scholarly journals Metagenomic Analysis Reveals the Shared and Distinct Features of Bacterial Communities and Resistomes in Corn Silage from Different Climate Zones in China

2021 ◽  
Author(s):  
Dongmei Xu ◽  
Hongyan Han ◽  
Chao Wang ◽  
Yixin Zhang ◽  
Fuhou Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
High Risk ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Climatic Factors ◽  
Antibiotic Resistance Gene ◽  
Corn Silage ◽  
Pollution Level ◽  
Microbial Composition ◽  
Climate Zones

Abstract Background: The emergence and spread of antibiotic resistance are a significant threat to global health. Silage is a major forage feed for ruminants, and its safety is an important guarantee that high-quality ruminant products will remain available to humans. However, little attention has been given to the silage resistome. To define the antibiotic resistome and its potential risk to silage from different climate zones and in response to the ensiling process, this study used metagenomics to investigate bacterial communities and the type and amount of antibiotic resistance gene (ARG) in corn silage harvested from six climate zones (Cfa, BWk, Dwc, Dwa, BSk, and Aw based on Köppen-Geiger climate classification) in China. Results: The composition and succession of silage bacterial communities varied significantly between different climate zones. Lactobacillus was the predominant bacteria during corn ensiling. A total of 134 ARGs were observed in corn silage, with the dominant classes being beta-lactamase and multidrug resistance and the primary mechanisms being efflux pump, inactivation, and target protection. Differences in the resistome were mainly attributed to disparities in microbial composition, which was indirectly affected by climatic factors and fermentation pH. ARG abundance was lower in 90-day silages than 5-day silages except in Hainan silage. The diversity and relative abundance (0.65-0.4% based on total gene number) of ARGs was lower in silage microbiota from Tibet than other climate zones. The dominant ARGs were tetM, oqxB, lmrD, lnuA, ermB, and tetS, and Enterobacter, Klebsiella, Staphylococcus, Lactobacillus and Lactococcus were the primary ARG hosts. Eleven high-risk ARGs were chosen to evaluate the pollution level of silages harvested from different climate zones. The highest relative abundance of high-risk ARGs belonging to Lactobacillus occurred in corn silages from Cfa, Dwa and BWk climate zones. Conclusions: The ensiling process decreased ARG abundance. While resistome contamination of silage from Tibet was relatively low, ARGs with high risk were abundant in silages from Cfa, Dwa and BWk climate zones.

scholarly journals Wastewater pollution differently affects the antibiotic resistance gene pool and biofilm bacterial communities across streambed compartments

2017 ◽  
Vol 26 (20) ◽  
pp. 5567-5581 ◽  
Author(s):  
Jèssica Subirats ◽  
Xavier Triadó-Margarit ◽  
Ladislav Mandaric ◽  
Vicenç Acuña ◽  
José Luis Balcázar ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Bacterial Communities ◽  
Gene Pool ◽  
Antibiotic Resistance Gene ◽  
Wastewater Pollution

scholarly journals Airborne bacterial communities and antibiotic resistance gene dynamics in PM2.5 during rainfall

2020 ◽  
Vol 134 ◽  
pp. 105318 ◽  
Author(s):  
Wei Ouyang ◽  
Bing Gao ◽  
Hongguang Cheng ◽  
Lei Zhang ◽  
Yidi Wang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Bacterial Communities ◽  
Antibiotic Resistance Gene

scholarly journals Formula alters preterm infant gut microbiota and increases its antibiotic resistance load

2019 ◽  
Author(s):  
Katariina Pärnänen ◽  
Jenni Hultman ◽  
Reetta Satokari ◽  
Samuli Rautava ◽  
Regina Lamendella ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Community ◽  
High Risk ◽  
Antibiotic Resistance Gene ◽  
Microbial Community Composition ◽  
Bifidobacterium Bifidum ◽  
Pathogenic Species ◽  
Bacterial Strains ◽  
Antibiotic Resistant ◽  
Feeding Choices

SummaryInfants are at a high risk of acquiring infections caused by antibiotic resistant bacterial strains. Antibiotic resistance gene (ARG) load is typically higher in newborns than in adults, but it is unknown which factors besides antibiotic treatment affect the load. Our study demonstrates that inclusion of any formula in the newborn diet causes shifts in microbial community composition that result in higher ARG loads in formula-fed infants compared to infants not fed formula. The effect of formula was especially strong in premature newborns and newborns treated with antibiotics. Interestingly, antibiotics alone without formula did not have a detectable impact on the ARG load of the newborn gut. We also observed that formula-fed infants had enriched numbers of pathogenic species and were depleted in typical infant gut species such as Bifidobacterium bifidum. The results suggest infant feeding choices should include assessment of risks associated with elevated ARG abundance.

scholarly journals Biodiversity of Soil Bacterial Communities from the Sasso Fratino Integral Nature Reserve

2021 ◽  
Vol 12 (4) ◽  
pp. 862-877
Author(s):  
Lara Mitia Castronovo ◽  
Sara Del Duca ◽  
Sofia Chioccioli ◽  
Alberto Vassallo ◽  
Donatella Fibbi ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Dna Analysis ◽  
Nature Reserve ◽  
Random Amplified Polymorphic Dna ◽  
Soil Samples ◽  
Microbial Composition ◽  
Rdna Sequencing ◽  
Soil Bacterial

The Sasso Fratino Integral Nature Reserve (Italy) aims to protect nature and territory. Since no anthropic activities are allowed, it represents a good model to study the bacterial community of a wild environment. The aim of this work was to characterise the cultivable and the total bacterial community of soil samples from the reserve in terms of taxonomy, composition, and structure. Seven soil samples were collected at different altitudes, and the chemical composition, the total and the cultivable microbiota, and the antibiotic resistance profiles of isolates were investigated. Total bacterial communities, studied through Next Generation Sequences analysis, included 390 genera. Samples differed in terms of microbial composition basing on the different altitude/vegetation of collection points. Random Amplified Polymorphic DNA Analysis (RAPD) allowed to identify 82 haplotypes out of 158 bacterial isolates. The taxonomic identification through 16S rDNA sequencing revealed that the strains were affiliated to 21 genera. Antibiotic resistance profiles of bacteria were also investigated, highlighting a high resistance against streptomycin and kanamycin. This work represents the first description of the soil bacterial community from the Natural Reserve of Sasso Fratino, and it is the first study considering the soil microbiota of an Italian integral nature reserve.

scholarly journals Metagenomic Analysis of Bacterial Communities and Antibiotic Resistance Genes in Penaeus monodon Biofloc-Based Aquaculture Environments

2022 ◽  
Vol 8 ◽  
Author(s):  
Xieyan Chen ◽  
Zihao He ◽  
Jichen Zhao ◽  
Minze Liao ◽  
Yuan Xue ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Waste Treatment ◽  
Gene Annotation ◽  
Antibiotic Resistance Gene ◽  
Penaeus Monodon ◽  
Antibiotic Resistance Genes ◽  
Absolute Abundance

Biofloc technology (BFT) is one of the most promising technologies in global aquaculture for the purpose of improving water quality, waste treatment, and disease prevention in intensive aquaculture systems. However, characterization of the microbial species and antibiotic resistance potentially present in biofloc-based aquaculture environments is needed. In this study, we used high-throughput sequencing technology to comprehensively compare the bacterial communities in mariculture ponds of Penaeus monodon (P. monodon), by testing of water, biofloc, and intestine of P. monodon. Operational taxonomic units (OTUs) cluster analysis showed that the nine samples tested divided into 45 phyla and 457 genera. Proteobacteria was the dominant bacteria in water, biofloc and prawn intestine. In biofloc and intestine, the Ruegeria (2.23–6.31%) genus represented the largest proportion of bacteria, with Marivita (14.01–20.94%) the largest group in water. Microbial functional annotation revealed that in all the samples, genes encoding metabolism were predominant. The antibiotic resistance gene annotation showed the highest absolute abundance of patB, adeF, OXA-243, and Brucella_suis_mprF from Proteobacteria. PatB (11.33–15.01%), adeF (15.79–18.16%), OXA-243 (35.65%), and Brucella_suis_mprF (10.03%) showed the highest absolute abundance of antibiotic resistance genes in water, biofloc, and intestines, respectively. These findings may greatly increase our understanding of the characteristics of the microbiota of shrimp biofloc-based aquaculture systems and the complex interactions among shrimp, ambient microflora, and environmental variables. It provides a reference basis for policy on breeding, environmental safety, and maintaining food safety in the production of P. monodon.

scholarly journals Different analysis strategies of 16S rRNA gene data from rodent studies generate contrasting views of gut bacterial communities associated with diet, health and obesity

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10372
Author(s):  
Jose F. Garcia-Mazcorro ◽  
Jorge R. Kawas ◽  
Cuauhtemoc Licona Cassani ◽  
Susanne Mertens-Talcott ◽  
Giuliana Noratto
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Future Research ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Analysis Strategies ◽  
The Impact

Background One of the main functions of diet is to nurture the gut microbiota and this relationship affects the health of the host. However, different analysis strategies can generate different views on the relative abundance of each microbial taxon, which can affect our conclusions about the significance of diet to gut health in lean and obese subjects. Here we explored the impact of using different analysis strategies to study the gut microbiota in a context of diet, health and obesity. Methods Over 15 million 16S rRNA gene sequences from published studies involving dietary interventions in obese laboratory rodents were analyzed. Three strategies were used to assign the 16S sequences to Operational Taxonomic Units (OTUs) based on the GreenGenes reference OTU sequence files clustered at 97% and 99% similarity. Results Different strategies to select OTUs influenced the relative abundance of all bacterial taxa, but the magnitude of this phenomenon showed a strong study effect. Different taxa showed up to 20% difference in relative abundance within the same study, depending on the analysis strategy. Very few OTUs were shared among the samples. ANOSIM test on unweighted UniFrac distances showed that study, sequencing technique, animal model, and dietary treatment (in that order) were the most important factors explaining the differences in bacterial communities. Except for obesity status, the contribution of diet and other factors to explain the variability in bacterial communities was lower when using weighted UniFrac distances. Predicted functional profile and high-level phenotypes of the microbiota showed that each study was associated with unique features and patterns. Conclusions The results confirm previous findings showing a strong study effect on gut microbial composition and raise concerns about the impact of analysis strategies on the membership and composition of the gut microbiota. This study may be helpful to guide future research aiming to investigate the relationship between diet, health, and the gut microbiota.

scholarly journals A Small Regulatory RNA Controls Cell Wall Biosynthesis and Antibiotic Resistance

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Jessica Borgmann ◽  
Sina Schäkermann ◽  
Julia Elisabeth Bandow ◽  
Franz Narberhaus
Keyword(s):  
Antibiotic Resistance ◽  
Agrobacterium Tumefaciens ◽  
Antibiotic Resistance Gene ◽  
Tumor Formation ◽  
Regulatory Rna ◽  
Beta Lactamase ◽  
Microbial Composition ◽  
Ampicillin Resistance ◽  
Content Type ◽  
Small Regulatory Rna

ABSTRACT Small regulatory RNAs play an important role in the adaptation to changing conditions. Here, we describe a differentially expressed small regulatory RNA (sRNA) that affects various cellular processes in the plant pathogen Agrobacterium tumefaciens. Using a combination of bioinformatic predictions and comparative proteomics, we identified nine targets, most of which are positively regulated by the sRNA. According to these targets, we named the sRNA PmaR for peptidoglycan biosynthesis, motility, and ampicillin resistance regulator. Agrobacterium spp. are long known to be naturally resistant to high ampicillin concentrations, and we can now explain this phenotype by the positive PmaR-mediated regulation of the beta-lactamase gene ampC. Structure probing revealed a spoon-like structure of the sRNA, with a single-stranded loop that is engaged in target interaction in vivo and in vitro. Several riboregulators have been implicated in antibiotic resistance mechanisms, such as uptake and efflux transporters, but PmaR represents the first example of an sRNA that directly controls the expression of an antibiotic resistance gene. IMPORTANCE The alphaproteobacterium Agrobacterium tumefaciens is able to infect various eudicots causing crown gall tumor formation. Based on its unique ability of interkingdom gene transfer, Agrobacterium serves as a crucial biotechnological tool for genetic manipulation of plant cells. The presence of hundreds of putative sRNAs in this organism suggests a considerable impact of riboregulation on A. tumefaciens physiology. Here, we characterized the biological function of the sRNA PmaR that controls various processes crucial for growth, motility, and virulence. Among the genes directly targeted by PmaR is ampC coding for a beta-lactamase that confers ampicillin resistance, suggesting that the sRNA is crucial for fitness in the competitive microbial composition of the rhizosphere.

scholarly journals Comparison of bacterial communities and antibiotic resistance genes in oxidation ditches and membrane bioreactors

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lifang Luo ◽  
Junqin Yao ◽  
Weiguo Liu ◽  
Lixin Yang ◽  
Hailong Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Activated Sludge ◽  
Relative Abundance ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Wastewater Treatment Plants ◽  
Antibiotic Resistance Genes ◽  
Membrane Bioreactors ◽  
Metagenomic Sequencing ◽  
Process Selection

AbstractOxidation ditches (ODs) and membrane bioreactors (MBRs) are widely used in wastewater treatment plants (WWTPs) with bacteria and antibiotic resistance genes (ARGs) running through the whole system. In this study, metagenomic sequencing was used to compare the bacterial communities and ARGs in the OD and MBR systems, which received the same influent in a WWTP located in Xinjiang, China. The results showed that the removal efficiency of pollutants by the MBR process was better than that by the OD process. The composition and the relative abundance of bacteria in activated sludge were similar at the phylum and genus levels and were not affected by process type. Multidrug, fluoroquinolones and peptides were the main ARG types for the two processes, with macB being the main ARG subtype, and the relative abundance of ARG subtypes in MBR effluent was much higher than that in the OD effluent. The mobile genetic elements (MGEs) in the activated sludge were mainly transposons (tnpA) and insertion sequences (ISs; IS91). These results provide a theoretical basis for process selection and controlling the spread of ARGs.

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