The School of Biological Sciences Fall 2025 Seminar Series presents Dr. Kostas Konstantinidis

Abstract: Large scale surveys of natural prokaryotic communities (metagenomics) or isolate genomes have revealed species clusters around 95% Average Nucleotide Identity (ANI) of shared genes. That is, members of the same species tend to show >95% ANI among themselves and <85% to members of other species with a clear scarcity (gap) of genome pairs showing between 85-95% ANI. We have recently reported a similar ANI gap within species, around 99.5% ANI, revealing that discrete, intraspecies units may also exist. We suggested referring to these units as genomovars (Rodriguez-R, mBio 2024), and to employ a higher ANI value (99.9%) and level of shared genes (>99% of total genes) to define strains (Viver, Nat. Comms. 2024). Interestingly, similar patterns have been also observed for viruses, especially bacteriophages (Aldequer-Riquelme, mBio, 2024). Exceptions to these main patterns are generally rare, and typically attributable to the unique ecology and/or evolution of the corresponding organisms. To further understand and model these patterns of diversity, however, the underlying genetic and/or ecological mechanisms that maintain discrete units at the species and intraspecies levels need to be elucidated (Konstantinidis, mLife, 2023). By analyzing closely related isolate genomes from the same or related samples we show that high ecological cohesiveness among the genomes, coupled to functionally and spatially (across the genome) unrestricted homologous recombination, likely underly these ANI units (Conrad et al., Nat. Comms. 2024). Therefore, our results represent a departure compared to previous models of microbial speciation that attributed speciation to either recombination or ecological cohesiveness but not their synergistic effect. Collectively, these findings should facilitate future micro-diversity studies across clinical or environmental settings because they provide more natural definitions of the species- and intra-species units of microbial and viral diversity. I will also take this opportunity to briefly highlight other projects that are ongoing in the Konstantinidis Lab.