Biofloc regulates shrimp intestinal microbiota homeostasis and host health through manipulation of environmental microbial communities

The health of ecosystems is fundamental to the productivity and sustainability of aquaculture. However, there is still limited understanding of both the key indicators that signal ecosystem health and the micro-level processes required to effectively restore it. Maintaining the health of ecosystem is crucial for aquaculture animal development, especially for shrimp farming. Here, we delineate the microecological characteristics that define healthy shrimp culture ecosystems and elucidate the microecological mechanisms by which biofloc technology restores health from diseased shrimp. We found that bacterial community structure of shrimp intestine exhibited greater stability under healthy state compared to diseased state. Rhodobacterales serve as key healthy indicator microbes within the shrimp intestine, demonstrating greater abundance and wider niche in both shrimp healthy and restored states. The Ruegeria arenilitoris , which belongs to the Rhodobacterales order, was isolated and confirmed to enhance shrimp resistance to Vibrio parahaemolyticus infection. The application of biofloc technology could facilitate the recovery of diseased shrimp to a healthy state. This recovery was reflected in key microecological shifts within the intestinal community: increased community similarity, enhanced network complexity, elevated niche width and network participant ratio of Rhodobacterales, collectively indicating a restoration of ecosystem health. More importantly, source tracking and partial least squares path modeling analyses indicate that applying biofloc technology regulates aquaculture water and environmental microbes, which thereby shapes shrimp intestinal bacterial community (notably enriching Rhodobacterales), and further manipulates shrimp's health status. Our findings demonstrate that regulating environmental microecology can effectively restore and sustain the ecological health of both aquaculture systems and the animals within them, and establish a vital theoretical foundation and a practical reference for advancing healthy aquaculture practices.