The mystery of rich human gut antibiotic resistome in the Yellow River with hyper-concentrated sediment-laden flow

Abstract

Human gut antibiotic resistome widely occur in anoxic environments characterized by high density of bacterial cells and frequent transmission of antibiotic resistance genes (ARGs). Such resistome is greatly diluted, degraded, and restrained in the aerobic habitats within most natural rivers (regarded as “terrestrial guts”) connecting continents and the oceans. Here we implemented a large-scale monitoring campaign extending 5,200 km along the Yellow River, and provide the first integral biogeographic pattern for both ARGs and their hosts. We identified plentiful ARGs (24 types and 809 subtypes) and their hosts (24 phyla and 757 MAGs) in three media (water, suspended particulate matter (SPM), and sediment). Unexpectedly, we found diverse human gut bacteria (HGB) acting as supercarriers of ARGs in this oxygen-rich river. We further discovered that numerous microhabitats were created within stratified biofilms that surround SPMs, particularly regarding the aggregation of anaerobic HGB. These microhabitats provide numerous ideal sinks for anaerobic bacteria and facilitate horizontal transfer of ARGs within the stratified biofilms, Furthermore, the stratification of biofilms surrounding SPMs has facilitated synergy between human gut flora and denitrifiers for propagation of ARGs in the anoxic atmospheres, leading to high occurrence of human gut antibiotic resistome. SPMs play active roles in the dynamic interactions of river water and sediment, thus accelerating the evolution of riverine resistome and transmission of human gut antibiotic resistome. This study revealed the special contribution of SPMs to the propagation of ARGs, and highlighted the necessity of making alternative strategies for sustainable management of large rivers with hyper-concentrated sediment-laden flows.