What has high-throughput sequencing ever done for us?

@article{Parkhill2013WhatHH,
  title={What has high-throughput sequencing ever done for us?},
  author={J. Parkhill},
  journal={Nature Reviews Microbiology},
  year={2013},
  volume={11},
  pages={664-665}
}
  • J. Parkhill
  • Published 2013
  • Biology, Medicine
  • Nature Reviews Microbiology
This month's Genome Watch looks back over the past 10 years and highlights how the incredible advances in sequencing technologies have transformed research into microbial genomes. 

Topics from this paper

Twenty years of bacterial genome sequencing
TLDR
The social history of sequencing is summarized and its impact on the authors' understanding of the biology, diversity and evolution of bacteria is summarized, while also highlighting spin-offs and translational impact in the clinic. Expand
Proteomic tools to decipher microbial community structure and functioning
TLDR
In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented. Expand
New Approaches for Needed Vaccines: Bacteria
TLDR
The science of genomics is providing new approaches, including reverse vaccinology, identifying new candidate antigens, and assessing potential vaccine coverage that are stimulating a reappraisal of the field and new candidate vaccines are emerging. Expand
A Robust Framework for Microbial Archaeology
TLDR
The fundamental concepts and theoretical framework of microbial archaeology are introduced, then applied methodologies for pathogen identification and microbiome characterization from archaeological samples are discussed, with special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Expand
Next-Generation Sequencing for Pathogen Detection and Identification
TLDR
There are an increasing number of examples whereby NGS is employed to discover novel pathogens, and these cases provide precedent for the use of NGS in microbial diagnostics, which has many advantages over traditional microbial diagnostic methods, such as unbiased rather than pathogen-specific protocols, ability to detect fastidious or non-culturable organisms, and can detect co-infections. Expand
Evolutionary insight from whole-genome sequencing of Pseudomonas aeruginosa from cystic fibrosis patients.
TLDR
Recent work that has applied whole-genome sequencing to understand P. aeruginosa population genomics, within-host microevolution and diversity, mutational mechanisms, genetic adaptation and transmission events is reviewed. Expand
Genome reconstruction and gene expression of "Candidatus Accumulibacter phosphatis" Clade IB performing biological phosphorus removal.
TLDR
The preliminary metatranscriptomic results revealed that the most significantly up-regulated genes of CAP IB HKU-1 from the anaerobic to the aerobic phase were responsible for assimilatory sulfate reduction, genetic information processing and phosphorus absorption, while the down- regulated genes were related to N2O reduction, PHA synthesis and acetyl-CoA formation. Expand
BMX: a tool for computing bacterial phyletic composition from orthologous maps
TLDR
Bacterial Makeup eXplorer (BMX) implements an algorithm that swiftly and efficiently facilitates the determination of the number of orthologs in prokaryotic genomes employing a reference free approach, which may be further exploited to transfer of gene annotations. Expand
Modelling the effects of mass drug administration on the molecular epidemiology of schistosomes.
TLDR
How genetic and genomic data have the potential to shape future research is considered, highlighting key areas where data is lacking, and how future molecular epidemiology knowledge can aid understanding of transmission dynamics and the effects of MDA, ultimately informing public health policy makers of the best interventions for NTDs. Expand
The gut microbiome, diet, and links to cardiometabolic and chronic disorders
TLDR
Data is summarized suggesting a link between the gut microbiota and derived metabolites with food intake patterns, metabolic alterations, and chronic CMDs. Expand
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Comparison of the whole-genome sequence ofBacillus anthracis isolated from a victim of a recent bioterrorist anthrax attack with a reference reveals 60 new markers that include single nucleotideExpand
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Reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II and analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment. Expand
Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
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W whole-genome sequencing data were used to propose and confirm that MRSA carriage by a staff member had allowed the outbreak to persist during periods without known infection on the SCBU and after a deep clean. Expand
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli
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  • Medicine, Biology
  • Proceedings of the National Academy of Sciences of the United States of America
  • 2002
TLDR
The complete genome sequence of uropathogenic Escherichia coli, strain CFT073 is presented and Comparisons indicate that extraintestinal pathogenic E. coli arose independently from multiple clonal lineages. Expand
A metagenome-wide association study of gut microbiota in type 2 diabetes
TLDR
MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. Expand
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TLDR
The complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium Porphyromonas gingivalis strain W83, a major contributor to periodontal disease, was determined and confirms the close relationship between the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum and the green-sulfur bacteria. Expand
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
TLDR
Several chromosomally encoded proteins that may contribute to pathogenicity—including haemolysins, phospholipases and iron acquisition functions—and numerous surface proteins that might be important targets for vaccines and drugs are found. Expand
Emergence and global spread of epidemic healthcare-associated Clostridium difficile
TLDR
This analysis identifies key genetic changes linked to the rapid transcontinental dissemination of epidemic C. difficile 027/BI/NAP1 and highlights the routes by which it spreads through the global healthcare system. Expand
Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica
TLDR
The authors' analysis indicates that B. parapertussis and B. pertussis are independent derivatives of B. bronchiseptica-like ancestors; host adaptation seems to be a consequence of loss, not gain, of function, and differences in virulence may be related to loss of regulatory or control functions. Expand
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