The importance of genome sequence quality to microbial comparative genomics

Smits, Theo H. M.

doi:10.1186/s12864-019-6014-5

Cited by 50 publications

(44 citation statements)

References 36 publications

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“…The core genome (which is almost 90% of total genome) refers to the conserved genes present in a species [ 57 ] which might differ in each individual strain within that species. Additionally, SNPs can be a result of poor sequencing quality and hence it is important to have a good sequencing depth at those positions to identify them as a mutation rather than sequencing error [ 58 ]. Grouping of all the isolates including ocular and non-ocular remained the same in both core and pan genome phylogeny.…”

Section: Discussionmentioning

confidence: 99%

Antibiotic Resistance Characteristics of Pseudomonas aeruginosa Isolated from Keratitis in Australia and India

et al. 2020

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This study investigated genomic differences in Australian and Indian Pseudomonas aeruginosa isolates from keratitis (infection of the cornea). Overall, the Indian isolates were resistant to more antibiotics, with some of those isolates being multi-drug resistant. Acquired genes were related to resistance to fluoroquinolones, aminoglycosides, beta-lactams, macrolides, sulphonamides, and tetracycline and were more frequent in Indian (96%) than in Australian (35%) isolates (p = 0.02). Indian isolates had large numbers of gene variations (median 50,006, IQR = 26,967–50,600) compared to Australian isolates (median 26,317, IQR = 25,681–33,780). There were a larger number of mutations in the mutL and uvrD genes associated with the mismatch repair (MMR) system in Indian isolates, which may result in strains losing their efficacy for DNA repair. The number of gene variations were greater in isolates carrying MMR system genes or exoU. In the phylogenetic division, the number of core genes were similar in both groups, but Indian isolates had larger numbers of pan genes (median 6518, IQR = 6040–6935). Clones related to three different sequence types—ST308, ST316, and ST491—were found among Indian isolates. Only one clone, ST233, containing two strains was present in Australian isolates. The most striking differences between Australian and Indian isolates were carriage of exoU (that encodes a cytolytic phospholipase) in Indian isolates and exoS (that encodes for GTPase activator activity) in Australian isolates, large number of acquired resistance genes, greater changes to MMR genes, and a larger pan genome as well as increased overall genetic variation in the Indian isolates.

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Section: Discussionmentioning

confidence: 99%

Antibiotic Resistance Characteristics of Pseudomonas aeruginosa Isolated from Keratitis in Australia and India

et al. 2020

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“…With the use of long-read sequencing technologies, recent studies have been able to resolve the complete genomes of cherry pathogens into chromosomal and plasmid sequences (Hulin et al, 2018a;Ruinelli et al, 2019). Complete genomes can greatly improve the accuracy of downstream analyses by resolving highly repetitive regions and providing structural context to gene locations (Baltrus and Clark, 2019;Smits, 2019).…”

Section: Chang Ing Fru Its: the Role Of Horizontal G Ene Tr Ans Fermentioning

confidence: 99%

Cherry picking by pseudomonads: After a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits

et al. 2020

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Pseudomonas syringae is a bacterial species complex associated with plants and aquatic environments that has been reported to cause disease on over 180 plant species (Berge et al., 2014). The pathogen is important globally as it infects most major crops. Host-adapted strains are responsible for damaging disease epidemics when invading new territories, for example the outbreak of horse chestnut bleeding canker in northern Europe (Green et al., 2010; Steele et al., 2010) and kiwifruit canker in New Zealand (McCann et al., 2017). P. syringae strains were traditionally classified based on host of isolation into groups of pathogenic varieties (pathovars) that generally infect one or a few related plant species (Sarkar et al., 2006). Classification is now supported by genotypic data, leading to the proposal for distinct genomospecies, phylogroups or phylogenomic species based on DNA-DNA hybridization, multilocus sequence analysis (MLSA) or more recently, whole genome sequence data comparisons (Gomila et al., 2017). Nineteen phylogenomic species

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“…Newly sequenced genomes should be deposited and made publicly available via standard central databases (e.g., GenBank 1 , DDBJ 2 , ENA 3 ). A rigorous sequence quality control and annotation should be carried out (Smits, 2019) identifying the mobile and other genetic elements (e.g., CRISPR arrays) and predicting their functional properties, thereby estimating the safety of probiotic candidates regarding virulence factors and possible antibiotic resistance gene transfer. The European Food Safety Authority (EFSA) and recent publications recommend WGS to improve the monitoring of foodborne antimicrobial resistance (Collineau et al, 2019;Efsa et al, 2019) and workflows to assess risk-related gene traits based on WGS are available (Salvetti et al, 2016).…”

Section: Genetic Characterization and Modification Of Probioticsmentioning

confidence: 99%

Future of Probiotics and Prebiotics and the Implications for Early Career Researchers

et al. 2020

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The opportunities in the fields of probiotics and prebiotics to a great degree stem from what we can learn about how they influence the microbiota and interact with the host. We discuss recent insights, cutting-edge technologies and controversial results from the perspective of early career researchers innovating in these areas. This perspective emerged from the 2019 meeting of the International Scientific Association for Probiotics and Prebiotics-Student and Fellows Association (ISAPP-SFA). Probiotic and prebiotic research is being driven by genetic characterization and modification of strains, stateof-the-art in vitro, in vivo, and in silico techniques designed to uncover the effects of probiotics and prebiotics on their targets, and metabolomic tools to identify key molecules that mediate benefits on the host. These research tools offer unprecedented insights into the functionality of probiotics and prebiotics in the host ecosystem. Young scientists need to acquire these diverse toolsets, or form interconnected teams to perform comprehensive experiments and systematic analysis of data. This will be critical to identify microbial structure and co-dependencies at body sites and determine how administered probiotic strains and prebiotic substances influence the host. This and other strategies proposed in this review will pave the way for translating the health benefits observed during research into real-life outcomes. Probiotic strains and prebiotic products can contribute greatly to the amelioration of global issues threatening society. The intent of this article is to provide an early career researcher's perspective on where the biggest opportunities lie to advance science and impact human health.

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The importance of genome sequence quality to microbial comparative genomics

Cited by 50 publications

References 36 publications

Antibiotic Resistance Characteristics of Pseudomonas aeruginosa Isolated from Keratitis in Australia and India

Antibiotic Resistance Characteristics of Pseudomonas aeruginosa Isolated from Keratitis in Australia and India

Cherry picking by pseudomonads: After a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits

Future of Probiotics and Prebiotics and the Implications for Early Career Researchers

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