scholarly journals Investigation of the Evolutionary Development of the Genus Bifidobacterium by Comparative Genomics

2014 ◽  
Vol 80 (20) ◽  
pp. 6383-6394 ◽  
Author(s):  
Gabriele Andrea Lugli ◽  
Christian Milani ◽  
Francesca Turroni ◽  
Sabrina Duranti ◽  
Chiara Ferrario ◽  
...  
Keyword(s):  
Sequence Comparison ◽  
Core Genome ◽  
Genetic Relatedness ◽  
Single Gene ◽  
Evolutionary Development ◽  
Genome Sequences ◽  
Separate Species ◽  
Content Type ◽  
Relative Paucity ◽  
A Genome

ABSTRACTTheBifidobacteriumgenus currently encompasses 48 recognized taxa, which have been isolated from different ecosystems. However, the current phylogeny of bifidobacteria is hampered by the relative paucity of genotypic data. Here, we reassessed the taxonomy of this bacterial genus using genome-based approaches, which demonstrated that the previous taxonomic view of bifidobacteria contained several inconsistencies. In particular, high levels of genetic relatedness were shown to exist between particularBifidobacteriumtaxa which would not justify their status as separate species. The results presented are here based on average nucleotide identity analysis involving the genome sequences for each type strain of the 48 bifidobacterial taxa, as well as phylogenetic comparative analysis of the predicted core genome of theBifidobacteriumgenus. The results of this study demonstrate that the availability of complete genome sequences allows the reconstruction of a more robust bifidobacterial phylogeny than that obtained from a single gene-based sequence comparison, thus discouraging the assignment of a new or separate bifidobacterial taxon without such a genome-based validation.

scholarly journals Characterization of HypermutatorPseudomonas aeruginosaIsolates from Patients with Cystic Fibrosis in Australia

2019 ◽  
Vol 63 (4) ◽  
Author(s):  
Vanessa E. Rees ◽  
Deanna S. Deveson Lucas ◽  
Carla López-Causapé ◽  
Yuling Huang ◽  
Tom Kotsimbos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Health Care ◽  
Cystic Fibrosis ◽  
Core Genome ◽  
Genetic Relatedness ◽  
Phylogenetic Analyses ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type

ABSTRACTHypermutablePseudomonas aeruginosaisolates (hypermutators) have been identified in patients with cystic fibrosis (CF) and are associated with reduced lung function. Hypermutators display a greatly increased mutation rate and an enhanced ability to become resistant to antibiotics during treatment. Their prevalence has been established among patients with CF, but it has not been determined for patients with CF in Australia. This study aimed to determine the prevalence of hypermutableP. aeruginosaisolates from adult patients with CF from a health care institution in Australia and to characterize the genetic diversity and antibiotic susceptibility of these isolates. A total of 59 P. aeruginosaclinical isolates from patients with CF were characterized. For all isolates, rifampin (RIF) mutation frequencies and susceptibility to a range of antibiotics were determined. Of the 59 isolates, 13 (22%) were hypermutable. Whole-genome sequences were determined for all hypermutable isolates. Core genome polymorphisms were used to assess genetic relatedness of the isolates, both to each other and to a sample of previously characterizedP. aeruginosastrains. Phylogenetic analyses showed that the hypermutators were from divergent lineages and that hypermutator phenotype was mostly the result of mutations inmutLor, less commonly, inmutS. Hypermutable isolates also contained a range of mutations that are likely associated with adaptation ofP. aeruginosato the CF lung environment. Multidrug resistance was more prevalent in hypermutable than nonhypermutable isolates (38% versus 22%). This study revealed that hypermutableP. aeruginosastrains are common among isolates from patients with CF in Australia and are implicated in the emergence of antibiotic resistance.

Classification of Pasteurella species B as Pasteurella oralis sp. nov.

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1396-1401 ◽  
Author(s):  
Henrik Christensen ◽  
Mads F. Bertelsen ◽  
Anders Miki Bojesen ◽  
Magne Bisgaard
Keyword(s):  
Related Species ◽  
Sequence Comparison ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Species Status ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
A Genome

Pasteurella species B has so far only been reported from the oral cavity of dogs, cats and a ferret. In the present study, information from 15 recent isolates from different sources, including African hedgehogs (Atelerix albiventris), banded mongoose (Mungos mungo), Moholi bushbabies (Galago moholi) and pneumonia of a cat, were compared to five strains investigated previously from bite wounds in humans inflicted by a cat and dog and from gingiva of a cat. rpoB gene sequence comparison showed that 17 isolates, including the reference strain (CCUG 19794T), had identical sequences, whereas two were closely related and demonstrated 97.9 and 99.6 % similarity to strain CCUG 19794T, respectively; the type strain of Pasteurella stomatis was the most closely related strain, with 92.3 % similarity. This is within the mean range (76–100 %) of rpoB gene sequence similarity between species of the same genus within the family Pasteurellaceae . 16S rRNA gene sequencing of four strains selected based on rpoB sequence comparison showed at least 99.7 % similarity between strains of Pasteurella species B, with 96.2 % similarity to the type strain of the closest related species ( Pasteurella canis ), indicating that Pasteurella species B should have separate species status. Separate species status was also documented when recN sequence comparisons were converted to a genome similarity of 93.7 % within Pasteurella species B and 59.0 % to the type strain of the closest related species ( P. canis ). Based on analysis of the phylogenetic and phenotypic data, and since most isolates originate from the oral cavities of a diverse group of animals, it is suggested that these bacteria be classified as Pasteurella oralis sp. nov.; the type strain is P683T ( = CCUG 19794T = CCM 7950T = strain 23193T = MCCM 00102T), obtained from a cat. Previous reports of the type strain have shown ubiquinone-8, demethylmenaquinone-8 and menaquinone-8 as the major quinones. Polyamines in the type strain were reported as diaminopropane, putrescine, cadaverine, sym-norspermidine, spermidine and spermine in a previous investigation, and the major fatty acids of the type strain were reported to be C16 : 0, C16 : 1ω7c and C14 : 0, with minor amounts of C18 : 0 and C18 : 1ω9c. The DNA G+C content of the type strain has been reported to be 40.0 mol%.

scholarly journals Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Kenan Jijakli ◽  
Paul A. Jensen
Keyword(s):  
Streptococcus Mutans ◽  
Single Gene ◽  
Metabolic Model ◽  
The United States ◽  
Defined Medium ◽  
Oral Microbiome ◽  
Tooth Decay ◽  
Oral Pathogen ◽  
Content Type ◽  
A Genome

ABSTRACT Streptococcus mutans is a Gram-positive bacterium that thrives under acidic conditions and is a primary cause of tooth decay (dental caries). To better understand the metabolism of S. mutans on a systematic level, we manually constructed a genome-scale metabolic model of the S. mutans type strain UA159. The model, called iSMU, contains 675 reactions involving 429 metabolites and the products of 493 genes. We validated iSMU by comparing simulations with growth experiments in defined medium. The model simulations matched experimental results for 17 of 18 carbon source utilization assays and 47 of 49 nutrient depletion assays. We also simulated the effects of single gene deletions. The model’s predictions agreed with 78.1% and 84.4% of the gene essentiality predictions from two experimental data sets. Our manually curated model is more accurate than S. mutans models generated from automated reconstruction pipelines and more complete than other manually curated models. We used iSMU to generate hypotheses about the S. mutans metabolic network. Subsequent genetic experiments confirmed that (i) S. mutans catabolizes sorbitol via a sorbitol-6-phosphate 2-dehydrogenase (SMU_308) and (ii) the Leloir pathway is required for growth on complex carbohydrates such as raffinose. We believe the iSMU model is an important resource for understanding the metabolism of S. mutans and guiding future experiments. IMPORTANCE Tooth decay is the most prevalent chronic disease in the United States. Decay is caused by the bacterium Streptococcus mutans, an oral pathogen that ferments sugars into tooth-destroying lactic acid. We constructed a complete metabolic model of S. mutans to systematically investigate how the bacterium grows. The model provides a valuable resource for understanding and targeting S. mutans’ ability to outcompete other species in the oral microbiome.

scholarly journals Hash-Based Core Genome Multilocus Sequence Typing for Clostridium difficile

2019 ◽  
Vol 58 (1) ◽  
Author(s):  
David W. Eyre ◽  
Tim E. A. Peto ◽  
Derrick W. Crook ◽  
A. Sarah Walker ◽  
Mark H. Wilcox
Keyword(s):  
Clostridium Difficile ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Genetic Relationships ◽  
Nucleotide Polymorphisms ◽  
Content Type ◽  
Recent Transmission ◽  
A Genome ◽  
Performance Penalty

ABSTRACT Pathogen whole-genome sequencing has huge potential as a tool to better understand infection transmission. However, rapidly identifying closely related genomes among a background of thousands of other genomes is challenging. Here, we describe a refinement to core genome multilocus sequence typing (cgMLST) in which alleles at each gene are reproducibly converted to a unique hash, or short string of letters (hash-cgMLST). This avoids the resource-intensive need for a single centralized database of sequentially numbered alleles. We test the reproducibility and discriminatory power of cgMLST/hash-cgMLST compared to those of mapping-based approaches in Clostridium difficile, using repeated sequencing of the same isolates (replicates) and data from consecutive infection isolates from six English hospitals. Hash-cgMLST provided the same results as standard cgMLST, with minimal performance penalty. Comparing 272 replicate sequence pairs using reference-based mapping, there were 0, 1, or 2 single-nucleotide polymorphisms (SNPs) between 262 (96%), 5 (2%), and 1 (<1%) of the pairs, respectively. Using hash-cgMLST, 218 (80%) of replicate pairs assembled with SPAdes had zero gene differences, and 31 (11%), 5 (2%), and 18 (7%) pairs had 1, 2, and >2 differences, respectively. False gene differences were clustered in specific genes and associated with fragmented assemblies, but were reduced using the SKESA assembler. Considering 412 pairs of infections with ≤2 SNPS, i.e., consistent with recent transmission, 376 (91%) had ≤2 gene differences and 16 (4%) had ≥4. Comparing a genome to 100,000 others took <1 min using hash-cgMLST. Hash-cgMLST is an effective surveillance tool for rapidly identifying clusters of related genomes. However, cgMLST/hash-cgMLST generate more false variants than mapping-based approaches. Follow-up mapping-based analyses are likely required to precisely define close genetic relationships.

scholarly journals Draft Genome Sequences and Complete Sequences of Two Plasmids of Escherichia coli Strain BOq 01, a Multiple-Antibiotic-Resistant Strain Isolated from a Poultry Farm in Mexico

2018 ◽  
Vol 7 (20) ◽  
Author(s):  
Armando Hernández-Mendoza ◽  
Daniel Rivera Mendoza ◽  
Abimael Moran-Vazquez ◽  
Edgar Dantán-González
Keyword(s):  
Escherichia Coli ◽  
Draft Genome ◽  
Gc Content ◽  
Coli Strain ◽  
Poultry Farm ◽  
Genome Sequences ◽  
Antibiotic Resistant ◽  
Content Type ◽  
A Genome ◽  
Complete Sequences

We report here the draft genome sequence of Escherichia coli strain BOq 01, a bacterium isolated from a poultry farm; the genome includes two plasmids conferring antibiotic resistances. This bacterium has a GC content of 50.89% and a genome size of 4.6 Mb.

scholarly journals Clostridioides difficile Whole-Genome Sequencing Reveals Limited Within-Host Genetic Diversity in a Pediatric Cohort

2019 ◽  
Vol 57 (9) ◽  
Author(s):  
Aakash Balaji ◽  
Egon A. Ozer ◽  
Larry K. Kociolek
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Core Genome ◽  
Genetic Relatedness ◽  
The Other ◽  
Whole Genome ◽  
Content Type ◽  
Clostridioides Difficile ◽  
Host Genetic

ABSTRACT Whole-genome sequencing (WGS) is a highly sensitive method for identifying genetic relatedness and transmission of Clostridioides difficile strains. Previous studies suggest that as few as 3 core genome single-nucleotide variants (SNVs) discriminate between genetically distinct isolates. Because a single C. difficile colony is selected from culture for WGS, significant within-host genetic diversity could preclude identification of transmission events. To evaluate the likelihood of missed transmission events using WGS of single colonies from culture, we examined within-host genetic diversity among C. difficile isolates collected from children. We performed WGS using an Illumina MiSeq instrument on 8 C. difficile colonies randomly selected from each culture performed on stool collected from 10 children (8 children diagnosed with C. difficile infection and 2 children with asymptomatic carriage); 77/80 (96%) isolate sequences were successfully assembled. Among 8/10 (80%) children, all isolates were the same sequence type (ST). The other 2 children each had mixed infection with two STs, although one ST predominated. Among 9/10 (90%) children, isotypic isolates differed by ≤2 SNVs; an isotypic isolate in the remaining child differed by 3 to SNVs relative to the other isolates from that child. Overall, among the 77 isolates collected from 10 stool cultures, 74/77 (96%) were clonal (i.e., same ST and ≤2 core genome SNVs) to other isolates in stool culture. In summary, we identified rare C. difficile within-host genetic diversity in children, suggesting that WGS of a single colony from stool is likely to appropriately characterize isolate clonality and putative transmission events in the majority of cases.

scholarly journals A Genome-Based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Nathan B. Pincus ◽  
Egon A. Ozer ◽  
Jonathan P. Allen ◽  
Marcus Nguyen ◽  
James J. Davis ◽  
...  
Keyword(s):  
Machine Learning ◽  
Pseudomonas Aeruginosa ◽  
Core Genome ◽  
Learning Models ◽  
Single Nucleotide Variants ◽  
Bacterial Genomes ◽  
Content Type ◽  
Accessory Genome ◽  
A Genome ◽  
Machine Learning Models

ABSTRACT Variation in the genome of Pseudomonas aeruginosa, an important pathogen, can have dramatic impacts on the bacterium’s ability to cause disease. We therefore asked whether it was possible to predict the virulence of P. aeruginosa isolates based on their genomic content. We applied a machine learning approach to a genetically and phenotypically diverse collection of 115 clinical P. aeruginosa isolates using genomic information and corresponding virulence phenotypes in a mouse model of bacteremia. We defined the accessory genome of these isolates through the presence or absence of accessory genomic elements (AGEs), sequences present in some strains but not others. Machine learning models trained using AGEs were predictive of virulence, with a mean nested cross-validation accuracy of 75% using the random forest algorithm. However, individual AGEs did not have a large influence on the algorithm’s performance, suggesting instead that virulence predictions are derived from a diffuse genomic signature. These results were validated with an independent test set of 25 P. aeruginosa isolates whose virulence was predicted with 72% accuracy. Machine learning models trained using core genome single-nucleotide variants and whole-genome k-mers also predicted virulence. Our findings are a proof of concept for the use of bacterial genomes to predict pathogenicity in P. aeruginosa and highlight the potential of this approach for predicting patient outcomes. IMPORTANCE Pseudomonas aeruginosa is a clinically important Gram-negative opportunistic pathogen. P. aeruginosa shows a large degree of genomic heterogeneity both through variation in sequences found throughout the species (core genome) and through the presence or absence of sequences in different isolates (accessory genome). P. aeruginosa isolates also differ markedly in their ability to cause disease. In this study, we used machine learning to predict the virulence level of P. aeruginosa isolates in a mouse bacteremia model based on genomic content. We show that both the accessory and core genomes are predictive of virulence. This study provides a machine learning framework to investigate relationships between bacterial genomes and complex phenotypes such as virulence.

scholarly journals The Divided Bacterial Genome: Structure, Function, and Evolution

2017 ◽  
Vol 81 (3) ◽  
Author(s):  
George C. diCenzo ◽  
Turlough M. Finan
Keyword(s):  
Meta Analysis ◽  
Bacterial Genome ◽  
Genome Structure ◽  
Dna Molecules ◽  
Human Pathogens ◽  
Genome Sequences ◽  
Bacterial Genomes ◽  
Content Type ◽  
A Genome ◽  
And Function

SUMMARY Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure.

scholarly journals Complete Genome Sequences of Microbacterium Bacteriophages Danno, Otwor, and Scumberland, Isolated in Clarksville, Tennessee

2021 ◽  
Vol 10 (13) ◽  
Author(s):  
Sergei A. Markov ◽  
James C. Church ◽  
Leong Lee ◽  
Cole M. Bell ◽  
Sarah D. Binkley ◽  
...  
Keyword(s):  
Complete Genome ◽  
Soil Samples ◽  
Genome Sequences ◽  
Content Type ◽  
A Genome

ABSTRACT This paper reports the genome sequences of bacteriophages isolated from soil samples using Microbacterium foliorum. Phages Danno and Otwor (cluster EE) have genomes of 17,452 bp and 17,454 bp, respectively, and 25 predicted genes. The phage Scumberland (cluster EC) has a genome of 53,276 bp with 92 predicted genes.

scholarly journals Genome Sequences of the Mycobacteriophages Awesomesauce and LastJedi

2020 ◽  
Vol 9 (34) ◽  
Author(s):  
Madison E. Davis ◽  
Véronique A. Delesalle ◽  
Kayla D. Blankenship ◽  
Jeffrey T. Good ◽  
Clayr M. Kroenke ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Mycobacterium Smegmatis ◽  
Sequence Comparison ◽  
Whole Genome ◽  
Genome Sequences ◽  
Protein Coding ◽  
Content Type ◽  
Nucleotide Sequence Comparison ◽  
Protein Coding Genes

ABSTRACT Bacteriophages Awesomesauce and LastJedi infect Mycobacterium smegmatis mc2155. While the Awesomesauce genome is 57,054 bp with 94 protein-coding genes, the LastJedi genome is 55,149 bp with 94 protein-coding genes. Nucleotide sequence comparison in Phamerator detected synteny between Awesomesauce gp49 to gp61 and singleton LilSpotty. Whole-genome BLASTn alignments revealed that LastJedi strongly resembles Clifton (99.41% identity).

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