Preface
Genomics, microbiomes, single cell analysis and next-generation sequencing

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Introduction

In less than a decade, new sequencing technologies have revolutionized our understanding of the highly complex nature of microbial communities inhabiting environments such as soil or the mammalian gastrointestinal tract. Only the advent of the so-called next-generation sequencing (NGS) allowed for massively parallel sequencing approaches that made the characterization of the human microbiome a feasible task within reasonable time and effort. NGS in combination with new, easier and affordable benchtop instruments has opened many avenues to genomics and microbiome research for an exponential growth of research groups. Nevertheless, challenges remain, in particular, with highly complex microbial communities, analyses of metagenomes or metatranscriptomes. In addition to population-based approaches, analyses at the single cell level have become possible, albeit with new challenges to overcome. This special issue encompasses a selection of reviews and original articles on these technologies as tools for environmental and medical microbiology and scientific advancement in general.

Di Bella et al. (2013) present a comprehensive guide on current high-throughput sequencing technologies. The review includes discussions of the entire workflow from study design and nucleic acid extraction to bioinformatic analyses of sequencing data. While an excellent baseline is provided for the fast evolving spectrum of microbiome research, areas that need further development are also highlighted.

Padmanabhan et al. (2013) discuss the growing impact of genomics and metagenomics on medical microbiology. The authors provide an overview how NGS technologies are being used for pathogen identification and epidemiology, detection of virulence factors, development of vaccines, and elucidation of the roles of microbial communities in health and disease.

Gürtler and Grando (2013) summarize progress in PCR-ribotyping of the intestinal pathogen Clostridium difficile with emphasis on how whole genome sequencing allows for detection of intra- and intergenomic variations in ribosomal RNA operons at the strain, ribotype, and operon level. In addition, a ribotyping app is introduced as a powerful tool for epidemiological studies.

Ramos et al. (2013) introduce a mate-pair library approach for improving de novo assembly of a prokaryotic genome from a single Ion Torrent PGM™ sequencing run. Whole genome sequencing of Corynebacterium tuberculosis was used to demonstrate the advantages of this approach.

Gómez-Raja and Larriba (2013) compare clone-by-clone gene sequencing and direct sequencing for identification of spontaneous mutations in Candida albicans and Saccharomyces cerevisiae. It appears that the choice of sequencing approach and PCR enzymes might introduce unexpected mutations which could interfere with haplotype determinations and analyses of point mutations.

Peng et al. (2013) present a direct boiling method for fecal DNA extraction as a cost-effective alternative to commercial kits. The authors performed a detailed evaluation of DNA extraction methods using Illumina sequencing of 16S rRNA tags for analysis of fecal microbiota.

A crucial prerequisite for NGS-based microbial diversity analyses in soil is efficient recovery of microorganisms. Lentendu et al. (2013) report on a novel workflow using high-density centrifugation and flow cytometry to isolate unicellular eukaryotes, which represent a component of soil microbial communities that is rarely studied because of the paucity of specific enrichment methods.

The analysis of single microbial cells in microfluidic systems is an intriguing research area currently emerging in microbiology. Probst et al. (2013) provide a detailed protocol for the generation of microfluidic growth chambers and manipulation of individual cells in these devices with optical tweezers in order to study evolving microbes at the single cell level.

This special issue would not have been possible without the excellent assistance from the editorial and publishing teams at Elsevier. In particular we would like to thank Judyth Howard, Editorial Coordinator, and Dr. Alvin Fox, Editor-in-Chief, for their patience and excellent guidance as well as Jerusha Aranha, Global Journal Manager, Dr. Sheba Agarwal-Jans, Publisher, Stella Yan, Senior Publishing Content Specialist, and Ramprasad Anbazhagan, Publishing Content Specialist, for helping us to navigate the review and publishing process. We are especially grateful to all reviewers who were at the heart of the peer review process and helped us to keep high standards for the selection of the articles in this special issue. Last but not least we thank all contributors including those who missed the inclusion in this issue.

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This Special Issue is dedicated to the leadership and gentlemanship of Dr. Alvin Fox. As Editor in Chief, Dr. Fox has provided invaluable service to this issue, the Journal of Microbiological Methods, and the entire scientific community.

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