To further investigate the bacterial community and identify the bacterial biomarkers between venom secretion and non-venom secretion snakes, 50 intestinal samples (25 large intestine, 25 small intestine) were obtained from 29 snakes (13 gut samples from
Deinagkistrodon
, 26 from
Naja
and 11 from
Ptyas mucosa
). 16S rDNA high-throughput sequencing results showed that 29 bacterial phyla, 545 bacterial genera, and 1,725 OTUs (operational taxonomic units) were identified in these samples. OTU numbers and the Ace, Chao, Shannon, and Simpson indexes were very similar among the three breeds of snakes included in this study. The
Bacteroidetes
,
Firmicutes
,
Fusobacteria
and
Proteobacteria
were predominant bacterial phyla. The relative abundance at the phylum level among these samples was similar, and the difference between small and large intestinal samples was not obvious. However, at the genus level, venom secretion snakes
Deinagkistrodon
and
Naja
clustered together according to different breeds. 27, 24, and 16 genera were identified as core microbes for
Deinagkistrodon
,
Naja
, and
Ptyas mucosa
, respectively. Interestingly, the relative abundances of genera
Hafnia_Obesumbacterium
,
Providencia
, and
Ureaplasma
were found to be significantly higher in non-venom secretion snakes, and the genera
Achromobacter
,
Cetobacterium
,
Clostridium innocuum
group,
Fusobacterium
,
Lachnoclostridium
,
Parabacteroides
, and
Romboutsia
were only detected in venom secretion snakes. The function of these bacteria in venom secretion needs to be further studied, and these venom secretion related genera may be the promising target to improve venom production.