Gut microbial communities associated with the molting stages of the giant freshwater prawn Macrobrachium rosenbergii

•This is the first study that investigates the dynamics of the gut microbe community during the prawn molt cycle.•Major changes in the M. rosenbergii freshwater prawn gut bacterial community structure coincide with molting stage C

The reciprocal interaction between host organisms' physiology and their gut microorganism community is of great interest in aquatic animal biology and aquaculture but for crustaceans, it remains understudied. This study enhances our understanding of this community of microorganisms as it changes during the molt cycle. Because crustaceans shed a major component of their gut, and the associated microbiome, with each molt this adds a level of complexity heretofore unexamined. We have identified the bacterial communities that are affected by the changing gut environment and that may in turn, exert some control over aspects of the molt cycle. We investigated the structural changes of the resident gut bacterial communities, using the diversity of the 16S rRNA gene by 454 pyrosequencing, in the freshwater prawn Macrobrachium rosenbergii during its four-stage molt cycle. The number of bacterial operational taxonomic units (OTUs) increased from stages A to C. Stage C the intermolt and longest lasting stage was different in the gut bacterial community structure having the (a) highest number of total OTUs, (b) highest number of unique and newly introduced OTUs, (c) highest percentage of estimated specialists OTUs, i.e. that are more ecologically restricted. Moreover, stage C was characterized by greater contribution of Actinobacteria-related and unaffiliated OTUs. The most dominant OTUs found in stage C of the gut of M. rosenbergii were related to microorganisms involved in fermentation and food material processing originating from similar, i.e. gut, or habitats of terrestrial and freshwater animals. Thus, the distinct gut bacterial communities found in molting stage C corroborate with the physiological significance of this molting stage. The abiotic factors and the exact role of the corresponding specific bacterial communities in the animal's physiology and growth are areas that remain to be elucidated.Statement of relevanceA thorough understanding of M. rosenbergii digestive physiology is essential to achieve better growth performance when cultured. This paper provides information that could be useful for developing effective strategies to manipulate gut microbial communities to promote prawn's growth and health and improve aquaculture productivity.