scholarly journals Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota

2018 ◽  
Author(s):  
Bálint Kintses ◽  
Orsolya Méhi ◽  
Eszter Ari ◽  
Mónika Számel ◽  
Ádám Györkei ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Horizontal Transfer ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Genetic Exchange ◽  
Human Gut ◽  
Human Gut Microbiota

AbstractThe human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs) that are ancient components of immune defence. Despite important medical relevance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here we show that AMP- and antibiotic-resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics revealed that AMP resistance genes originating from phylogenetically distant bacteria only have a limited potential to confer resistance inEscherichia coli, an intrinsically susceptible species. Third, the phenotypic impact of acquired AMP resistance genes heavily depends on the genetic background of the recipient bacteria. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota with implications for disease risks.

scholarly journals Horizontal transfer of antibiotic resistance genes in the human gut microbiome

2020 ◽  
Vol 53 ◽  
pp. 35-43 ◽  
Author(s):  
Ross S McInnes ◽  
Gregory E McCallum ◽  
Lisa E Lamberte ◽  
Willem van Schaik
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Horizontal Transfer ◽  
Antibiotic Resistance Genes ◽  
Human Gut ◽  
Human Gut Microbiome

scholarly journals Metagenomics-Based Analysis of the Age-Related Cumulative Effect of Antibiotic Resistance Genes in Gut Microbiota

Antibiotics ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1006
Author(s):  
Lei Wu ◽  
Xinqiang Xie ◽  
Ying Li ◽  
Tingting Liang ◽  
Haojie Zhong ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Tetracycline Resistance ◽  
Cumulative Effect ◽  
Resistance Mechanisms ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Age Related

Antibiotic resistance in bacteria has become a major global health problem. One of the main reservoirs of antibiotic resistance genes is the human gut microbiota. To characterise these genes, a metagenomic approach was used. In this study, a comprehensive antibiotic resistome catalog was established using fecal samples from 246 healthy individuals from world’s longevity township in Jiaoling, China. In total, 606 antibiotic resistance genes were detected. Our results indicated that antibiotic resistance genes in the human gut microbiota accumulate and become more complex with age as older groups harbour the highest abundance of these genes. Tetracycline resistance gene type tetQ was the most abundant group of antibiotic resistance genes in gut microbiota, and the main carrier of antibiotic resistance genes was Bacteroides. Antibiotic efflux, inactivation, and target alteration were found to be the dominant antimicrobial resistance mechanisms. This research may help to establish a comprehensive antibiotic resistance catalog that includes extremely long-lived healthy people such as centenarians, and may provide potential recommendations for controlling the use of antibiotics.

scholarly journals The human gut resistome

2015 ◽  
Vol 370 (1670) ◽  
pp. 20140087 ◽  
Author(s):  
Willem van Schaik
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Resistance Genes ◽  
Horizontal Transfer ◽  
Genetic Material ◽  
Antibiotic Resistance Genes ◽  
Strictly Anaerobic ◽  
Donor Strain ◽  
Human Gut ◽  
Frequent Event

In recent decades, the emergence and spread of antibiotic resistance among bacterial pathogens has become a major threat to public health. Bacteria can acquire antibiotic resistance genes by the mobilization and transfer of resistance genes from a donor strain. The human gut contains a densely populated microbial ecosystem, termed the gut microbiota, which offers ample opportunities for the horizontal transfer of genetic material, including antibiotic resistance genes. Recent technological advances allow microbiota-wide studies into the diversity and dynamics of the antibiotic resistance genes that are harboured by the gut microbiota (‘the gut resistome’). Genes conferring resistance to antibiotics are ubiquitously present among the gut microbiota of humans and most resistance genes are harboured by strictly anaerobic gut commensals. The horizontal transfer of genetic material, including antibiotic resistance genes, through conjugation and transduction is a frequent event in the gut microbiota, but mostly involves non-pathogenic gut commensals as these dominate the microbiota of healthy individuals. Resistance gene transfer from commensals to gut-dwelling opportunistic pathogens appears to be a relatively rare event but may contribute to the emergence of multi-drug resistant strains, as is illustrated by the vancomycin resistance determinants that are shared by anaerobic gut commensals and the nosocomial pathogen Enterococcus faecium .

scholarly journals Putative mobilized colistin resistance genes in the human gut microbiome

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bruno G. N. Andrade ◽  
Tobias Goris ◽  
Haithem Afli ◽  
Felipe H. Coutinho ◽  
Alberto M. R. Dávila ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Antibiotic Resistance Genes ◽  
Future Research ◽  
Human Populations ◽  
Bacterial Strains ◽  
Colistin Resistance ◽  
Human Gut ◽  
Human Gut Microbiome

Abstract Background The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes. Results A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings. Conclusion This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.

scholarly journals Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota

2018 ◽  
Vol 4 (3) ◽  
pp. 447-458 ◽  
Author(s):  
Bálint Kintses ◽  
Orsolya Méhi ◽  
Eszter Ari ◽  
Mónika Számel ◽  
Ádám Györkei ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Antimicrobial Peptide ◽  
Resistance Genes ◽  
Horizontal Transfer ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Antimicrobial Peptide Resistance

scholarly journals Rice Bran and Quercetin Produce a Positive Synergistic Effect on Human Gut Microbiota, Elevate the Level of Propionate, and Reduce the Population of Enterobacteriaceae family when Determined using a Bioreactor Model

2020 ◽  
Author(s):  
Sudeep Ghimire ◽  
Supapit Wongkuna ◽  
Ranjini Sankaranarayanan ◽  
Elizabeth P. Ryan ◽  
G. Jayarama Bhat ◽  
...  
Keyword(s):  
Synergistic Effect ◽  
Gut Microbiota ◽  
Rice Bran ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Human Gut ◽  
Food Ingredients ◽  
Microbiome Composition ◽  
Human Gut Microbiota ◽  
Host Health

AbstractDiet is one of the prominent determinants of gut microbiota composition significantly impacting human health. Recent studies with dietary supplements such as rice bran and quercetin have been shown to provide a beneficial impact on the host by positively influencing the gut microbiota. However, the specific bacterial species impacted when rice bran or quercetin is present in the diet is not well understood. Therefore, in this study, we used a minibioreactor array system as a model to determine the effect of quercetin and rice bran individually, as well as in combination, on gut microbiota without the confounding host factors. We found that rice bran exerts higher shift in gut microbiome composition when compared to quercetin. At the species level, Acidaminococcus intestini was the only significantly enriched taxa when quercetin was supplemented, while 15 species were enriched in rice bran supplementation and 13 were enriched when quercetin and rice bran were supplemented in combination. When comparing the short chain fatty acid production, quercetin supplementation significantly enriched isobutyrate production while propionate dominated the quercetin and rice bran combined group. Higher levels of propionate were highly correlated to the lower abundance of the potentially pathogenic Enterobacteriaceae family. These findings suggest that the combination of rice bran and quercetin serve to enrich beneficial bacteria and reduce potential opportunistic pathogens. However, further in vivo studies are necessary to determine the synergistic effect of rice bran and quercetin on host health and immunity.ImportanceRice bran and quercetin are dietary components that shape host health by interacting with the gut microbiome. Both these substrates have been reported to provide nutritional and immunological benefits individually. However, considering the complexity of the human diet, it is useful to determine how the combination of food ingredients such as rice bran and quercetin influences the human gut microbiota. Our study provides insights into how these ingredients influence microbiome composition alone and in combination in vitro. This will allow us to identify which species in the gut microbiome are responsible for biotransformation of these dietary ingredients.. Such information is helpful for the development of synbiotics to improve gut health and immunity.

scholarly journals Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters

2022 ◽  
Vol 8 (1) ◽  
Author(s):  
Wei Yan ◽  
A. Brantley Hall ◽  
Xiaofang Jiang
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Phase Variation ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Human Gut ◽  
Bacterial Populations ◽  
Human Gut Microbiome ◽  
Metagenomic Assembly

AbstractAntibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.

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