Topic: Bioinformatics Applied to Microbiota-based Science

During the past two decades, the evolution of DNA sequencing technologies has allowed the gathering of a vast amount of metagenomic data, laying the foundation to study complex microbial communities, also known as microbiomes. At the dawn of the metagenomic classification era, DNA sequences were mainly used to unveil the composition of the bacterial communities inhabiting specific environments through analysis based on the amplification of microbial marker genes. Recently, the more informative shotgun metagenomics approach allowed the reconstruction of the functional contribution of the bacteria harbored in the biological samples without the necessity to compromise data during sample preparation. To date, the interest of the scientific community is rapidly moving to a complete overview of the microbiomes, involving multiple bioinformatic pipelines aiming at understanding complex dynamics between members of the same environmental niche and their host.

This Special Issue aims to gather projects that rely on bioinformatics strategies to investigate bacteria, archaea, protists, and fungi in the frame of microbiome research, highlighting applications in the field of the human microbiome as well as more unexplored microbiomes, such as non-human animals.

We welcome original or review manuscripts, perspectives, opinions, and commentaries on different aspects of this Special Issue, including but not limited to:
Microbiota investigation using bioinformatic approaches:
● Microbial profiling of human and animal microbiomes
● Genome reconstruction of microorganisms from complex environments
● DNA enrichment studies of microbiomes
● Investigation of the microbial dark matter among microbiomes
● Functional profiling of host-related microbiomes
● Host-microbiome and microbiome-microbiome relationships

Bioinformatic pipelines and microbiomes:
● Development of bioinformatic pipeline in the field
● Comparisons between bioinformatic pipelines
● Innovative approaches to microbiome data management