Effects of diet shift on the gut microbiota of the critically endangered Siberian Crane

Wetlands worldwide have suffered from serious degradation and transformation, leading to waterbirds increasingly dependent on agricultural fields for feeding. Although gut microbiota is an essential component of host health, the impacts of agricultural feeding on gut microbial community and pathogen transmission remain poorly understood. To fill this knowledge gap, we used 16S rRNA sequencing to characterize the fecal bacterial community of the Siberian Crane (Grus leucogeranus), a Critically Endangered species, that recently has shifted its foraging from largely Vallisneria tubers in Poyang Lake natural wetlands to crops (i.e., rice seeds and lotus rhizomes) in agricultural fields. We compared the bacterial communities between tuber foraging cranes and crop foraging cranes. Our results indicate that diet shift greatly modified the gut microbiota diversity, composition and function. Crop foraging cranes had higher microbiota diversity than tuber foraging cranes. The alteration in microbiota composition and function were correlated with change in food nutrition. Tuber (i.e., high in fiber) foraging cranes were enriched in Clostridiaceae with fiber digestion ability, and crop (i.e., high in carbohydrate) foraging cranes were enriched in bacterial taxa and functions related to carbohydrate metabolism. The flexibility of gut microbiota might enhance Siberian Cranes’ ability to adapt to novel diet and environment. However, many enriched families in crop foraging cranes were pathogenic bacteria, which might increase the susceptibility of cranes to pathogenic infection. Special caution should be taken to agricultural feeding waterbirds in Asia, where the widespread poultry-keeping in over-harvested rice fields might increase the transmission probability of pathogenetic bacteria among wild birds, domestic poultry and humans.