Advances in Techniques and Analyses to Characterize Host-Specific and Environmental Microbiomes

Dear Colleagues,

Microbiome research has exponentially increased over the last two decades and provided insights into microbial community structure, genome composition, phylogenetic relationships, and functions in numerous (eco)systems. While efforts to advance microbiome research have primarily resulted from the application of 16S rRNA gene (16S), shotgun metagenomic, and metatranscriptomic sequencing within human-centric samples and analysis tools, there has been limited development of host-specific tools to provide greater taxonomic and functional information. Research into host- and environment-specific microbiome applications has resulted in the generation of datasets that have limited resolution as human-centric bioinformatic databases and tools lack microbial information associated with non-human systems and require further development and benchmarking of analysis tools to enable the characterization of these microbiomes.

Further understanding of potential host–microbe and microbe–microbe interactions within specific host systems, such as mice and canines, as well as within specific systems, such as skin, vaginal, or environmental samples, is needed to elucidate associations between these microbiomes and health and disease states. Moreover, there is a continued need for the development and benchmarking of bioinformatic tools incorporating robust statistical analysis for the analysis of these complex datasets. Host- and environment-specific microbiomes may also go hand in hand with the generation of additional omics datasets (e.g., metabolomics and proteomics); thus, bioinformatic tools enabling the integration of multiple omics are also needed.

The present Special Issue welcomes studies characterizing host- and environmental-specific microbiomes (e.g., canine, vaginal, skin, and environmental) using specialized analysis tools. Submission of studies demonstrating comparison of results using different analytical techniques, such as bioinformatics techniques, databases, statistical tools, chemical extractions, analytical chemistry techniques, and microbial techniques, is encouraged. Articles presenting a novel bioinformatic tool or benchmarking an existing one for the analysis of host-specific microbiomes and those integrating additional omes are also welcome.

Prof. Dr. Carl Gordon Johnston
Dr. Tasha M. Santiago-Rodriguez
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

• bioinformatics
• metagenomics
• metatranscriptomics
• microbiome
• omics