The gut microbiome is crucial for health, but understanding its modulation is complex due to high inter-individual variation. Recent studies reveal that environmental and host factors account for less than 20% of microbial composition variation, highlighting the importance of stochastic factors and ecological rules. While diet and lifestyle impact the host-microbiome relationship, resilience is key in maintaining its structure over a lifetime. Our analysis of 35,000 gut samples showed the microbiome as branch-structured, with different states connected to host and environmental factors. This structure can identify transitions to less healthy states linked with diversity and function changes. Next-gen engines may need to consider identified gut-tipping elements to prevent reaching unhealthy states. Thinking of the microbiome as branch-connected ecological states paves the way more than ever for personalized nutritional and therapeutic interventions.