16S rRNA sequence based identification of pathogenic gut microbiota of rohu labeo rohita (hamilton‐buchanan 1822) and silver carp hypophthalmichthys molitrix (valenciennes 1844)

Abstract

Rohu (Labeo rohita) and Silver carp (Hypophthalmichthys molitrix) are the most
common, popular and commercially important fish of Bangladesh. Pathogenic
gastrointestinal bacteria indicate the acceptability or quality hence it influences
the economic status of these fish. To investigate the pathogenic gastrointestinal
bacteria of these economically important fish of Bangladesh was carried out. Gut
microbiota of indigenous Rohu and exotic Silver carp of three different markets
of Dhaka metropolitan city were studied using various selective agar media,
classical biochemical tests and 16S rRNA sequencing. Antibiotic susceptibility of
selected isolates was also carried out against 14 antibiotics. Firstly, 216 colonies
were differentiated morphologically and among them, 18 isolates were
characterized by biochemical properties. Finally, the identification of 10 isolates
were confirmed by sequencing the 16S rRNA gene. Total bacterial count (TBC),
total Salmonella‐Shigella and total Staphylococcal count exhibited significant
difference (p < 0.05) between the species but not among markets. TBC of Rohu
samples was 5.27 ± 2.01 × 107 cfu/g and in Silver carp was 3.02 ± 1.42 × 107 cfu/g,
total Salmonella and Shigella was 6.94 ± 7.15 × 106 cfu/g from Rohu and 1.11 ± 0.97
× 106 cfu/g from Silver carp. Total Staphylococcal count was found 1.03 ± 0.52 ×
107 cfu/g in Rohu and 5.48 ± 3.98 × 106 cfu/g in Silver carp. Biochemical assays
provisionally determined 7 different bacterial genera from Rohu and 7 from
Silver carp. Six different genera of Gram‐negative bacteria (4 genera from Rohu
and 2 from Silver carp) were identified as Aeromonas, Proteus, Pseudomonas,
Enterobacter, Citrobacter, Klebsiella sp. by 16S rRNA sequencing. The results
revealed that all the 18 representative isolates including reference strain (E. coli
DH5α) were sensitive to ciprofloxacin and resistant to sulphamethoxazole. These
findings might be due to the poor quality of the aqueous environment and
reflects fish as the potential reservoir of pathogenic bacteria causing fish‐borne
disease outbreaks.