Year: 2026
Type: article
Study design: Systematic Review
Abstract: Epidemiological surveillance is essential for the early detection of outbreaks. Integrating bacterial diversity indicators into surveillance systems could improve outbreak prediction by identifying ecosystem changes that alter microbial communities. This systematic review aimed to identify bacterial diversity assessment methods reported in the literature and determine the most commonly used diversity indicators. A systematic review of articles published in PubMed/Medline between 2015 and 2024 was conducted using the keywords bacterial AND (diversity OR biodiversity). Of the 154 records identified, 90 relevant studies were included, covering humans (29.0%), animals (28.0%), soil (22.0%), water (11.0%), air (5.6%), and plants (3.3%). Alpha diversity was assessed in all studies, beta diversity in 85.6%, and genetic diversity in 56.7%. The most frequently used metrics were species richness (94.4%), the Shannon index (80.0%), and relative abundance (77.8%). Phylogenetic and taxonomic diversity were evaluated in 41.1 and 26.7% of the studies, respectively. Most studies used 16S rRNA/rDNA gene sequencing for bacterial identification. Alpha diversity remains the predominant focus of bacterial diversity research, whereas genetic diversity is comparatively underexplored. Future studies should incorporate additional diversity metrics, particularly indicator species and dark diversity, to provide a more comprehensive assessment of bacterial communities. Key words: Bacterial diversity, bacterial species, diversity measures, bacteria.
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: diamond
OpenAlex ID: W7212005331