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Over recent years, genomic information has increasingly been used for prokaryotic species definition and classification. Genome sequence-based alternatives to the gold standard DNA–DNA hybridization (DDH) relatedness have been developed, notably average nucleotide identity (ANI), which is one of the most useful measurements for species delineation in the genomic era. However, the strictly intracellar lifestyle, the few measurable phenotypic properties and the low level of genetic heterogeneity made the current standard genomic criteria for bacterial species definition inapplicable to Rickettsia species. We evaluated a range of whole genome sequence (WGS)-based taxonomic parameters to develop guidelines for the classification of Rickettsia isolates at genus and species levels. By comparing the degree of similarity of 74 WGSs from 31 Rickettsia species and 61 WGSs from members of three closely related genera also belonging to the order Rickettsiales ( Orientia , 11 genomes; Ehrlichia , 22 genomes; and Anaplasma , 28 genomes) using digital DDH (dDDh) and ANI by orthology (OrthoANI) parameters, we demonstrated that WGS-based taxonomic information, which is easy to obtain and use, can serve for reliable classification of isolates within the Rickettsia genus and species. To be classified as a member of the genus Rickettsia , a bacterial isolate should exhibit OrthoANI values with any Rickettsia species with a validly published name of ≥83.63 %. To be classified as a new Rickettsia species, an isolate should not exhibit more than any of the following degrees of genomic relatedness levels with the most closely related species: >92.30 and >99.19 % for the dDDH and OrthoANI values, respectively. When applied to four rickettsial isolates of uncertain status, the above-described thresholds enabled their classification as new species in one case. Thus, we propose WGS-based guidelines to efficiently delineate Rickettsia species, with OrthoANI and dDDH being the most accurate for classification at the genus and species levels, respectively.

Rickettsia species are endosymbionts hosted by arthropods and are known to cause mild to fatal diseases in humans. Here, we analyse the evolution and diversity of 34 Rickettsia species using a pangenomic meta-analysis (80 genomes/41 plasmids). Phylogenomic trees showed that Rickettsia spp. diverged into two Spotted Fever groups, a Typhus group, a Canadensis group and a Bellii group, and may have inherited their plasmids from an ancestral plasmid that persisted in some strains or may have been lost by others. The results suggested that the ancestors of Rickettsia spp. might have infected Acari and/or Insecta and probably diverged by persisting inside and/or switching hosts. Pangenomic analysis revealed that the Rickettsia genus evolved through a strong interplay between genome degradation/reduction and/or expansion leading to possible distinct adaptive trajectories. The genus mainly shared evolutionary relationships with α-proteobacteria, and also with γ/β/δ-proteobacteria, cytophagia, actinobacteria, cyanobacteria, chlamydiia and viruses, suggesting lateral exchanges of several critical genes. These evolutionary processes have probably been orchestrated by an abundance of mobile genetic elements, especially in the Spotted Fever and Bellii groups. In this study, we provided a global evolutionary genomic view of the intracellular Rickettsia that may help our understanding of their diversity, adaptation and fitness.

In this study, we assessed the presence of vector-borne microorganisms in different species of fleas collected from different hosts in diverse areas of South-Western Europe by molecular methods. A total of 319 fleas belonging to eight different species was tested for the presence of eight microorganisms. Wolbachia spp. endosymbionts were detected in Ctenocephalides felis, Pulex irritans, Archaeopsylla erinacei and Ctenophthalmus baeticus boisseauorum specimens. Rickettsia felis, an emerging pathogen, was detected in C. felis, A. erinacei and Ct. b. boisseauorum. Rickettsia typhi, the agent of murine typhus was detected for the first time in A. erinacei and Mycobacterium spp. were detected for the first time in fleas (C. felis, P. irritans and A. erinacei). Lastly, five different species of Bartonella were detected in fleas' DNA in this study, including a possible new bacterium belonging to this genus. With this study, we updated the knowledge of the flea-borne bacteria present in the South-West of Europe reinforcing the idea about the necessity to expand and increase the current knowledge on flea-borne pathogens.

International audience

Over recent years, genomic information has increasingly been used for prokaryotic species definition and classification. Genome sequence-based alternatives to the gold standard DNA-DNA hybridization (DDH) relatedness have been developed, notably average nucleotide identity (ANI), which is one of the most useful measurements for species delineation in the genomic era. However, the strictly intracellar lifestyle, the few measurable phenotypic properties and the low level of genetic heterogeneity made the current standard genomic criteria for bacterial species definition inapplicable to

Truffles are edible mushrooms with similar morphological characteristics, that make it difficult to distinguish between highly prized truffles (such as the Périgord black T. melanosporum) and inexpensive truffles (such as the Asian Black T. indicum). These biological and economic features have led to several misidentifications and/or fraudulent profit in the truffle markets. In this paper, we investigate Matrix-assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) biotyping to identify 34 commercial fresh truffles from Europe and Asia. The MALDI-TOF MS clustering rapidly distinguished seven Tuber species identified by ITS phylogenetic analysis. The tasty T. melanosporum was clearly differentiated from the Chinese and less expensive truffles. These cheaper mushrooms were marketed as T. indicum but corresponded to a mix of three species. In total, the method confirmed misidentifications in 26% of commercial specimens. Several unknown blind-coded truffles were rapidly identified, with scores >= 2, using the Bruker Biotyper algorithm against MS databases. This study demonstrates that MALDI-TOF MS is a reliable, rapid and cheaper new tool compared with molecular methods for the identification of truffle species and could be used to control frauds in the truffle markets. It could also be useful for the certification of truffle-inoculated seedlings and/or diversity in forest ecosystems.

International audience; Rickettsiales are obligate intracellular bacteria originally found in metazoans, but more recently recognized as widespread endosymbionts of various protists. One genus was detected also in several green algae, but reports on rickettsialean endosymbionts in other algal groups are lacking. Here we show that several distantly related eustigmatophytes (coccoid algae belonging to Ochrophyta, Stramenopiles) are infected by Candidatus Phycorickettsia gen. nov., a new member of the family Rickettsiaceae. The genome sequence of Ca. Phycorickettsia trachydisci sp. nov., an endosymbiont of Trachydiscus minutus CCALA 838, revealed genomic features (size, GC content, number of genes) typical for other Rickettsiales, but some unusual aspects of the gene content were noted. Specifically, Phycorickettsia lacks genes for several components of the respiration chain, haem biosynthesis pathway, or c-di-GMP-based signalling. On the other hand, it uniquely harbours a six-gene operon of enigmatic function that we recently reported from plastid genomes of two distantly related eustigmatophytes and from various non-rickettsialean bacteria. Strikingly, the eustigmatophyte operon is closely related to the one from Phycorickettsia, suggesting a gene transfer event between the endosymbiont and host lineages in early eustigmatophyte evolution. We hypothesize an important role of the operon in the physiology of Phycorickettsia infection and a long-term eustigmatophyte-Phycorickettsia coexistence.

International audience; A rickettsial organism harboured by Amblyomma triguttatum ticks on Barrow Island, Western Australia, was discovered after reports of possible rickettsiosis among local workers. Subsequent isolation of this rickettsia (strain BWI-1) in cell culture and analysis of its phylogenetic, genotypic and phenotypic relationships with type strains of Rickettsia species with standing in nomenclature suggested that it was sufficiently divergent to warrant its classification as a new species. Multiple gene comparison of strain BWI-1 revealed degrees of sequence similarity with Rickettsia raoultii, its closest relative, of 99.58, 98.89, 97.03, 96.93 and 95.73% for the 16S rRNA, citrate synthase, ompA, ompB and sca4 genes, respectively. Serotyping in mice also demonstrated that strain BWI-1(T) was distinct from Rickettsia raoultii. Thus, we propose the naming of a new species, Rickettsia gravesii sp. nov., based on its novel genotypic and phenotypic characteristics. Strain BWI-1(T) was deposited in the ATCC, CSUR and ARRL collections under reference numbers VR-1664, CSUR R172 and RGBWI-1, respectively.

Coxiella-like bacteria have been recently proposed as human pathogens. Using molecular techniques, we detected Coxiella-like bacteria in the blood and serum samples of a patient with a scalp eschar, neck lymphadenopathy, severe urticaria, edema, fever, and arthralgia indicating that this organism can provide systemic complications.

Bartonella senegalensis sp. nov. strain OS02(T) is the type strain of B. senegalensis sp. nov., a new species within the genus Bartonella. This strain, whose genome is described here, was isolated in Senegal from the soft tick Ornithodoros sonrai, the vector of relapsing fever. B. senegalensis is an aerobic, rod-shaped, Gram-negative bacterium. Here we describe the features of this organism, together with the complete genome sequence and its annotation. The 1,966,996 bp-long genome contains 1,710 protein-coding and 46 RNA genes, including 6 rRNA genes.

International audience; Coxiella-like bacteria have been recently proposed as human pathogens. Using molecular techniques, we detected Coxiella-like bacteria in the blood and serum samples of a patient with a scalp eschar, neck lymphadenopathy, severe urticaria, edema, fever, and arthralgia indicating that this organism can provide systemic complications.

Enterobacter massiliensis strain JC163(T) sp. nov. is the type strain of E. massiliensis sp. nov., a new species within the genus Enterobacter. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. E. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,922,247 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 55.1% and contains 4,644 protein-coding and 80 RNA genes, including 5 rRNA genes.

Rickettsia raoultii is a tick-associated spotted fever group (SFG) organism, causing scalp eschar and neck lymphadenopathy after tick bite (SENLAT) in humans. We report here the genome sequence of R. raoultii strain Khabarovsk T (CSUR R3 T , ATCC VR-1596 T ), which was isolated from a Dermacentor silvarum tick collected in Russia.

In cell culture, Rickettsia felis grows only at low temperatures (< 31 °C). Therefore, its ability to enter, survive and grow in cell lines has primarily been tested in cells derived from amphibians and arthropods, which naturally grow at low temperatures, and only infrequently in mammalian cells. We subcultured R. felis in mammalian cells for more than 10 passages using media supplemented with tryptose phosphate broth (TPB) and found that TPB is critical for optimal growth of R. felis in mammalian cells.

Rickettsia prowazekii, the agent of epidemic typhus, is an obligate intracellular bacterium that is transmitted to human beings by the body louse. Several strains that differ considerably in virulence are recognized, but the genetic basis for these variations has remained unknown since the initial description of the avirulent vaccine strain nearly 70 yr ago. We use a recently developed murine model of epidemic typhus and transcriptomic, proteomic, and genetic techniques to identify the factors associated with virulence. We identified four phenotypes ofR. prowazekiithat differed in virulence, associated with the up-regulation of antiapoptotic genes or the interferon I pathway in the host cells. Transcriptional and proteomic analyses ofR. prowazekiisurface protein expression and protein methylation varied with virulence. By sequencing a virulent strain and using comparative genomics, we found hotspots of mutations in homopolymeric tracts of poly(A) and poly(T) in eight genes in an avirulent strain that split and inactivated these genes. These includedrecO, putative methyltransferase, and exported protein. Passage of the avirulent Madrid E strain in cells or in experimental animals was associated with a cascade of gene reactivations, beginning withrecO, that restored the virulent phenotype. An area of genomic plasticity appears to determine virulence inR. prowazekiiand represents an example of adaptive mutation for this pathogen.

Rickettsia species are strictly intracellular Gram-negative bacteria that infect a variety of mammalian hosts, including humans. Many Rickettsia species are associated to arthropod vectors. Their adaptation to life within eukaryotic cells resulted in a progressive genomic degradation via pseudogenization of genes involved in various metabolisms. Paradoxically, some species exhibit conjugative plasmids and gene duplications. As the genomes from most species have been sequenced, we review here the main characteristics of rickettsial genomes.

We examined the below-ground mycorrhizal diversity of P. pinea seedlings inoculated with S. collinitus six years after out- planting in a disturbed site, located at La Petite-Camargue (Gard, France). This was performed using the polymerase chain reaction (PCR), the restriction fragment length polymorphism (RFLP) and the sequencing of the nuclear ribosomal internal transcribed spacer (ITS). Seven and one plants corresponding, respectively, to inoculated and non-inoculated (control) treatments were chosen randomly. Examinations were carried out directly from ectomycorrhizae. A total number of 233 root tips was examined. Five ITS RFLP taxa were detected. The ITS taxon I corresponded to the ectomycorrhizal species Rhizopogon rubescens. This fungus was abundant (55%) in the P. pinea ectomycorrhizal community. The other ITS taxa were rare and remained unidentified. The current P. pinea plantation showed a restricted diversity of the ectomycorrhizal community which is typical of ectomycorrhizal communities in young plantations established in disturbed stands.

Rickettsia hoogstraalii is a tick-associated member of the spotted fever group rickettsiae that is geographically widely distributed. We report here the draft genome of R. hoogstraalii strain Croatica(T) (=DSM 22243 = UTMB 00003), which was isolated from Haemaphysalis sulcata ticks collected in Croatia.

Rickettsia tamurae is a member of the spotted fever group rickettsiae, which was reported in 2011 to cause human infections in Japan. We report the draft genome sequence of R. tamurae strain AT-1 T , isolated from Amblyomma testudinarium ticks.

Rickettsia aeschlimannii is a tick-associated human pathogen. We report here the draft genome of R. aeschlimannii strain MC16, isolated from Hyalomma marginatum marginatum ticks collected in Morocco.

Kurthia massiliensis strain JC30(T) sp. nov. is the type strain of K. massiliensis sp. nov., a new species within the genus Kurthia. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. K. massiliensis is a Gram-positive aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,199,090 bp long genome contains 3,240 protein-coding genes and 86 RNA genes, including between 3 and 4 rRNA genes.

Kingella kingae is a betaproteobacterium from the order Neisseriales , and it is an agent of invasive infections in children. We sequenced the genome from the septic arthritis strain 11220434. It is composed of a 1,990,794-bp chromosome but no plasmid, and it contains 2,042 protein-coding genes and 52 RNA genes, including 3 rRNA genes.

Rickettsia australisstrain PhillipsTwas isolated in Queensland, Australia, in 1950. It is the tick-borne agent of Queensland tick typhus, a disease endemic in Australia. The 1.29-Mb genome sequence of this bacterium is highly similar to that ofRickettsia akaribut contains two plasmids.

The present study reports the complete and annotated genome sequence of the human pathogen Rickettsia slovaca strain 13-B, which was isolated from a Dermacentor tick in Slovakia in 1968. The 1.27-Mb genome provides further insights into the acquisition of virulence related to genome reduction in Rickettsia species.

In cell culture, Rickettsia felis grows only at low temperatures (31 °C). Therefore, its ability to enter, survive and grow in cell lines has primarily been tested in cells derived from amphibians and arthropods, which naturally grow at low temperatures, and only infrequently in mammalian cells. We subcultured R. felis in mammalian cells for more than 10 passages using media supplemented with tryptose phosphate broth (TPB) and found that TPB is critical for optimal growth of R. felis in mammalian cells.

Background Rickettsia raoultii is a novel Rickettsia species recently isolated from Dermacentor ticks and classified within the spotted fever group (SFG). The inability of R. raoultii to spread within L929 cells suggests that this bacterium is unable to polymerize host cell actin, a property exhibited by all SFG rickettsiae except R. peacocki. This result led us to investigate if RickA, the protein thought to generate actin nucleation, was expressed within this rickettsia species. Methodology/Principal Findings Amplification and sequencing of R. raoultii rickA showed that this gene encoded a putative 565 amino acid protein highly homologous to those found in other rickettsiae. Using immunofluorescence assays, we determined that the motility pattern (i.e. microcolonies or cell-to-cell spreading) of R. raoultii was different depending on the host cell line in which the bacteria replicated. In contrast, under the same experimental conditions, R. conorii shares the same phenotype both in L929 and in Vero cells. Transmission electron microscopy analysis of infected cells showed that non-motile bacteria were free in the cytosol instead of enclosed in a vacuole. Moreover, western-blot analysis demonstrated that the defect of R. raoultii actin-based motility within L929 cells was not related to lower expression of RickA. Conclusion/Significance These results, together with previously published data about R. typhi, strongly suggest that another factor, apart from RickA, may be involved with be responsible for actin-based motility in bacteria from the Rickettsia genus.

This work presents DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat unit which are useful for the identification of five European and Asiatic truffles ( Tuber magnatum , T. melanosporum , T. indicum , T. aestivum , and T. mesentericum ). Truffles are edible mycorrhizal ascomycetes that show similar morphological characteristics but that have distinct organoleptic and economic values. A total of 36 out of 46 ITS1 or ITS2 sequence motifs have allowed an accurate in silico distinction of the five truffles to be made (i.e., by pattern matching and/or BLAST analysis on downloaded GenBank sequences and directly against GenBank databases). The motifs considered the intraspecific genetic variability of each species, including rare haplotypes, and assigned their respective species from either the ascocarps or ectomycorrhizas. The data indicate that short ITS1 or ITS2 motifs (≤50 bp in size) can be considered promising tools for truffle species identification. A dot blot hybridization analysis of T. magnatum and T. melanosporum compared with other close relatives or distant lineages allowed at least one highly specific motif to be identified for each species. These results were confirmed in a blind test which included new field isolates. The current work has provided a reliable new tool for a truffle oligonucleotide bar code and identification in ecological and evolutionary studies.

Summary The study examined the diversity of ectomycorrhizal fungi, naturally established on roots of containerised Pinus seedlings in a nursery, using PCR–RFLP and sequencing of the nuclear ribosomal internal transcribed spacer. Seventy-two samples, including ectomycorrhizae and fruit bodies, were examined. Molecular typing assigned the fungal symbionts to four ectomycorrhizal Boletales: Rhizopogon rubescens , Suillus bovinus , S. variegatus , and R. luteolus. R. rubescens was abundant (37.5%), while Suillus and R. luteolus species were moderately established (25–26%) and rare (2.8%), respectively. In addition, Rhizopogon species colonised P. nigra ssp. salzmannii seedlings , whereas Suillus species were identified on Pinus nigra ssp. nigra seedlings. The diversity and the ability of these naturally established symbionts under artificial nursery conditions were discussed. The molecular survey investigated here should contribute to successful monitoring of mycorrhizal application under both nursery and plantation conditions.

International audience; BACKGROUND INFORMATION: The MIPs (major intrinsic proteins) constitute a large family of membrane proteins that facilitate the passive transport of water and small neutral solutes across cell membranes. Since water is the most abundant molecule in all living organisms, the discovery of selective water-transporting channels called AQPs (aquaporins) has led to new knowledge on both the physiological and molecular mechanisms of membrane permeability. The MIPs are identified in Archaea, Bacteria and Eukaryota, and the rapid accumulation of new sequences in the database provides an opportunity for large-scale analysis, to identify functional and/or structural signatures or to infer evolutionary relationships. To help perform such an analysis, we have developed MIPDB (database for MIP proteins), a relational database dedicated to members of the MIP family. RESULTS: MIPDB is a motif-oriented database that integrates data on 785 MIP proteins from more than 200 organisms and contains 230 distinct sequence motifs. MIPDB proposes the classification of MIP proteins into three functional subgroups: AQPs, glycerol-uptake facilitators and aquaglyceroporins. Plant MIPs are classified into three specific subgroups according to their subcellular distribution in the plasma membrane, tonoplast or the symbiosome membrane. Some motifs of the database are highly selective and can be used to predict the transport function or subcellular localization of unknown MIP proteins. CONCLUSIONS: MIPDB offers a user-friendly and intuitive interface for a rapid and easy access to MIP resources and to sequence analysis tools. MIPDB is a web application, publicly accessible at http://idefix.univ-rennes1.fr:8080/Prot/index.html

Ectomycorrhizal diversity (ED) associated with Pinus halepensis trees was examined 1.5 years after outplanting at a fire-disturbed site of Rieucoulon (Herault, France). ED analysis was examined on non-inoculated and Suillus collinitus-inoculated plants, and on naturally regenerated trees. A total of 461 single ectomycorrhizas was typed using PCR-RFLP analysis and sequencing of the internal transcribed spacer ( ITS) of the nuclear rDNA. Twelve ITS RFLP-taxa were detected. The ectomycorrhizal fungus S. collinitus ( ITS RFLP-taxon 1) was the most abundant (45.8 - 59.7%) species in the three treatments, suggesting that it is a strong ectomycorrhizal competitor in this site. S. mediterraneensis ( ITS RFLP-taxon 2) was restricted to control and naturally regenerated trees and was unequally moderate (11.7 - 31.9%). The remaining below-ground ITS RFLP-taxa were uncommon and rare (0.0 - 9.6%). The current experimental P. halepensis plantation showed a species-poor community dominated by two Suillus species. Ecological strategies of these symbionts are discussed., Diversité ectomycorhizienne dans une plantation à Pinus halepensis. La diversité génétique des ectomycorhizes de plants de P. halepensis a été examinée une année et demie après introduction dans un site incendié de Rieucoulon (Hérault, France). Cette diversité a été caractérisée à l’aide du polymorphisme de fragments de restriction (RFLP) et du séquençage de l’espaceur interne transcrit (ITS) de l’ADN ribosomal nucléaire. Trois traitements ont été examinés : des plants témoins, des plants mycorhizés avec Suillus collinitus et des plants en régénération naturelle. Au total, 461 ectomycorhizes ont été soumises au typage moléculaire. Douze ribotypes d’ITS ont été détectés. S. collinitus (ribotype 1) est l’espèce dominante (45,8–59,7 %) dans les trois traitements suggérant une forte capacité de colonisation dans ce site. La présence de S. mediterraneensis (ribotype 2) est limitée aux plants témoins et aux autres issus de la régénération naturelle et sa fréquence est modérée (11,7–31,9 %). Les autres symbiotes ectomycorhiziens sont rares (0,0–9,6 %) et leur abondance diffère d’un traitement à l’autre. Cette étude révèle une faible diversité des symbiotes ectomycorhiziens dans la plantation à P. halepensis; elle est dominée par deux espèces du genre Suillus. Les stratégies écologiques de ces symbiotes sont discutées.

Rickettsia conoriisubsp.israelensisis the agent of Israeli spotted fever. The present study reports the draft genome ofRickettsia conoriisubsp.israelensisstrain ISTT CDC1, isolated from aRhipicephalus sanguineustick collected in Israel.

Rickettsia conorii subsp. caspia is the agent of Astrakhan fever, a spotted fever group rickettsiosis endemic to Astrakhan, Russia. The present study reports the draft genome of Rickettsia conorii subsp. caspia strain A-167.

“ Rickettsia sibirica subsp. mongolitimonae ” is the agent of lymphangitis-associated rickettsiosis, an emerging human disease that has been diagnosed in Europe and Africa. The present study reports the draft genome of Rickettsia sibirica subsp. mongolitimonae strain HA-91.

Rickettsia japonica strain YH, isolated in 1984 in Japan, is the type strain of R. japonica , the tick-borne agent of Japanese spotted fever. Here, we report the 1.33-Mb genome of this rickettsial species.

Rickettsia honei strain RB T was isolated from a febrile patient on Flinders Island, Australia, in 1991 and has been demonstrated to be the agent of Flinders Island spotted fever, a disease transmitted to humans by ticks. The comparison of this 1.27-Mb genome with other Rickettsia genomes provides additional insight into the mechanisms of evolution in Rickettsia species.

Rickettsia sibirica sibirica is the causative agent of Siberian or North Asian tick typhus, a tick-borne rickettsiosis known to exist in Siberia and eastern China. Here we present the draft genome of Rickettsia sibirica sibirica strain BJ-90 isolated from Dermacentor sinicus ticks collected in Beijing, China.

We report the complete and annotated genome sequence of Rickettsia helvetica strain C9P9, which was first isolated in 1979 from Ixodes ricinus ticks in Switzerland and is considered a human pathogen.

Summary In the mediterranean region, the strong edaphic, climatic and economic constraints lead to the increase of the transplantation crisis of young trees. The use of controlled mycorrhizal infection is one of the means open to reduce the effects of this crisis by improving the quality of the forest trees grown in nursery, and the reforestation. To achieve this objective, a research/development programme was started and preliminary results are presented: screening of mycorrhizal isolates using physiological criteria; controlled mycorrhizal infection including the study of enzymic polymorphism in mycorrhizae as a tool for characterization of these organs; measurement of the effects of mycorrhizal infection on the nutrition of trees in nursery; ecophysiological study of experimental wood lots.

Bartonella florenciae sp. nov. strain R4(T) is the type strain of B. florenciae sp. nov., a new species within the genus Bartonella. This strain, whose genome is described here, was isolated in France from the spleen of the shrew Crocidura russula. B. florenciae is an aerobic, rod-shaped, Gram-negative bacterium. Here we describe the features of this organism, together with the complete genome sequence and its annotation. The 2,010,844 bp-long genome contains 1,909 protein-coding and 46 RNA genes, including two rRNA operons.

Background The Rickettsia genus includes 25 validated species, 17 of which are proven human pathogens. Among these, the pathogenicity varies greatly, from the highly virulent R. prowazekii, which causes epidemic typhus and kills its arthropod host, to the mild pathogen R. africae, the agent of African tick-bite fever, which does not affect the fitness of its tick vector. Results We evaluated the clonality of R. africae in 70 patients and 155 ticks, and determined its genome sequence, which comprises a circular chromosome of 1,278,540 bp including a tra operon and an unstable 12,377-bp plasmid. To study the genetic characteristics associated with virulence, we compared this species to R. prowazekii, R. rickettsii and R. conorii. R. africae and R. prowazekii have, respectively, the less and most decayed genomes. Eighteen genes are present only in R. africae including one with a putative protease domain upregulated at 37°C. Conclusion Based on these data, we speculate that a loss of regulatory genes causes an increase of virulence of rickettsial species in ticks and mammals. We also speculate that in Rickettsia species virulence is mostly associated with gene loss. The genome sequence was deposited in GenBank under accession number [GenBank: NZ_AAUY01000001].