Assessing the intestinal bacterial community of farmed Nile tilapia (Oreochromis niloticus) by high-throughput absolute abundance quantification

Abstract

Intestinal microbiota studies based on high-throughput sequencing have attracted increasing attention due to its vital impact on host health. However, the taxonomical profile in relative proportion does not reflect the quantity of the intestinal bacteria and the inter-sample differences among taxa. In this study, we applied a high-throughput absolute abundance quantification method that used an internal standard strain to simultaneously obtain both the relative and absolute abundances in the intestinal bacterial community of farmed Nile tilapia (Oreochromis niloticus). The results showed that the structure, relative and absolute abundances, and function of the intestinal indigenous microbiota didn’t change significantly after adding a low concentration of internal standard strain, and a comprehensive quantitative intestinal bacterial ecology was obtained. We first found that the total absolute abundance of the intestinal indigenous bacteria in farmed Nile tilapia was 2.95 × 108 cells g−1, and most genera concentrations were in the range of 103 to 105 cells g−1. The intestinal bacterial community was dominated by Cetobacterium with a concentration of 108 cells g−1, followed by Plesiomonas, Romboutsia, and Escherichia-Shigella with concentrations of over 107 cells g−1. The potential intestinal pathogens Aeromonas and Streptococcus reached 105 cells g−1 in the tilapia intestines, while the potential probiotics such as Lactobacillus and Enterococcus with a high concentration of over 106 cells g−1 were detected. Furthermore, PICRUSt analysis revealed that functional genes involved in membrane transport, carbohydrate metabolism, and amino acid metabolism were enriched in the intestinal microbiota of tilapia. This study characterized the intestinal quantitative bacterial ecology of farmed Nile tilapia, providing foundational support for an in-depth understanding of the intestinal microbiota and its interaction mechanism with the host.