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Results for “core genome phylogeny”

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PubMed2026

Deciphering the genomic landscape of novel Acinetobacter non-baumannii lineages causing neonatal septicemia: carbapenem resistance and virulence.

BACKGROUND: Acinetobacter non-baumannii (Anb) species are reported worldwide to cause infections in both adults and neonates, although less frequently than Acinetobacter baumannii. However, limited information is available on their genomic diversity, resistance mechanisms, and virulence potential. This study investigates novel Anb isolates causing neonatal septicemia in India to characterize their resistance and pathogenic traits. METHODS: Anb isolates from neonatal blood cultures (2007-2025) were identified by VITEK2 Compact system, MALDI-TOF MS, and Whole-genome sequencing (WGS). Antimicrobial susceptibility was tested by VITEK2. Genomic analysis included MLST, resistome, virulome, plasmid typing, integrons, and core-genome phylogeny analysis. In vitro and in vivo studies assessed pathogenic potential of Anb species. RESULTS: Anb infections were low (11%) among the neonates during the study period. WGS revealed 11 novel Sequence Types (STs) which include A. indicus, A. variabilis, A. schindleri, and A. bereziniae. Six out of these eleven Anbs harbored carbapenemases such as bla NDM-1 and/or bla OXA-58-like genes (bla OXA-58, bla OXA-420). bla NDM-1 was acquired via Tn125 transposon. ISAba125 was located upstream of bla NDM-1, and a conserved structure extending to IS91 family transposase was detected in bla NDM-1-harboring genomes. bla OXA-58-like genes were found to be associated with ISAba3. Most carbapenemases were likely located on chromosome. Class 1 integrons carrying multiple antimicrobial resistance genes (ARGs) and diverse plasmid replicase families were detected in Anbs. Core genome phylogeny showed that the study Anbs were not closely related to the global Anbs. In vitro virulence-associated assays (biofilm formation, surface motility, adherence/invasion, apoptosis) and in vivo lethality in murine infection model showed reduced pathogenicity, reinforcing earlier observations that Anb species are generally less virulent than A. baumannii. Several virulence factors (VFs) were detected; however, no clear correlation was observed between virulence genes, in vitro pathogenicity, and in vivo lethality. CONCLUSION: These results indicate the multifactorial nature of Anb pathogenicity and the current limitations of knowledge of its VFs. However, the presence of numerous VFs suggests a capacity to cause disease, particularly in vulnerable host populations such as neonates. Furthermore, the presence of multiple ARGs indicates a strong potential for persistence and dissemination in hospital environments with high antibiotic pressure. Overall, these findings underscore the importance of continued AMR surveillance, genome characterization and further investigations into Anb pathogenicity.

Acinetobacter non-baumannii↗

PubMed2026

Genomic Characterization of Aeromonas dhakensis Isolated From a Fatal Dolphin Case.

Aeromonas dhakensis has emerged as a significant pathogen affecting both aquatic animals and humans; however, genomic data for isolates from marine mammals remain scarce. In this study, we characterised the genome of A. dhakensis strain KDL-001, isolated from a fatal dolphin case, using whole-genome sequencing and comparative genomics. Taxonomic analyses, including MLST and average nucleotide identity (ANI), confirmed the isolate as A. dhakensis. Core-genome phylogeny further revealed that KDL-001 is closely related to strains derived from fish and aquatic environments. Notably, in silico screening of virulence-associated genes showed that the virulence-associated gene profile of the dolphin isolate was broadly comparable to those of other A. dhakensis strains, with no isolate-specific virulence-associated genes being identified within the limits of this analysis. These findings demonstrate that the dolphin-derived isolate is genomically comparable to previously described A. dhakensis strains and possesses conserved virulence-associated genes commonly found within the species.

Animals↗

PubMed2026

Proposal of three novel species of the family Xanthobacteraceae: Xanthobacter pollutisoli sp. nov., Xanthobacter luteus sp. nov. and Aquabacter albus sp. nov., isolated from oil-contaminated soils.

Three Gram-stain-negative bacterial strains, KR7-65T, KR7-225T and CN5-332T isolated from oil-contaminated soil in Korea and China were identified. Phylogenetic analysis based on 16S rRNA gene sequences placed the strains within the family Xanthobacteraceae, with KR7-65T and KR7-225T affiliated with the genus Xanthobacter and CN5-332T with the genus Aquabacter. Sequence similarities to type strains of validly published species were below 98.5%. Core genome phylogeny showed that the four strains formed distinct clusters occupying different positions in the phylogenetic tree and exhibited different closest relatives. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization (dDDH) values between KR7-65T and KR7-225T and members of Xanthobacter were 78.7-87.0%, 74.8-87.8% and 22.7-32.3%, respectively, whereas those between CN5-332T and members of Aquabacter were 80.2-80.7%, 79.6-80.5% and 23.4-23.9%, supporting their assignment as novel species. The DNA G+C contents were 68.0, 69.9 and 66.5 mol% for KR7-65T, KR7-225T and CN5-332T, respectively. Strains KR7-65T and KR7-225T contained phosphatidylcholine, phosphatidylglycerol, phosphatidyl monomethyl ethanolamine, diphosphatidylglycerol (DPG) and an unidentified glycolipid as major polar lipids, whereas DPG was absent in strain CN5-332T. The primary fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), cyclo C19 : 0ω8c and C16 : 0. On the basis of phylogenetic, genomic and phenotypic evidence, strains KR7-65T and KR7-225T represent two novel species of the genus Xanthobacter, for which the names Xanthobacter pollutisoli sp. nov. (type strain KR7-65T=KACC 23453T=NBRC 116939T) and Xanthobacter luteus sp. nov. (type strain KR7-225T=KACC 23282T=NBRC 116940T) are proposed. Strain CN5-332T represents a novel species of the genus Aquabacter, for which the name Aquabacter albus sp. nov. (type strain CN5-332T=KACC 23276T=CCTCC AB 2024343T) is proposed.

Phylogeny↗

PubMed2005

Phylogenetic characterization of virulence and resistance phenotypes of Pseudomonas syringae.

Individual strains of the plant pathogenic bacterium Pseudomonas syringae vary in their ability to produce toxins, nucleate ice, and resist antimicrobial compounds. These phenotypes enhance virulence, but it is not clear whether they play a dominant role in specific pathogen-host interactions. To investigate the evolution of these virulence-associated phenotypes, we used functional assays to survey for the distribution of these phenotypes among a collection of 95 P. syringae strains. All of these strains were phylogenetically characterized via multilocus sequence typing (MLST). We surveyed for the production of coronatine, phaseolotoxin, syringomycin, and tabtoxin; for resistance to ampicillin, chloramphenicol, rifampin, streptomycin, tetracycline, kanamycin, and copper; and for the ability to nucleate ice at high temperatures via the ice-nucleating protein INA. We found that fewer than 50% of the strains produced toxins and significantly fewer strains than expected produced multiple toxins, leading to the speculation that there is a cost associated with the production of multiple toxins. None of these toxins was associated with host of isolation, and their distribution, relative to core genome phylogeny, indicated extensive horizontal genetic exchange. Most strains were resistant to ampicillin and copper and had the ability to nucleate ice, and yet very few strains were resistant to the other antibiotics. The distribution of the rare resistance phenotypes was also inconsistent with the clonal history of the species and did not associate with host of isolation. The present study provides a robust phylogenetic foundation for the study of these important virulence-associated phenotypes in P. syringae host colonization and pathogenesis.

Adaptation, Physiological↗

PubMed2025

Diversity of Salmonella enterica isolates from urban river and sewage water in Blantyre, Malawi.

BACKGROUND: Salmonella enterica encompasses over 2,600 serovars, including several commonly associated with severe infection in humans. Salmonella is a major cause of sepsis in Africa; however, diagnosis requires clinical microbiology facilities. Environmental surveillance has the potential to play a role in Salmonella surveillance. METHODS: We undertook water-based environmental surveillance in Blantyre, Malawi, from 2018-2020, taking samples from rivers (87.9%), a sewage plant (8.85%) and other water sources (3.24%), isolating and storing 1,042 non-typhoidal Salmonella (NTS) isolates in this period. Of these, 341 NTS isolates were whole genome sequenced, genome quality was checked, duplicate genomes from any given sample were removed and core genome phylogeny was reconstructed. AMRFinder, PathogenWatch and SISTR were used to further investigate serovar, sequence type and antimicrobial resistance determinants. RESULTS: After quality checks, and removal of duplicate genomes, 270 NTS genomes remained for further analysis. Multiple Salmonella serovars associated with human infection were detected, of which S. Typhimurium (55/270 isolates) was the most common, including 44 of Sequence Type (ST) 313, a serovar commonly associated with severe invasive disease (iNTS). Six lineage 2 ST313 genomes possessed AMR genes predicting multidrug resistance (MDR), while 29 lineage 3 isolates contained no AMR predictive genes. PCR based detection of staG has been proposed as a diagnostic marker of S. Typhi; however, all eight genomes that contained staG identified as Salmonella enterica serovar Orion, raising concerns about the specificity of this marker as a monoplex for environmental surveillance of S. Typhi. DISCUSSION: The study identified diverse Salmonella serovars in the environment, including those reported to cause invasive disease, emphasizing the complex but potentially valuable contribution of implementing environmental surveillance for Salmonella in high burden areas lacking diagnostic microbiology capacity.

Sewage↗

PubMed2006

Comparative genomics of host-specific virulence in Pseudomonas syringae.

While much study has gone into characterizing virulence factors that play a general role in disease, less work has been directed at identifying pathogen factors that act in a host-specific manner. Understanding these factors will help reveal the variety of mechanisms used by pathogens to suppress or avoid host defenses. We identified candidate Pseudomonas syringae host-specific virulence genes by searching for genes whose distribution among natural P. syringae isolates was statistically associated with hosts of isolation. We analyzed 91 strains isolated from 39 plant hosts by DNA microarray-based comparative genomic hybridization against an array containing 353 virulence-associated (VA) genes, including 53 type III secretion system effectors (T3SEs). We identified individual genes and gene profiles that were significantly associated with strains isolated from cauliflower, Chinese cabbage, soybean, rice, and tomato. We also identified specific horizontal gene acquisition events associated with host shifts by mapping the array data onto the core genome phylogeny of the species. This study provides the largest suite of candidate host-specificity factors from any pathogen, suggests that there are multiple ways in which P. syringae isolates can adapt to the same host, and provides insight into the evolutionary mechanisms underlying host adaptation.

Gene Expression Profiling↗

PubMed2026

Lineage structure and penicillin-binding protein variability in clinical Streptococcus pneumoniae isolates from Southwest China exhibiting reduced susceptibility to penicillin.

BACKGROUND: Reduced susceptibility to penicillin in Streptococcus pneumoniae is mediated primarily by alterations in penicillin-binding proteins (PBPs) and often coexists with multidrug resistance within successful lineages. The region-specific genomic characterization of clinically relevant pneumococci with reduced penicillin susceptibility in Southwest China remains limited. METHODS: We performed whole-genome sequencing of 204 clinical S. pneumoniae isolates collected from five institutions in Southwest China (2018-2022) that met our operational screening definition of reduced susceptibility to penicillin (PEN MIC ≥0.12 μg/mL). Molecular serotypes, MLST types, and Global Pneumococcal Sequence Clusters (GPSCs) were assigned; virulence and antimicrobial resistance determinants were profiled; and a core genome phylogeny was reconstructed with international contextualization through the use of PubMLST genomes meeting the same MIC criterion. Amino acid variability in PBP1a/PBP2b/PBP2x was quantified using TIGR4 numbering, and highly variable noncatalytic residues located within 15 Å of catalytic motifs were prioritized via structure-guided screening. RESULTS: The isolates showed a high burden of resistance to non-β-lactam antibiotics (erythromycin, 98.5%; tetracycline, 82.8%; trimethoprim-sulfamethoxazole, 64.7%), while fluoroquinolone susceptibility was largely preserved (≥97%), and vancomycin/linezolid resistance was not detected. Twenty-seven serotypes were identified, among which 19F (23.5%) and 19A (14.2%) were dominant, and the estimated PCV13 coverage was 69.6%. GPSC1 was the dominant lineage (36.8%), and the lineage composition among our isolates differed markedly from those in the PubMLST-USA and PubMLST-Thailand subsets. Virulence and resistance gene carriage differed markedly between GPSC1 and non-GPSC1 isolates, with enrichment of pilus operons, mef(A)/msr(D), and folA/folP in GPSC1. PBP variations were clustered in transpeptidase domains and motif-adjacent regions while essential catalytic residues were conserved; with the structure-guided filter, 12, 11, and 11 motif-proximal noncatalytic candidate sites were prioritized in PBP1a, PBP2b, and PBP2x, respectively. CONCLUSION: Clinical S. pneumoniae isolates with reduced penicillin susceptibility collected in Southwest China demonstrated resistance and accessory gene profiles that were strongly structured by a GPSC-defined lineage background. Our site-resolved, structure-guided PBP analysis provides a regional PBP variability landscape and a compact set of recurrent motif-proximal candidate substitutions to support surveillance and downstream functional validation.

Streptococcus pneumoniae↗

PubMed2026

Carbapenemase-producing Acinetobacter baumannii from Spanish hospitals, 2016-2020: Interregional spread of ST2PAS isolates co-harbouring blaOXA-23, blaOXA-66 and armA genes.

INTRODUCTION AND AIMS: Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a serious global threat, prioritized by the World Health Organization for new antibiotic development. The European Centre for Disease Prevention and Control proposed the integration of genomic sequencing into surveillance. This study characterizes phenotypic and genotypic features of nationwide-collected CRAB isolates from Spanish hospitals (2016-2020). MATERIALS AND METHODS: A total of 822 CRAB isolates sent to the Spanish reference laboratory were analysed, and 108 representative isolates were selected from 48 hospitals in 25 Spanish provinces. Antibiotic susceptibility was determined according to European Committee on Antimicrobial Susceptibility Testing guidelines, and WGS was performed by Illumina. Resistome, virulome, phylogeny (core-genome Multi-Locus Sequence-Typing; 2390 genes), insertion sequences and plasmids were analysed. RESULTS: Of the 108 representative isolates, 68.5% produced OXA-23, 10.2% OXA-24, 7.4% OXA-58, 1.9% NDM-1 and 2.7% others. 3.7% co-produced two acquired carbapenemases, and six that did not have them showed the ISAba1 upstream of the blaOXA-51 like. The predominant sequence types were ST2pas (82.4%) and ST218Oxf (61.1%). blaOXA-66 chromosomal carbapenemase allele was present in 75% of the 108 isolates, armA 16 s rRNA methyltransferase gene in 61.1%, and the kL-7/OCL-18 was present in 59.3% of the isolates. The most active antibiotic was colistin. Overall, 65.4% of invasive cases were caused by isolates harbouring all 38 virulence genes tested. In 64.8% of isolates a plasmid type was detected, mainly pS32-1-like (54.6%). CONCLUSIONS: In Spain, CRAB dissemination is driven by interregional spread of isolates belonging to the ST218Oxf/ST2Pas clones, characterized by the blaOXA-23/blaOXA-66 genotype, the presence of armA, the KL7/OCL18 capsular profile and the presence of pS32-1 plasmid.

K Locus↗

PubMed2005

An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences.

BACKGROUND: The concept of a genomic core, defined as the set of genes ubiquitous in all genomes of a monophyletic group, has become crucial in comparative and evolutionary genomics. However, it is still a matter of debate whether lateral gene transfers (LGT) may affect the components of genomic cores, preventing their use to retrace species evolution. We have recently reconstructed the phylogeny of Archaea by using two large concatenated datasets of core proteins involved in translation and transcription, respectively. The resulting trees were largely congruent, showing that informational gene components of the archaeal genomic core belonging to two distinct molecular systems contain a coherent signal for archaeal phylogeny. However, some incongruence remained between the two phylogenies. This may be due either to undetected LGT and/or to a lack of sufficient phylogenetic signal in the datasets. RESULTS: We present evidence strongly favoring of the latter hypothesis. In fact, we have updated our transcription and translation datasets with five new archaeal genomes for a total of 6384 and 2928 amino acid positions, respectively, and 25 taxa. This increase in taxonomic sampling led to the nearly complete convergence of the transcription-based and translation-based trees on a single phylogenetic pattern for archaeal evolution. In fact, only a single incongruence persisted between the two phylogenies. This concerned Methanopyrus kandleri, whose placement remained strongly biased in the transcription tree due to its above average evolutionary rates, and could not be counterbalanced due to the lack of availability of closely related and/or slower-evolving relatives. CONCLUSION: To our knowledge, this is the first report of evidence that the phylogenetic signal harbored by components of the archaeal translation apparatus is confirmed by additional markers belonging to a second molecular system (i.e. transcription). This rules out the risk of circularity when inferring species evolution by small subunit ribosomal RNA and ribosomal protein sequences, since it has been suggested that concerted LGT may affect these markers. Our results strongly support the existence of a core of proteins that has evolved mainly through vertical inheritance in Archaea, and carries a bona fide phylogenetic signal that can be used to retrace the evolutionary history of this domain. The identification and analysis of additional molecular markers not affected by LGT should continue defining the emerging picture of a genuine phylogenetic core for the third domain of life.

Algorithms↗

PubMed2026

Characterisation of Carbapenem-Resistant Raoultella planticola and Structural Analysis of NDM Composite Plasmids.

OBJECTIVE: This study aimed to investigate the molecular characteristics, resistant plasmid structures and phylogeny of a carbapenem-resistant Raoultella planticola (CRRP) strain from a patient with pneumonia to inform antimicrobial resistance control strategies. METHODS: We performed strain identification using MALDI-TOF MS, the BD Phoenix 100 system and whole-genome sequencing (WGS). We assessed antimicrobial susceptibility and resistance gene transfer using PCR, conjugation and stability assays, plasmid structure using a bioinformatics tool and phylogeny using a core-genome phylogenetic tree. RESULTS: WGS confirmed the isolate as R. planticola (average nucleotide identity (ANI) > 98.9% with reference type strains), co-harbouring blaKPC-2 and blaNDM-1. It was resistant to 19 antimicrobial agents and susceptible to only polymyxin, amikacin and chloramphenicol. Resistance genes were present on two conjugative plasmids: pzwx_KPC (IncFIA) and pzwx_NDM (a novel repFIB/repHI5B hybrid assembled via non-homologous end joining). Both plasmids demonstrated efficient transfer and stable inheritance over 12 passages. pzwx_KPC was highly homologous to plasmids from Klebsiella pneumoniae. Phylogenetic analysis revealed the closest relationship with German R. planticola strains. CONCLUSION: CRRP carries highly transmissible and stable resistance plasmids. Strengthened monitoring in immunocompromised patients and improved environmental disinfection are recommended. The risk of misidentification by automated systems underscores the importance of WGS for accurate pathogen identification.

Carbapenem resistance↗

PubMed2026

Comparative genomics of ESKAPE pathogen species: Integrating pan-genome architecture, antimicrobial resistance, and virulence factor repertoires.

BACKGROUND: ESKAPE pathogens are major causes of hospital-acquired infections and are characterized by extensive antimicrobial resistance (AMR) and diverse virulence mechanisms. Although species-specific pan-genome studies have revealed substantial genomic diversity, the relationships among genome plasticity, resistance burden, and virulence remain incompletely understood across the ESKAPE complex. METHODS: We analyzed 120 high-quality genomes representing six single-species ESKAPE groups (20 genomes per species). Genome quality was assessed using CheckM2. Species-specific pan-genomes were constructed with Roary, AMR genes were identified using AMRFinderPlus, and virulence factors were detected against the VFDB database using DIAMOND. AMR genes were mapped to core and accessory genome compartments through integration of Prokka annotations and Roary outputs. Statistical associations were evaluated using Fisher's exact tests and correlation analyses, with false discovery rate correction applied within each test family. Core-genome maximum-likelihood phylogenies were reconstructed to provide an evolutionary framework. RESULTS: Pan-genome sizes ranged from 4720 to 17,272 genes, with Enterobacter and Pseudomonas possessing the largest accessory genomes. Multidrug resistance (MDR; resistance to ≥3 antimicrobial classes) was detected in 93.3% of strains. After false discovery rate correction, AMR genes remained significantly enriched in the accessory genomes of Enterobacter, Enterococcus, Klebsiella, and Staphylococcus, whereas Acinetobacter and Pseudomonas did not show significant enrichment in either genome compartment. Within-species analyses identified significant positive associations between accessory genome size and AMR class burden in Staphylococcus, Enterococcus, and Enterobacter, whereas the moderate Pearson correlation observed in Pseudomonas was not significant after FDR correction. Virulence factor repertoires varied markedly among species, with Pseudomonas exhibiting the highest burden and Enterococcus the lowest. CONCLUSIONS: ESKAPE pathogens display distinct patterns of resistance and virulence. Accessory genome expansion was associated with higher AMR burden in several species, whereas other species showed no significant association between accessory genome size and AMR burden and no significant enrichment of AMR genes in either genome compartment, highlighting the species-specific nature of AMR evolution.

Virulence Factors↗

PubMed2003

Horizontal gene transfer and phylogenetics.

The initial analysis of complete genomes has suggested that horizontal gene transfer events are very frequent between microorganisms. This could potentially render the inference, and even the concept itself, of the organismal phylogeny impossible. However, a coherent phylogenetic pattern has recently emerged from an analysis of about a hundred genes, the so-called 'core', strongly suggesting that it is possible to infer the phylogeny of prokaryotes. Also, estimation of the frequency of horizontal gene transfers at the genome level in a phylogenetic context seems to indicate that it is rather low, although of significant biological impact. Nevertheless, it should be emphasized that the history of microorganisms cannot be properly represented by the phylogeny of the core, which represents only a tiny fraction of the genome. This history, even if horizontal gene transfers are rare, should be represented by a network surrounding the core phylogeny.

Bacteria↗

PubMed2026

Whole-Genome Analysis Reveals Antimicrobial Resistance and Population Structure of Environmental and Veterinary Acinetobacter baumannii.

Acinetobacter (A.) baumannii is an important multidrug-resistant pathogen increasingly recognized across animal and environmental settings, and carbapenem-resistant A. baumannii (CRAB) is classified as a critical-priority pathogen by the World Health Organization. This study investigated the antimicrobial resistance (AMR) and genomic characteristics of 122 A. baumannii isolates comprising 72 veterinary and 50 environmental isolates collected in Andhra Pradesh, India. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), resistance and virulence gene profiling, multilocus sequence typing (MLST), core-genome analysis, single nucleotide polymorphism (SNP) phylogeny, and pan-genome analysis were performed. Overall, 58.2% of isolates were multidrug-resistant (MDR), and 41.8% were extensively drug-resistant (XDR). Sequence type (ST) 52 predominated among veterinary isolates, whereas ST2 was more frequent among environmental isolates. The presence of carbapenem-resistant isolates along with the ST2 lineage enhances the similarity to clinical A. baumannii. Several intrinsic resistance genes, including blaOXA-23, armA, aph(3″)-Ib, aph(6)-Id, tet(B), mph(E), and msr(E), were more prevalent in the ST2-associated population. Virulence-associated determinants were widely conserved. Core-genome MLST (cgMLST) and core-genome SNP (cgSNP) analyses identified highly related isolates within both lineages, while pairwise SNP differences were 0-7. Pan-genome analysis identified 4204 gene clusters and distinct accessory gene patterns between ST2 and ST52. These findings indicate that resistance gene distribution was closely associated with lineage structure and support integrated genomic surveillance of A. baumannii across animal and environmental reservoirs.

Acinetobacter baumannii↗

PubMed2026

Comprehensive genomic and computational insights into Brucella suis: pan-genome analysis, evolutionary perspectives, and in-silico vaccine design.

BACKGROUND: Brucella suis is a zoonotic intracellular pathogen responsible for brucellosis, mainly in swine and humans. Although numerous genome sequences are publicly available, an integrative genomic analysis combining pan-genome architecture, structural organization, evolutionary relationships, and vaccine-associated targets remains limited. RESULTS: In this study, we analyzed 91 publicly available B.suis genomes to characterize their pan-genome composition and genomic structure. The pan-genome exhibited an open configuration, indicating continued genomic diversification. A total of 2,146 core genes were identified, representing conserved functions essential for species maintenance, while the accessory genome reflected strain-level variability. Phylogenetic reconstruction based on single-copy orthologs revealed distinct evolutionary clades among the strains. A complementary phylogenetic analysis of pan-genome gene presence-absence patterns further supported clade differentiation and highlighted variation in accessory gene repertoires. Comparative synteny and genome structural analyses demonstrated largely conserved chromosomal organization with localized rearrangements across strains. Screening of the core proteome identified 64 putative antigenic proteins with predicted surface localization and immunogenic properties. Additionally, resistance-associated determinants related to tetracycline and doxycycline were detected in one genome within the dataset. CONCLUSIONS: This comprehensive genomic analysis defines the pan-genome structure, evolutionary relationships, and genome organization of B.suis. The integration of core and pan-genome-based phylogenies provides complementary insights into strain diversification, while the identified conserved antigenic candidates offer a foundation for future experimental validation and rational vaccine development strategies.

Genome, Bacterial↗

PubMed2002

A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history.

It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data. For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogies by using a BLAST reciprocal best hit definition of orthology. In addition, concatenation of sequences of different genes as well as building of consensus trees only consider the few genes that are shared among all organisms. Here we present an attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny. This led us to perform a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny. We then used this core of genes to infer a tree. This phylogeny presents several differences with the rRNA phylogeny, notably for the position of hyperthermophilic bacteria.

Computational Biology↗

PubMed2006

The genome of Rhizobium leguminosarum has recognizable core and accessory components.

BACKGROUND: Rhizobium leguminosarum is an alpha-proteobacterial N2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. RESULTS: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens. CONCLUSION: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.

ATP-Binding Cassette Transporters↗

PubMed1996

Anoxygenic phototrophy across the phylogenetic spectrum: current understanding and future perspectives

The phylogenetic heterogeneity of anoxygenic phototrophic bacteria has been revealed by 16S rRNA sequence analysis, the results of which have led to extensive taxonomic rearrangements within previously defined taxa of phototrophs and stimulated interest in this group of organisms. Anoxygenic photosynthetic bacteria can be found within 4 of the 12 phylogenetic lineages, and in some cases are highly related to non-photosynthetic members of these groups. The largest number of phototrophs are found in the class Proteobacteria. Comparative phylogenetic analysis using 23S rDNA sequences generally supports the topology obtained from 16S rDNA sequences. The photosynthetic reaction centers are conserved in all photosynthetic bacteria, and are of two types. One is shared by the Proteobacteria and Chloroflexus aurantiacus and is similar to Photosystem II of cyanobacteria, while heliobacteria and Chlorobium and relatives possess a reaction center similar to the cyanobacterial Photosystem I. These similarities are supported by sequence analysis of core reaction center peptides, but contradict phylogenies reconstructed from rRNA sequence analysis. Genome analysis by means of physical mapping has been performed for only three species of anoxygenic phototrophs. Some conservation of operon structure and gene sequence has been found within the Proteobacteria, but does not extend to other phototrophs.

Journal Article↗

PubMed2002

Genomic and phylogenetic analyses of an adenovirus isolated from a corn snake (Elaphe guttata) imply a common origin with members of the proposed new genus Atadenovirus.

Approximately 60% of the genome of an adenovirus isolated from a corn snake (Elaphe guttata) was cloned and sequenced. The results of homology searches showed that the genes of the corn snake adenovirus (SnAdV-1) were closest to their counterparts in members of the recently proposed new genus ATADENOVIRUS: In phylogenetic analyses of the complete hexon and protease genes, SnAdV-1 indeed clustered together with the atadenoviruses. The characteristic features in the genome organization of SnAdV-1 included the presence of a gene homologous to that for protein p32K, the lack of structural proteins V and IX and the absence of homologues of the E1A and E3 regions. These characteristics are in accordance with the genus-defining markers of atadenoviruses. Comparison of the cleavage sites of the viral protease in core protein pVII also confirmed SnAdV-1 as a candidate member of the genus ATADENOVIRUS: Thus, the hypothesis on the possible reptilian origin of atadenoviruses (Harrach, Acta Veterinaria Hungarica 48, 484-490, 2000) seems to be supported. However, the base composition of DNA sequence (>18 kb) determined from the SnAdV-1 genome showed an equilibrated GC content of 51%, which is unusual for an atadenovirus.

Adenoviridae↗