About this Research Topic

Background

The study of microbial diversity has traditionally relied on the cultivation of microorganisms in the laboratory. However, it is now widely recognized that a significant portion of microbial life cannot yet be cultivated using conventional methods. This "microbial dark matter" comprises diverse prokaryotic organisms that remain elusive to traditional isolation techniques.

To overcome this challenge, researchers have turned to omics approaches, which allow for the analysis of genetic material (metabarcoding, metagenomics, and single-cell genomics) or their encoded products (metatranscriptomics and metaproteomics) directly from environmental samples. By sequencing and analyzing the genetic material and encoded products of these uncultivated microorganisms, scientists can gain insights into their genomic composition, metabolic potential, and ecological roles.

These as-yet-uncultured (and perhaps uncultivable) organisms play a crucial role in shaping microbial ecosystems. Though the absence of axenic cultures only allow assignment of provisional "Candidatus" names for these organisms under the International Code of Nomenclature of Prokaryotes, the recently established SeqCode has emerged as a means to obtain standing in nomenclature for these names, thus facilitating communication, taxonomic classification, and improving our understanding of their diversity.

To gain insights into the hidden uncultivated prokaryotic world by integrating omics approaches into our exploration and characterization efforts of the microbial unknown. This includes:

1- Identifying and describing the genetic makeup, metabolic capabilities, and ecological roles of previously underexplored and uncultivated prokaryotic organisms.

2- Defining and classifying new taxonomic units that are named within the Candidatus category, or under the SeqCode, leading to a more comprehensive understanding of microbial diversity and evolutionary relationships.

3- Gaining insights into the functions and contributions of uncultivated microorganisms in various ecological processes, such as nutrient cycling, symbiotic interactions, and disease pathogenesis.

4- Enhancing knowledge of microbial communities and their interactions in complex ecosystems, contributing to broader ecological studies, and understanding the roles of microorganisms in ecosystem balance.

5- Informing the development of novel techniques and approaches to isolate and cultivate previously elusive microorganisms, potentially leading to the discovery of bioactive compounds, enzymes, and other biotechnological applications.

We seek contributions that advance our understanding of uncultivated Prokaryotes, including their genetic diversity, functional potential, and ecological roles, while addressing the challenges associated with their recalcitrance to most of the classical microbiological approaches.

Specific themes that can be addressed include:

1-Taxonomic classification and nomenclature: Manuscripts proposing new taxonomic units within the Candidatus category, or named under the SeqCode, based on sequence data, emphasizing the genetic distinctiveness and evolutionary relationships of uncultured microorganisms using up to date taxogenomics.

2-Functional potential and ecological roles: Manuscripts investigating the functional significance of uncultivated microorganisms, including their involvement in biogeochemical cycling, host-microbe interactions, symbiosis, and disease pathogenesis.

3-Comparative genomics and evolution: Manuscripts exploring the evolutionary relationships, genetic adaptations, and dynamics of uncultivated microorganisms through comparative genomics and phylogenetic/phylogenomic analyses.

4-Innovative genome-enabled cultivation strategies: Manuscripts discussing novel techniques to isolate and cultivate previously uncultivated microorganisms, such as specialized media, co-culture methods, and enrichment strategies.

5-Biotechnological applications: Manuscripts highlighting the biotechnological potential of uncultivated microorganisms, such as the discovery of bioactive compounds, enzymes, or metabolic pathways with applications in medicine, industry, or environmental remediation.

Keywords: uncultivated, bacteria, archaea, omics, SeqCode, Candidatus, taxonogenomics, taxogenomics, metabarcoding, metagenomics, metatranscriptomics, metaproteomics, genomics

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.

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