avian pathogen B. avium . The motility of the latter two species is due to peritrichous flagella. Here we show that strains of all four species contain DNA sequences homologous to flagellin genes. Two types of gene probe were hybridised to Bordetella chromosomal DNA in Southern blots: the structural gene for H1 flagellin of Salmonella typhimurium and an oligonucleotide derived from the conserved N-terminal amino acid sequences of various flagellin proteins. Cla I-digested DNA from all four Bordetella species hybridised with both probes in Southern blots, although each species gave a characteristic pattern of hybridisation. This indicates that the non-motile B. pertussis and B. parapertussis species contain non-expressed flagellin genes.     

Comparative whole-genome hybridization reveals genomic islands in Brucella species

Brucella species are responsible for brucellosis, a worldwide zoonotic disease causing abortion in domestic animals and Malta fever in humans. Based on host preference, the genus is divided into six species. Brucella abortus, B. melitensis, and B. suis are pathogenic to humans, whereas B. ovis and B. neotomae are nonpathogenic to humans and B. canis human infections are rare. Limited genome diversity exists among Brucella species. Comparison of Brucella species whole genomes is, therefore, likely to identify factors responsible for differences in host preference and virulence restriction. To facilitate such studies, we used the complete genome sequence of B. melitensis 16M, the species highly pathogenic to humans, to construct a genomic microarray. Hybridization of labeled genomic DNA from Brucella species to this microarray revealed a total of 217 open reading frames (ORFs) altered in five Brucella species analyzed. These ORFs are often found in clusters (islands) in the 16M genome. Examination of the genomic context of these islands suggests that many are horizontally acquired. Deletions of genetic content identified in Brucella species are conserved in multiple strains of the same species, and genomic islands missing in a given species are often restricted to that particular species. These findings suggest that, whereas the loss or gain of genetic material may be related to the host range and virulence restriction of certain Brucella species for humans, independent mechanisms involving gene inactivation or altered expression of virulence determinants may also contribute to these differences.     

Community Sampling and Integrative Taxonomy Reveal New Species and Host Specificity in the Army Ant-Associated Beetle Genus Tetradonia (Coleoptera,Staphylinidae, Aleocharinae)

Army ant colonies host a diverse community of arthropod symbionts. Among the best-studied symbiont communities are those of Neotropical army ants of the genus Eciton. It is clear, however, that even in these comparatively well studied systems, a large proportion of symbiont biodiversity remains unknown. Even more striking is our lack of knowledge regarding the nature and specificity of these host-symbiont interactions. Here we surveyed the diversity and host specificity of rove beetles of the genus Tetradonia Wasmann, 1894 (Staphylinidae: Aleocharinae). Systematic community sampling of 58 colonies of the six local Eciton species at La Selva Biological Station, Costa Rica, combined with an integrative taxonomic approach, allowed us to uncover species diversity, host specificity, and co-occurrence patterns of symbionts in unprecedented detail. We used an integrative taxonomic approach combining morphological and genetic analyses, to delineate species boundaries. Mitochondrial DNA barcodes were analyzed for 362 Tetradonia specimens, and additional nuclear markers for a subset of 88 specimens. All analyses supported the presence of five Tetradonia species, including two species new to science. Host specificity is highly variable across species, ranging from generalists such as T. laticeps, which parasitizes all six local Eciton species, to specialists such as T. lizonae, which primarily parasitizes a single species, E. hamatum. Here we provide a dichotomous key along with diagnostic molecular characters for identification of Tetradonia species at La Selva Biological Station. By reliably assessing biodiversity and providing tools for species identification, we hope to set the baseline for future studies of the ecological and evolutionary dynamics in these species-rich host-symbiont networks.     

In situ localization of the evolutionary conserved Cpy/Cty gene in the subfamily Chironominae (Chironomidae, Diptera): establishment of chromosomal homologies

The homologous sites on the salivary gland chromosomes of 13 species from three genera: Chironomus, Glyptotendipes, Kiefferulus have been mapped by means of fluorescent in situ hybridization using the evolutionary conserved gene Cpy/Cty (clone Cla1.1). In all species of genus Chironomus and genus Kiefferulus , the Cty/Cpy gene is located on arm F of chromosome EF. The relocation of the gene among the species of genus Chironomus can be done by simple or complex homozygous inversions which occurred during the divergent evolution of the chromosome of the species. In the genus Glyptotendipes , the Cty/Cpy gene was localized in arm E of chromosome EF. Since the banding patterns of salivary gland chromosomes between genus Chironomus and genus Glyptotendipes cannot be compared directly, in situ hybridization with clone of conservative gene was performed to be established some homologous chromosomes. The results obtained indicate that the chromosome arm F of Chironomus and chromosome arm E of Glyptotendipes may be homologous.     

New evolutionary lineages, unexpected diversity, and host specificity in the parabasalid genus Tetratrichomonas

We studied morphological and molecular polymorphism of 53 Tetratrichomonas isolates obtained from amphibian, reptilian, mammalian hosts, and from a slug with the aid of protargol staining and analyses of ITS1-5.8S rRNA-ITS2, SSU rRNA, and alpha-tubulin gene sequences. The phylogenetic tree based on the concatenate of all sequences showed the monophyly of the genus Tetratrichomonas with respect to the genus Trichomonas. Our data suggest that two parabasalid genera, Pentatrichomonoides and Trichomonoides, may belong to the genus Tetratrichomonas. Tetratrichomonas isolates were divided into 16 robust host-specific and monophyletic groups that probably represent separate, mostly new, species. As only five Tetratrichomonas species were described from the examined host taxa so far, our study uncovered considerable species diversity within the genus. The wide host range, high level of species-specific host specificity, and newly revealed biodiversity make the genus Tetratrichomonas a valuable model for studying evolution of parasites.     

Variation in symbiont distribution between closely related coral species over large depth ranges

Symbiotic algae in coral species distributed over a large depth range are confronted with major differences in light conditions. We studied the genetic variation of Symbiodinium in the coral genus Madracis over depth (5-40 m) and at two different colony surface positions. Using polymerase chain reaction-denaturing gradient gel electrophoresis ITS2 nuclear ribosomal DNA analyses, we consistently identified three symbiont genotypes with distributions that reveal patterns of host specificity and depth-based zonation. ITS2 type B7 Symbiodinium is the generalist type, occurring in all zooxanthellate Madracis corals and at all depths. Type B13 is restricted to the shallow water specialist Madracis mirabilis. Type B15 is typical of deep reef environments and replaces B7 in the depth generalist Madracis pharensis. Contrasting with variation over depth, we found strong functional within-colony uniformity in symbiont diversity. Relating symbiont distributions to measured physical factors (irradiance, light spectral distribution, temperature), suggests depth-based ecological function and host specificity for Symbiodinium ITS2 types, even among closely related coral species.