Recent breakthroughs suggest that the single-celled microbial ancestor of all complex life was far more sophisticated than previously believed. For decades, scientists assumed this primitive organism, which lived billions of years ago in an anoxic world, resembled a simple bacterium. New research, published in Nature Microbiology and Nature, reveals that this ancestor actually possessed an extensive molecular toolkit, laying a much more advanced foundation for the evolution of eukaryotes—the domain of life that includes humans, animals, fungi, and plants. Since no direct fossil record exists for this critical moment in history, researchers led by Thijs Ettema, a microbiology professor at Wageningen University & Research, adopted a comparative approach. They examined the relationship between eukaryotes and their distant evolutionary cousins, the Asgard archaea. Discovered only a decade ago, Asgard archaea are single-celled microorganisms found in deep-sea sediments. Although both lineages share a common ancestor, their DNA sequences appear quite distinct after approximately two billion years of independent evolution. To uncover deeper similarities, the team shifted their focus from DNA to protein structures. While DNA sequences change rapidly over time, the three-dimensional shapes of proteins, which determine their function, remain far more stable. Leveraging artificial intelligence tools like AlphaFold, the researchers predicted the structures of over 35,000 proteins from more than 400 Asgard archaeal samples collected in China and Mexico. The analysis uncovered a startling finding: Asgard archaea contain approximately 1,300 proteins that were thought to exist exclusively in eukaryotes. These include proteins essential for intracellular transport, storage, and the formation of cellular compartments—features that define complex cells. The presence of these shared proteins indicates that the ancient ancestor already possessed the machinery necessary for complex cellular organization. This molecular evidence is now being supported by microscopic observations. Cultivating Asgard archaea in the lab is notoriously difficult due to their slow growth rates and preference for oxygen-poor environments. However, recent successes have allowed scientists to observe these microbes directly. Microscopy reveals that some species exhibit tentacle-like protrusions for movement and internal vesicles and membranes reminiscent of the compartments found in human cells. Furthermore, the understanding of these ancient microbes is evolving regarding their relationship with oxygen. Historically, Asgard archaea were only found in oxygen-free environments, where oxygen is toxic. The new study, however, identified Asgard archaea thriving in oxygen-rich settings, carrying genes involved in oxygen processing. While it remains unclear whether this oxygen-handling ability was inherited from the common ancestor or evolved independently, some evidence suggests certain species may even be capable of respiring oxygen to generate energy. This comprehensive picture was made possible by a technological revolution. Ten years ago, when Asgard archaea were first discovered, researchers had only the genome of a single specimen, offering weak and inconclusive evidence of their link to complex life. Today, advanced DNA sequencing and AI-driven protein prediction have enabled the analysis of vast datasets, confirming early intuitions with robust data. While questions remain about the exact appearance of the ancestor and whether its ancient proteins performed identical functions to those in modern eukaryotes, the consensus is clear. The microbial ancestor of complex life was not a simple primitive cell but a sophisticated organism that already held the potential to evolve into the diverse, multicellular world we inhabit today.