About this Research Topic
The broad application of sequencing technologies has significantly expanded our portfolio to analyze microbes and the responses of their hosts to health and disease. Rapid technological advances lead to growing opportunities to sequence and analyze DNA and RNA quickly and at high resolution. Researchers analyze isolates, metagenomic and metatranscriptomic samples from various environmental settings, including human, animal, and agricultural environments. While well-established approaches and tools still provide robust insights, the possibility to perform real-time sequencing and analysis opens up entirely new applications in the field of molecular surveillance and outbreak analysis. We had never had access to such incredible tools for molecular monitoring of emerging pathogens, mobile genetic elements, virulence and resistance factors, and antibiotic resistance genes. We started this transitional era by combining well-established sequencing technologies with new developments that now allow single-molecule real-time approaches and combined insights from multi-omic areas.
However, due to the novelty and rapid development of molecular technologies, there are still many challenges in data acquisition, standardization, and reproducibility; especially concerning downstream bioinformatics analysis. Appropriate platforms, tools, workflows, and databases must fully exploit and integrate sequencing and other molecular technologies for advanced monitoring in different areas.
With this Research Topic, we target original research, review, mini-review, Hypothesis and Theory, Perspective, and Opinion articles on the edge of the transition era to new sequencing technologies and their application to integrative omics in molecular surveillance. We invite researchers from the field of molecular surveillance in human health, animal health, food safety and related areas utilizing well-established short-read and novel long-read sequencing technologies and the integration of different omics data sources. Thus, submissions should focus on the applications, challenges, limitations, and future aspects of sequencing and multi-omics-based microbial characterization, in particular in the context of molecular surveillance.
This Research Topic includes, but is not limited to:
- Molecular surveillance & outbreak analysis
- Whole-Genome-Sequencing of isolates
- Short- & long-read sequencing approaches as well as hybrid settings
- Real-time sequencing & in-field applications
- Metagenomics & metatranscriptomics
- Multiomics applications & integrative omics
- Agricultural settings, e.g. investigations of genetically modified crops
- Food surveillance & microbial community studies, e.g. in fermented foods
- Rapid detection of emerging pathogens (bacteria, viruses, fungi)
- Mobile genetic elements (virulence factors, antimicrobial resistance)
- Integrated databases & resources
Keywords: sequencing, integrative omics, metagenomics, molecular surveillance, microbes, metatranscriptomics, bioinformatics analysis, whole genome sequencing, multiomics, agriculture, food surveillance, emerging pathogens, mobile genetic elements
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.