Increasing evidence has revealed a close association between intestinal bacterial community and hosts health. However, it is unclear whether and what extend Baimang disease alters the intestinal microbiota in mud crab (
Scylla paramamosain
). Here, we conducted intestinal contents Illumina sequencing of healthy and Baimang diseased mud crab (
S. paramamosain
) to understand bacterial community variations among health status. In addition, bacterial functional predication was used to investigate whether and how the bacteria variations further change their functions? The phyla of
Proteobacteria
,
Fusobacteria
,
Cyanobacteria
,
Tenericutes
,
Firmicutes
,
Bacteroidetes
, and
Spirochaetae
constituted over 96.44% of the total intestinal bacteria, with being the dominant taxa. The 7 most significantly different orders, including the increased four orders of
Clostridiales
,
Entomoplasmatales
,
Bacteroidales
, and
Mycoplasmatales
and the decreased three orders of
Vibrionales
,
Campylobacterales
, and
Fusobacteriales
, accounted for 61.14% dissimilarity, probably being the indicator taxa of Baimang disease. Accordingly, 12 Kyoto Encyclopedia of Genes and Genomes orthologies in level 3 shifted significantly at the diseased crabs. Especially, bacterial secretion system, secretion system, lipopolysaccharide biosynthesis proteins and
Vibrio cholerae
pathogenic cycle, being related to bacterial virulence, were reduced. In addition, the reduced butanoate metabolism, and induced methane metabolism and one carbon pool by folate were important metabolic processes of probiotic, such as
Bacteroides
spp. and
Clostridium
spp., with playing critical roles in host health. This study suggests that Baimang disease coupled altered the intestinal bacterial communities and functions, providing timely information for further analysis the influencing mechanism of Baimang disease in mud crab (
S. paramamosain
).
Electronic supplementary material
The online version of this article (10.1186/s13568-019-0745-1) contains supplementary material, which is available to authorized users.