BIGSdb: Scalable analysis of bacterial genome variation at the population level

Jolley, Keith A.; Maiden, Martin C. J.

doi:10.1186/1471-2105-11-595

Cited by 2,082 publications

(1,962 citation statements)

References 55 publications

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“…BIGSdb is a database designed to store bacterial sequences, and perform pre-defined analysis rapidly on them 32 . Trees from genomes in this database can be produced with the GenomeComparator module.…”

Section: Resultsmentioning

confidence: 99%

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Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

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Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined “true tree” using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

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Section: Resultsmentioning

confidence: 99%

“…Distances between core gene alleles (add a distance of zero for each core gene with identical sequence, add a distance of one if non-identical), as used in the BIGSdb genome comparator module 32 .…”

Section: Methodsmentioning

confidence: 99%

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

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“…The barcode region is by far the best represented in the databases, and the correct subtype can be identified by BLAST analysis in either GenBank or the new Blastocystis MLST database (www.pubmlst.org/blastocystis; (Jolley and Maiden, 2010;Stensvold et al, 2012a). The latter has the added advantages of automatically assigning allele types to the SSU-rDNA as well as using the consensus subtype nomenclature (unlike GenBank where the subtype is included only if one was part of the accession submission and no attempt to impose a standard nomenclature is made).…”

Section: Blastocystismentioning

confidence: 99%

Recent Developments in Blastocystis Research

Clark

Giezen

Alfellani

et al. 2013

Advances in Parasitology

251

216

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Abstract:Blastocystis is a common parasite of the human large intestine but has an uncertain role in disease. In this review, we appraise the published evidence addressing this and its weaknesses. Genetic diversity studies have led to the identification of numerous subtypes within the genus Blastocystis and, recently, methods for studying variation within subtypes have been developed, with implications for our understanding of host specificity. The geographic distribution of subtypes is summarised and the impact this may have on investigations into the role of the organism in disease is discussed. Finally, we describe the organelle and nuclear genome characteristics and look to future developments in the field.

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“…The first MLST database software to be developed [66][67][68] stored only isolate information, and allele and ST definitions. Newer platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) 69 extend the MLST, or gene-by-gene, approach to WGS data. BIGSdb encompasses all the functionality of the software formerly used for the MLST databases hosted on PubMLST 67,70 .…”

Section: Gene-by-gene Typing Infrastructurementioning

confidence: 99%

MLST revisited: the gene-by-gene approach to bacterial genomics

et al. 2013

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Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.Advances in nucleotide-sequencing technology have provided unparalleled access to the enormous genetic diversity that has accumulated in the bacterial domain during 3.5-4 billion years of evolution 1 . Numerous sets of whole-genome sequencing (WGS) data for bacterial isolates (BOX 1) are available 2 , and metagenomic studies using these technologies continue to reveal further, seemingly boundless, diversity in bacterial communities 3 . Faced with this plethora of information, microbiologists must develop structured means of describing this diversity and of linking phenotype and genotype, thereby facilitating an improved understanding of the microbiological world. Given that we have precise information on the function of only a very small proportion of bacterial genes, and no knowledge at all about most, this is a formidable, if extremely exciting, challenge.Here, we focus primarily on pathogenic bacteria, although the concepts discussed are applicable more widely to all bacteria and archaea. Bacterial pathogens played a crucial part in the development of experimental microbiology and remain the most intensively studied prokaryotes more than 100 years later 4 . Pathogens have emerged across the diversity of the bacterial -but, interestingly, not the archaeal -domain on many occasions and are both polyphyletic and highly diverse. Thus, although pathogens represent only a tiny subset of the bacterial world, the challenges faced by the clinical microbiology laboratory are representative of those faced by microbiology as a whole.Taxonomic and functional analyses are based on the observations that diversity among bacteria is not continuous and that distinct, stable types with particular properties exist 5 . These founding principles of microbiology 6 have been upheld by much subsequent research, but the study of such clusters remains largely descriptive, and the evolutionary mechanisms that led to cluster emergence and persistence remain incompletely understood 7,8 . Structuring is also evident within bacterial genomes, as diversity is unevenly distributed among genes Pre-WGS cataloguing of diversityA major advance in defining bacterial diversity was the proposal, by the late Carl Woese and colleagues, of a universal and 'natural' -that is, genealogical -classification system based on small-su...

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BIGSdb: Scalable analysis of bacterial genome variation at the population level

Cited by 2,082 publications

References 55 publications

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Recent Developments in Blastocystis Research

MLST revisited: the gene-by-gene approach to bacterial genomics

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