Draft Genome Sequences from a Novel Clade of Bacillus cereus
            <i>Sensu Lato</i>
            Strains, Isolated from the International Space Station

Venkateswaran, Kasthuri; Sielaff, Aleksandra Checinska; Ratnayake, Shashikala; Pope, Robert K.; Blank, Thomas; Степанов, В. П.; Fox, George E.; Tongeren, Sandra P. van; Torres, Clinton; Allen, Jonathan; Jaing, Crystal; Pierson, Duane L.; Perry, Jay L.; Koren, Sergey; Phillippy, Adam M.; Klubnik, Joy; Treangen, Todd J.; Rosovitz, M. J.; Bergman, Nicholas H.

doi:10.1128/genomea.00680-17

Cited by 16 publications

(14 citation statements)

References 11 publications

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“…To demonstrate how difficult sequences from this group have been to classify over time, simulated reads were created for two Bacillus cereus strains. The first, B. cereus VD118, is a strain available in RefSeq version 60 and beyond, and the second, B. cereus ISSFR-23F 17 , was recently isolated from the International Space Station and is not present in any of the RefSeq releases tested. It is phylogenetically close to B. anthracis , but lacks the phylogenetic and species characteristics of B. anthracis.…”

Section: Resultsmentioning

confidence: 99%

“…To test the ability to classify reads from genomes not in the bacterial RefSeq database 10,000 simulated single-end Illumina reads (101 bp) were created using Grinder 24 with default settings from: (i) a Bacillus cereus genome, B. cereus VD118, not present in RefSeq until verion 60 and beyond; and (ii) a novel B. cereus genome, B. cereus ISSFR-23F 17 , never present in any of the RefSeq versions tested. We decided to use these genomes as they are members of the B. cereus sensu lato group, containing a collection of species that are known to be challenging for k-mer methods to distinguish between 19,20 .…”

Section: Methodsmentioning

confidence: 99%

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RefSeq database growth influences the accuracy of k-mer-based species identification

Nasko

Koren

Phillippy

et al. 2018

Preprint

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10Accurate species-level taxonomic classification and profiling of complex microbial communities 11 remains a challenge due to homologous regions shared among closely related species and a 12 sparse representation of non-human associated microbes in the database. Although the database 13 undoubtedly has a strong influence on the sensitivity of taxonomic classifiers and profilers, to 14 date, no study has carefully explored this topic on historical RefSeq releases and explored its 15 impact on accuracy. In this study, we examined the influence of the database, over time, on k-16 mer based sequence classification and profiling. We present three major findings: (i) database 17 growth over time resulted in more classified reads, but fewer species-level classifications and 18 more species-level misclassifications; (ii) Bayesian re-estimation of abundance helped to recover 19 species-level classifications when the exact target strain was present; and (iii) Bayesian re-20 estimation struggled when the database lacked the target strain, resulting in a notable decrease in 21 accuracy. In summary, our findings suggest that the growth of RefSeq over time has strongly 22 influenced the accuracy of k-mer based classification and profiling methods, resulting in 23 . CC-BY 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/304972 doi: bioRxiv preprint first posted online Apr. 19, 2018; 2 different classification results depending on the particular database used. These results suggest a 24 need for new algorithms specially adapted for large genome collections and better measures of 25 classification uncertainty. 26 27

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

RefSeq database growth influences the accuracy of k-mer-based species identification

Nasko

Koren

Phillippy

et al. 2018

Preprint

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“…Evaluation of a "first-pass" taxonomic classifier To demonstrate typical use of a first-pass taxonomic classification program, we analyzed all simulated reads from the B. cereus JEM-2 genome [34,35] with Kraken [36]. The majority of the reads (79%) were assigned to the Bacillus cereus group; of these, only 32% of the reads were assigned more specifically to B. cereus.…”

Section: Resultsmentioning

confidence: 99%

BLAST-based validation of metagenomic sequence assignments

Bazinet¹,

Ondov

Sommer³

et al. 2017

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When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments. Thus, in a bioforensic setting where correct assignments are paramount, assignments of interest made by "first-pass" classifiers should be confirmed using the most precise methods and comprehensive databases available. In this study we present a blast-based method for validating the assignments made by less precise sequence classification programs, with optimal parameters for filtering of blast results determined via simulation of sequence reads from genomes of interest, and we apply the method to the detection of four pathogenic organisms. The software implementing the method is open source and freely available.

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“…For example, all known pathogenic strains of B. anthracis contain a single nucleotide mutation that inactivates the PlcR gene. This feature was used to determine that a bacterium found during routine monitoring of the International Space Station (ISS) was not B. anthracis , as suggested by its morphological features, but instead a previously uncharacterized strain of Bacillus cereus , a usually non‐pathogenic relative of B. anthracis that is commonly found in soil and even on food .…”

Section: Databases Mattermentioning

confidence: 99%