Metagenomic and network analysis revealed wide distribution of antibiotic resistance genes in monkey gut microbiota

The effects of food provisioning on the gut microbiota community and antibiotic resistance genes of Yunnan snub-nosed monkey

Yunnan snub-nosed monkeys (Rhinopithecus bieti) are the highest elevation lived non-human primate, and their survival has been threatened for decades. To promote their population growth, a reserve provides a typical monkey population with supplemental food. However, the influences of this food provisioning on their gut microbiota and antibiotic resistance genes (ARGs) were unknown. Therefore, we investigated the gut microbiota and ARGs of the food-provisioned monkey population compared with another wild foraging population. We found that food provisioning significantly increased the gut microbiota diversity and changed the community composition, particularly increased both the Firmicutes abundance and Firmicutes/Bacteroidetes ratio. Meanwhile, the food provisioning decreased the complex and stable gut microbiota network. KEGG functions were also influenced by food provisioning, with wild foraging monkeys showing higher functions of metabolism and genetic information processing, especially the carbohydrate metabolism, while food-provisioned monkeys exhibited increased environmental information processing, cellular processes, and organismal systems, including valine, leucine, and isoleucine degradation. In addition, food provisioning increased the abundance of ARGs in the gut microbiota, with most increasing the abundance of bacA gene and changing the correlations between specific ARGs and bacterial phyla in each population. Our study highlights that even food provisioning could promote wildlife nutrient intake, and it is necessary to pay attention to the increased ARGs and potential effects on gut microbiota stability and functions for this human conservation measure.

Antibiotic resistance profiles of gut microbiota across various primate species in Guangxi

Introduction

Understanding the gut microbiota and antibiotic resistance gene (ARG) profiles in non-human primates (NHPs) is crucial for evaluating their potential impact on human health and the environment.

Methods

In this study, we performed metagenomic analysis of 203 primate fecal samples, including nine NHP species and humans, to comprehensively characterize their gut microbiota and ARGs.

Results

Our study reveals the prevailing phyla in primates as Firmicutes, Bacteroidetes, Euryarchaeota, and Proteobacteria. The captive NHPs exhibited higher ARG abundance compared to their wild counterparts, with tetracycline and beta-lactam resistance genes prevailing. Notably, ARG subtypes in Trachypithecus leucocephalus (T. leucocephalus) residing in karst limestone habitats displayed a more dispersed distribution compared to other species. Interestingly, ARG profiles of NHPs clustered based on geographic location and captivity status. Co-occurrence network analysis revealed intricate correlations between ARG subtypes and bacterial taxa. Procrustes analysis unveiled a significant correlation between ARGs and microbial phylogenetic community structure. Taxonomic composition analysis further highlighted differences in microbial abundance among NHPs and humans.

Discussion

Our study underscores the impact of lifestyle and geographical location on NHP gut microbiota and ARGs, providing essential insights into the potential risks posed by NHPs to antibiotic resistance dissemination. This comprehensive analysis enhances our understanding of the interplay between NHPs and the gut resistome, offering a critical reference for future research on antibiotic resistance and host-microbe interactions.

Combined network analysis and interpretable machine learning reveals the environmental adaptations of more than 10,000 ruminant microbial genomes

Background

The ruminant gastrointestinal contains numerous microbiomes that serve a crucial role in sustaining the host's productivity and health. In recent times, numerous studies have revealed that variations in influencing factors, including the environment, diet, and host, contribute to the shaping of gastrointestinal microbial adaptation to specific states. Therefore, understanding how host and environmental factors affect gastrointestinal microbes will help to improve the sustainability of ruminant production systems.

Results

Based on a graphical analysis perspective, this study elucidates the microbial topology and robustness of the gastrointestinal of different ruminant species, showing that the microbial network is more resistant to random attacks. The risk of transmission of high-risk metagenome-assembled genome (MAG) was also demonstrated based on a large-scale survey of the distribution of antibiotic resistance genes (ARG) in the microbiota of most types of ecosystems. In addition, an interpretable machine learning framework was developed to study the complex, high-dimensional data of the gastrointestinal microbial genome. The evolution of gastrointestinal microbial adaptations to the environment in ruminants were analyzed and the adaptability changes of microorganisms to different altitudes were identified, including microbial transcriptional repair.

Conclusion

Our findings indicate that the environment has an impact on the functional features of microbiomes in ruminant. The findings provide a new insight for the future development of microbial resources for the sustainable development in agriculture.

The fate of antibiotic resistance genes in the coastal lagoon with multiple functional zones

Coastal lagoons provide many important services to human society, but their year-round use for aquaculture introduces large amounts of sewage. The contamination of antibiotic resistance genes (ARGs) is therefore of great concern. In this study, 50 ARGs subtypes, two integrase genes (intl1, intl2), and 16S rRNA genes were detected by high-throughput quantitative PCR, and standard curves of all target genes were prepared for quantification. The occurrence and distribution of ARGs in a typical coastal lagoon (XinCun lagoon, China) were comprehensively explored. We detected 44 and 38 subtypes of ARGs in the water and sediment, respectively, and discuss the various factors influencing the fate of ARGs in the coastal lagoon. Macrolides-lincosamides-streptogramins B was the primary ARG type, and macB was the predominant subtype. Antibiotic efflux and antibiotic inactivation were the main ARG resistance mechanisms. The XinCun lagoon was divided into eight functional zones. The ARGs showed a distinct spatial distribution owing to the influence of microbial biomass and anthropogenic activity in different functional zones. Fishing rafts, abandoned fish ponds, the town sewage zone, and mangrove wetlands provided a large quantity of ARGs to the XinCun lagoon. Nutrients and heavy metals also significantly correlated with the fate of the ARGs, especially NO₂^--N and Cu, which cannot be ignored. It is noteworthy that lagoon-barrier systems coupled with persistent pollutant inputs result in coastal lagoons acting as a "buffer pool" for ARGs, which can then accumulate and threaten the offshore environment.

Captivity and geography influence the antibiotic resistome of non-human primates

INTRODUCTION

Antibiotic resistance poses a serious threat for animals and humans health worldwide. Yet a comprehensive exploration of the influence of captivity and geography on non-human primate (NPH) gut antibiotic resistance remains incomplete.

METHODS

In this study, 131 metagenomic sequencing datasets of five species of NHPs included different regions and lifestyles were selected to perform the antibiotic resistance analysis.

RESULTS

Nineteen related resistance antibiotics and 325 antibiotic resistance genes (ARGs) were obtained. A significantly higher abundance and diversity index of ARGs in the captive NHPs than in the wild was found but not for all of the samples. The biomarker-tracking of ARGs analysis identified key ARGs related to aminoglycoside resistance genes and tetracycline resistance genes.

DISCUSSION

These results suggest that captivity and geography changes associated with human activities can lead to marked changes in the ecology of the NHP gut flora ARGs.

Occurrence of antibiotics and bacterial resistance genes in wastewater: resistance mechanisms and antimicrobial resistance control approaches

Antimicrobial pharmaceuticals are classified as emergent micropollutants of concern, implying that even at low concentrations, long-term exposure to the environment can have significant eco-toxicological effects. There is a lack of a standardized regulatory framework governing the permissible antibiotic content for monitoring environmental water quality standards. Therefore, indiscriminate discharge of antimicrobials at potentially active concentrations into urban wastewater treatment facilities is rampant. Antimicrobials may exert selective pressure on bacteria, leading to resistance development and eventual health consequences. The emergence of clinically important multiple antibiotic-resistant bacteria in untreated hospital effluents and wastewater treatment plants (WWTPs) has been linked to the continuous exposure of bacteria to antimicrobials. The levels of environmental exposure to antibiotics and their correlation to the evolution and spread of resistant bacteria need to be elucidated to help in the formulation of mitigation measures. This review explores frequently detected antimicrobials in wastewater and gives a comprehensive coverage of bacterial resistance mechanisms to different antibiotic classes through the expression of a wide variety of antibiotic resistance genes either inherent and/or exchanged among bacteria or acquired from the reservoir of antibiotic resistance genes (ARGs) in wastewater systems. To complement the removal of antibiotics and ARGs from WWTPs, upscaling the implementation of prospective interventions such as vaccines, phage therapy, and natural compounds as alternatives to widespread antibiotic use provides a multifaceted approach to minimize the spread of antimicrobial resistance.