Advancements in Anaerobic Cultivation Techniques to Study Gut Microbiome

Microbiome research is transforming disease treatment and environmental solutions. Culturing microbes is essential for describing them and defining their functions. It also allows for controlled experiments to validate molecular data predictions. Current anaerobic culture techniques have been around since the 1960s, but new strategies are improving them. High-throughput anaerobic cultivation methods face implementation challenges. However, they can generate scientific breakthroughs, especially in gut microbiome studies. The gut microbiome is crucial for human health and dominated by anaerobic microbes. Next-generation cultivation methods can shift the field from association to causation. Scientists have been isolating gut bacteria for 60 years. 'Culturomics' emerged in the early 2010s to address the low fraction of cultured microbes. MALDI-TOF mass spectrometry facilitates rapid isolate identification. However, most culturomics approaches remain manual and throughput is low. A large fraction of bacteria remains undescribed (30-60% in gut environments). Even for described taxa, most functions are poorly defined. These microbial unknowns challenge microbiome-based innovation. Understanding strain evolution in a single host is crucial, as is controlled storage to prevent functional loss during in vitro cultivation. Innovative anaerobic cultivation methods face long-recognized challenges. We now have the knowledge and technologies to overcome them. Scaled-up techniques can boost isolation, identification, and storage. Specific platforms can improve culture conditions for difficult-to-grow species, enabling multiplexed functional comparisons, high-resolution analysis, and gene editing.