Bacterial adaptability and their interactions with various hosts, ranging from symbiosis to pathogenicity, dictate their lifestyle. The genetic factors involved in the colonization of animal and plant hosts by both pathogenic and mutualistic bacteria are also essential for discovering new drug targets for disease management and for developing innovative biostimulant strategies. Recent advances in genome-wide high-throughput technologies, such as transposon insertion sequencing, have resulted in the identification of pathways that facilitate efficient host colonization. However, the role of comparable genes in this process across different bacteria remains unclear.

To maximize the insights gained from these approaches, it is increasingly important to integrate complementary layers of regulation, such as transcriptomic responses and epigenetic modifications, which reveal context-dependent gene activity during colonization. Additionally, the implementation of single-cell technologies on bacterial offers unprecedented resolution to dissect phenotypic heterogeneity and cell-specific colonization patterns. Despite considerable progress, variability in laboratory environments often necessitates arduous, time-consuming adjustments to protocols, limiting the accessibility of these powerful techniques to a broader scientific audience.

The aim of this research topic is to enhance understanding of the genetic determinants involved in the colonization of animal and plant hosts by pathogenic and mutualistic bacteria and to explicitly identify the pathways that enable efficient host colonization. This can be accomplished by refining protocols and pinpointing key parameters that influence the complexity of mutant libraries, thus streamlining the process and enhancing accessibility. This includes adjusting electroporation parameters, post-electroporation conditions, and devising a simplified workflow for sequencing library preparation. To gain further insights into the genetic determinants of host colonization, we invite original research articles, reviews, mini-reviews and all type of articles accepted by the journal that address, but are not limited to, the following themes:

- The role of similar genes in host colonization across different bacteria.
- The impact of key parameters on the complexity of mutant libraries.
- The development of a simplified sequencing library preparation workflow.
- The refinement of protocols for genome-wide high-throughput technologies.
- Potential differences in the genetic basis of host colonization in symbionts and pathogens
- The role of genes for quorum sensing, biofilm formation, outer-membrane modification or metabolism of host-derived molecules in host colonization
- Integration of transcriptomic, proteomic, metabolomic, epigenetic and single-cell analyses to support functional genomic discoveries.
- Contribution of the accessory genome and horizontal gene transfer to colonization strategies, and their integration into functional genetic analyses.
- Genetic enablement of recalcitrant microbes: delivery, counter-selection, restriction–modification bypass.

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Streamlining Genetic Analysis for Bacterial Host Colonization