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

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbiomes".

Deadline for manuscript submissions: 30 April 2025 | Viewed by 920

Special Issue Editors


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Guest Editor
Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
Interests: human oral and gut microbiome; effects of probiotics & antibiotics; biodegradation of polycyclic aromatic hydrocarbons (PAHs); functional diversity of genes associated with pollutant degradation; water chemistry of riverine systems; tropical field ecology
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Special Issue Information

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

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Keywords

  • bioinformatics
  • metagenomics
  • metatranscriptomics
  • microbiome
  • omics

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Published Papers (1 paper)

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Research

19 pages, 2302 KiB  
Article
Mercury and Arctic Char Gill Microbiota Correlation in Canadian Arctic Communities
by Flora Amill, Patrice Couture and Nicolas Derome
Microorganisms 2024, 12(12), 2449; https://doi.org/10.3390/microorganisms12122449 - 28 Nov 2024
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Abstract
Arctic char is a top predator in Arctic waters and is threatened by mercury pollution in the context of changing climate. Gill microbiota is directly exposed to environmental xenobiotics and play a central role in immunity and fitness. Surprisingly, there is a lack [...] Read more.
Arctic char is a top predator in Arctic waters and is threatened by mercury pollution in the context of changing climate. Gill microbiota is directly exposed to environmental xenobiotics and play a central role in immunity and fitness. Surprisingly, there is a lack of literature studying the effect of mercury on gill microbiota. To fill this knowledge gap, our primary goal was to measure to what extent gill exposure to mercury may alter gill microbiota activity in Arctic char. Specifically, we calculated the correlation between the taxonomic distribution of gill-associated bacterial symbiont activity and total mercury concentration in livers and muscles in wild populations of Arctic char in the Canadian Arctic. Our results showed that total mercury concentrations in tissues were higher in Ekaluktutiak (Nunavut) than in the other sites in Nunavik. Proteobacteria was the main phylum correlated to mercury concentration in both tissues, followed by Bacteroidetes and Cyanobacteria. In the most contaminated sites, Aeromonas and Pseudomonas (Proteobacteria) were predominant, while mercury concentration negatively correlated with Photobacterium (Proteobacteria) or Cerasicoccus (Verrucomicrobia). In summary, we found that mercury contamination correlates with active gill microbiota composition, with potential implications of strains in modulating mercury toxicity, making them interesting for future biomarker studies. Full article
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