High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

Loman, Nicholas J.; Constantinidou, Chrystala; Chan, Jacqueline; Halachev, Mihail; Sergeant, Martin J.; Penn, Charles W.; Robinson, Esther; Pallen, Mark J.

doi:10.1038/nrmicro2850

Cited by 375 publications

(286 citation statements)

References 54 publications

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Section: Discussionmentioning

confidence: 99%

“…WGS studies of bacteria are currently in a golden age, with many resources and much interest being dedicated to the area as a whole and especially to WGS applications for clinical problems [36][37][38]63 . However, when this initial excitement has passed, it will be Europe PMC Funders Author Manuscripts necessary to move into a more prosaic exploitation phase, which will require the construction of sustainable infrastructures -sustainable both intellectually (that is, the concept of relating WGS data to typing and taxonomy) and physically (that is, the use of inter-operable data sets that are archived in accessible databases).…”

Section: Discussionmentioning

confidence: 99%

“…Current WGS technologies do not generate complete genome sequences; rather, they produce data that can be used to reconstruct most of the genome sequence 37 . The relative performances of different sequencing platforms have been recently reviewed 38,39 and are not further discussed here, but it is reasonable to suppose that the already very high data quality will continue to improve and that large numbers of very high-quality complete genomes are not too distant a prospect.…”

Section: Post-wgs Cataloguing Of Diversitymentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Post-wgs Cataloguing Of Diversitymentioning

confidence: 99%

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

et al. 2013

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“…The second group includes six techniques not based on PCR: CFE (Alessi et al 2011;Ocio and Brookes 1990), PLFA (Zhang et al 2007), FDA (Adam and Duncan 2001;Green et al 2006), SIP (Dumont and Murrell 2005), DNA arrays (Li and Liu 2003) and FISH (Moter and Göbel 2000). Finally, high-throughput sequencing technologies comprise six techniques: 454 (Mardis 2008), Illumina (Loman et al 2012), SOLiD (Magi et al 2010;Shokralla et al 2012), PGM (Egan et al 2012;Loman et al 2012), HeliScope (Magi et al 2010;Shokralla et al 2012) and SMRT (Schadt et al 2010). Some of these techniques are also applied to the study of plant genomics.…”

Section: Molecular Techniques For the Study Of Functional Groups Of Smentioning

confidence: 99%

Plant and microbe genomics and beyond: potential for developing a novel molecular plant nutrition approach

2015

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Classical soil science approaches have enabled us to establish basic principles of how the soil system functions and have answered numerous practical agricultural application questions. In recent years, efforts have been refocused on better understanding, managing and benefiting from this system that contains one of the most complex biological communities of the planet. Soil biology is seen as being at the center of scientific research of this century, with novel research objectives and goals being set. In addition, plant nutrition has enabled us to understand nutrient uptake, transport and mobilization mechanisms in plants, and both disciplines have converged on the area of microorganism-mediated plant nutrition. The challenge for these scientific areas is to identify microorganism communities and the roles they play in their habitats, as well as the mechanisms that plants have to make better use of nutrients. Genomics and metagenomics, along with microbiological techniques, are contributing greatly to advances in our understanding of living systems that exist in the soil and their interaction with plants. For its part, molecular plant nutrition has made significant progress in understanding the use of nutrients by plant cells, and has identified molecular mechanisms that can improve nutrient use efficiency. Together, molecular soil microbiology and molecular plant nutrition are projected to be a driving force in agriculture and sustainable food production in the coming years. Herewith, we aim to integrate recent literature on basic and applied research concerning plant and microbe genomics in terms of their potential for developing a novel molecular plant nutrition approach, with special emphasis on nitrogen, potassium and phosphorous as the major macronutrients for crop plants.

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“…After a period of lively competition (Loman et al ., 2012), the marketplace for high‐throughput sequencing has recently settled into a state of near‐monopoly, with Illumina short‐read sequencing dominating the field. While this technology may be highly suited to applications such as re‐sequencing of genomes, where attention is focused on detection of single nucleotide variants, it is poorly able to cope with the riotous diversity of microbial genomes and metagenomes, particularly when looking at mobile genetic elements or accessory genomes (Stoesser et al ., 2014).…”

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confidence: 99%

Microbial bioinformatics 2020

Pallen

2016

Microbial Biotechnology

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SummaryMicrobial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever‐growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale‐up to the million‐microbial‐genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user‐friendly outputs. The “internet of things” will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd‐sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand‐held sequencers will be analysed on mobile devices. Open‐source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty‐first century, microbial sequence space will remain the final frontier!

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High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

Cited by 375 publications

References 54 publications

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

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

Plant and microbe genomics and beyond: potential for developing a novel molecular plant nutrition approach

Microbial bioinformatics 2020

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