Horizontal gene transfer (HGT) is a key driver in the evolution of bacterial genomes. The acquisition of genes mediated by HGT may enable bacteria to adapt to ever-changing environmental conditions. Long-term application of antibiotics in intensive agriculture is associated with the dissemination of antibiotic resistance genes among bacteria with the consequences causing public health concern. Commensal farm-animal-associated gut microbiota are considered the reservoir of the resistance genes. Therefore, in this study, we identified known and not-yet characterized mobilized genes originating from chicken and porcine fecal samples using our innovative pipeline followed by network analysis to provide appropriate visualization to support proper interpretation.
- MeSH
- antibakteriální látky MeSH
- Bacteria genetika MeSH
- bakteriální geny MeSH
- genom bakteriální MeSH
- mikrobiota * MeSH
- prasata MeSH
- přenos genů horizontální * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Antibiotics are the most efficient type of therapy developed in the twentieth century. From the early 1960s to the present, the rate of discovery of new and therapeutically useful classes of antibiotics has significantly decreased. As a result of antibiotic use, novel strains emerge that limit the efficiency of therapies in patients, resulting in serious consequences such as morbidity or mortality, as well as clinical difficulties. Antibiotic resistance has created major concern and has a greater impact on global health. Horizontal and vertical gene transfers are two mechanisms involved in the spread of antibiotic resistance genes (ARGs) through environmental sources such as wastewater treatment plants, agriculture, soil, manure, and hospital-associated area discharges. Mobile genetic elements have an important part in microbe selection pressure and in spreading their genes into new microbial communities; additionally, it establishes a loop between the environment, animals, and humans. This review contains antibiotics and their resistance mechanisms, diffusion of ARGs, prevention of ARG transmission, tactics involved in microbiome identification, and therapies that aid to minimize infection, which are explored further below. The emergence of ARGs and antibiotic-resistant bacteria (ARB) is an unavoidable threat to global health. The discovery of novel antimicrobial agents derived from natural products shifts the focus from chemical modification of existing antibiotic chemical composition. In the future, metagenomic research could aid in the identification of antimicrobial resistance genes in the environment. Novel therapeutics may reduce infection and the transmission of ARGs.
The bacterial origin of mitochondria has been a widely accepted as an event that occurred about 1.45 billion years ago and endowed cells with internal energy producing organelle. Thus, mitochondria have traditionally been viewed as subcellular organelle as any other - fully functionally dependent on the cell it is a part of. However, recent studies have given us evidence that mitochondria are more functionally independent than other organelles, as they can function outside the cells, engage in complex "social" interactions, and communicate with each other as well as other cellular components, bacteria and viruses. Furthermore, mitochondria move, assemble and organize upon sensing different environmental cues, using a process akin to bacterial quorum sensing. Therefore, taking all these lines of evidence into account we hypothesize that mitochondria need to be viewed and studied from a perspective of a more functionally independent entity. This view of mitochondria may lead to new insights into their biological function, and inform new strategies for treatment of disease associated with mitochondrial dysfunction.
- MeSH
- bakteriální geny * MeSH
- lidé MeSH
- mitochondrie * MeSH
- quorum sensing MeSH
- virion MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- MeSH
- antibakteriální látky farmakologie MeSH
- antiinfekční látky * MeSH
- bakteriální geny MeSH
- lidé MeSH
- methicilin rezistentní Staphylococcus aureus * genetika MeSH
- mikrobiální testy citlivosti MeSH
- rezistence na methicilin genetika MeSH
- stafylokokové infekce * genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- dopisy MeSH
Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, many studies have been carried out to investigate the role of gut microbiota as a pool of antibiotic resistance genes (ARGs) in human and animals. Both the structure and function of the gut bacterial community and related ARGs in pig remain unknown. In this study, we characterized the gut microbiomes and resistomes of fecal samples collected from sixteen pig farms located in sixteen cities of Shandong Province by metagenomic sequencing. Alpha diversity indicated that fecal samples from Dezhou (DZ) and Jinan (J) showed higher alpha diversity, and the lowest was from pig farms of Rizhao (RZ). Other pig farms showed similar alpha diversity. Besides, we found that the composition of gut bacterial among these pig farms varied greatly. Helcococcus massiliensis was the dominant bacterial species in pig farms of RZ and Zibo (ZB), while Prevotella sp. P5-92 occupied a superior proportion in Binzhou (BZ) and Yantai (YT). The proportion of Lactobacillus johnsonii was similar among farms of Qingdao (QD), Linyi (LY), Taian (TA), Weifang (WF), Weihai (WH), and YT. In total, 1112 ARGs were obtained and classified into 69 groups from 48 fecal samples. ARG abundance was higher in farms of Dongying (DY) and WH than others, while the lowest farms in BZ and ZB. Interestingly, it is found that BZ pig farm was exclusive, so the tetQ gene showed a higher abundance. In contrast, the load of APH(3') - IIIa in fecal samples from DY, J-1, LC, WF, and WH was high. Meanwhile, the most relevant ARGs and the corresponding microbes were screened out. Our metagenomic sequencing data provides new insights into the abundance, diversity, and structure of bacterial community in pig farms. Meanwhile, we screened ARG-carrying bacteria and explored the correlation between ARGs and bacterial community, which provide a comprehensive view of the pig fecial ARGs and microbes in different farms of Shandong.
Persistent use of pesticides and animal manure in agricultural soils inadvertently introduced heavy metals and antibiotic/antibiotic resistance genes (ARGs) into the soil with deleterious consequences. The microbiome and heavy metal and antibiotic resistome of a pesticide and animal manure inundated agricultural soil (SL6) obtained from a vegetable farm at Otte, Eiyenkorin, Kwara State, Nigeria, was deciphered via shotgun metagenomics and functional annotation of putative ORFs (open reading frames). Structural metagenomics of SL6 microbiome revealed 29 phyla, 49 classes, 94 orders, 183 families, 366 genera, 424 species, and 260 strains with the preponderance of the phyla Proteobacteria (40%) and Actinobacteria (36%), classes Actinobacteria (36%), Alphaproteobacteria (18%), and Gammaproteobacteria (17%), and genera Kocuria (16%), Sphingobacterium (11%), and Brevundimonas (10%), respectively. Heavy metal resistance genes annotation conducted using Biocide and Metal Resistance Gene Database (BacMet) revealed the detection of genes responsible for the uptake, transport, detoxification, efflux, and regulation of copper, cadmium, zinc, nickel, chromium, cobalt, selenium, tungsten, mercury, and several others. ARG annotation using the Antibiotic Resistance Gene-annotation (ARG-ANNOT) revealed ARGs for 11 antibiotic classes with the preponderance of β-lactamases, mobilized colistin resistance determinant (mcr-1), macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside resistance genes, among others. The persistent use of pesticide and animal manure is strongly believed to play a major role in the proliferation of heavy metal and antibiotic resistance genes in the soil. This study revealed that agricultural soils inundated with pesticide and animal manure use are potential hotspots for ARG spread and may accentuate the spread of multidrug resistant clinical pathogens.
- MeSH
- aminoglykosidy MeSH
- antibakteriální látky farmakologie MeSH
- bakteriální geny MeSH
- beta-laktamasy genetika MeSH
- chrom MeSH
- dezinficiencia * MeSH
- glykopeptidy MeSH
- hnůj mikrobiologie MeSH
- kadmium MeSH
- kobalt MeSH
- kolistin MeSH
- linkosamidy MeSH
- makrolidy MeSH
- měď MeSH
- metagenomika MeSH
- mikrobiota * genetika MeSH
- nikl MeSH
- pesticidy * farmakologie MeSH
- půda chemie MeSH
- půdní mikrobiologie MeSH
- rtuť * MeSH
- selen * MeSH
- streptograminy MeSH
- wolfram MeSH
- zinek MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
The wild boar (Sus scrofa) population has increased dramatically over the last decades throughout Europe and it has become a serious pest. In addition, the common habitat of wild boar and of the tick, Ixodes ricinus, indicates the potential of wild boar to play a role in epidemiology of epizootic and zoonotic tick-borne pathogens, including Anaplasma phagocytophilum. In Europe, epidemiological cycles and reservoirs of A. phagocytophilum, including its zoonotic haplotypes, are poorly understood. In this study, we focused on detection and further genetic characterization of A. phagocytophilum and piroplasmids in 550 wild boars from eleven districts of Moravia and Silesia in the Czech Republic. Using highly sensitive nested PCR targeting the groEL gene, the DNA of A. phagocytophilum was detected in 28 wild boars (5.1 %) representing six unique haplotypes. The dominant haplotype was found in 21 samples from 7 different districts. All detected haplotypes clustered in the largest clade representing the European ecotype I and the dominant haplotype fell to the subclade with the European human cases and strains from dogs and horses. Nested PCR targeting the variable region of the 18S rRNA gene of piroplasmids resulted in one positive sample with 99.8 % sequence identity to Babesia divergens. The presence of these two pathogens that are primarily circulated by I. ricinus confirms the local participation of wild boar in the host spectrum of this tick and warrants experimental studies to address wild boar as a reservoir of zoonotic haplotypes of A. phagocytophilum.
- MeSH
- Anaplasma phagocytophilum genetika izolace a purifikace MeSH
- anaplasmóza epidemiologie mikrobiologie MeSH
- babezióza epidemiologie parazitologie MeSH
- bakteriální geny MeSH
- genetická variace * MeSH
- nemoci prasat epidemiologie mikrobiologie parazitologie MeSH
- Piroplasmida genetika izolace a purifikace MeSH
- prasata MeSH
- prevalence MeSH
- protozoální geny MeSH
- Sus scrofa MeSH
- zdroje nemoci parazitologie veterinární MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
Butyrate is formed in the gut during bacterial fermentation of dietary fiber and is attributed numerous beneficial effects on the host metabolism. We aimed to develop a method for the assessment of functional capacity of gut microbiota butyrate synthesis based on the qPCR quantification of bacterial gene coding butyryl-CoA:acetate CoA-transferase, the key enzyme of butyrate synthesis. In silico, we identified bacteria possessing but gene among human gut microbiota by searching but coding sequences in available databases. We designed and validated six sets of degenerate primers covering all selected bacteria, based on their phylogenetic nearness and sequence similarity, and developed a method for gene abundance normalization in human fecal DNA. We determined but gene abundance in fecal DNA of subjects with opposing dietary patterns and metabolic phenotypes-lean vegans (VG) and healthy obese omnivores (OB) with known fecal microbiota and metabolome composition. We found higher but gene copy number in VG compared with OB, in line with higher fecal butyrate content in VG group. We further found a positive correlation between the relative abundance of target bacterial genera identified by next-generation sequencing and groups of but gene-containing bacteria determined by specific primers. In conclusion, this approach represents a simple and feasible tool for estimation of microbial functional capacity.
- MeSH
- bakteriální geny * MeSH
- butyráty metabolismus MeSH
- DNA bakterií genetika MeSH
- dospělí MeSH
- feces mikrobiologie MeSH
- fenotyp MeSH
- fylogeneze MeSH
- genová dávka MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- neparametrická statistika MeSH
- obezita mikrobiologie MeSH
- polymerázová řetězová reakce * MeSH
- reprodukovatelnost výsledků MeSH
- střevní mikroflóra genetika MeSH
- vegani MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Routinely used typing methods including MLST, rep-PCR and whole genome sequencing (WGS) are time-consuming, costly, and often low throughput. Here, we describe a novel mini-MLST scheme for Eschericha coli as an alternative method for rapid genotyping. Using the proposed mini-MLST scheme, 10,946 existing STs were converted into 1,038 Melting Types (MelTs). To validate the new mini-MLST scheme, in silico analysis was performed on 73,704 strains retrieved from EnteroBase resulting in discriminatory power D = 0.9465 (CI 95% 0.9726-0.9736) for mini-MLST and D = 0.9731 (CI 95% 0.9726-0.9736) for MLST. Moreover, validation on clinical isolates was conducted with a significant concordance between MLST, rep-PCR and WGS. To conclude, the great portability, efficient processing, cost-effectiveness, and high throughput of mini-MLST represents immense benefits, even when accompanied with a slightly lower discriminatory power than other typing methods. This study proved mini-MLST is an ideal method to screen and subgroup large sets of isolates and/or quick strain typing during outbreaks. In addition, our results clearly showed its suitability for prospective surveillance monitoring of emergent and high-risk E. coli clones'.
- MeSH
- bakteriální geny * MeSH
- denaturace nukleových kyselin MeSH
- DNA bakterií chemie genetika MeSH
- DNA primery MeSH
- epidemický výskyt choroby MeSH
- Escherichia coli klasifikace genetika izolace a purifikace MeSH
- genom bakteriální MeSH
- genotypizační techniky * MeSH
- infekce vyvolané Escherichia coli mikrobiologie MeSH
- jednonukleotidový polymorfismus * MeSH
- multilokusová sekvenční typizace metody MeSH
- počítačová simulace MeSH
- polymerázová řetězová reakce metody MeSH
- repetitivní sekvence nukleových kyselin MeSH
- sekvenování celého genomu MeSH
- surveillance populace MeSH
- techniky typizace bakterií * MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase-α, β, β'. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β' subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.
- MeSH
- Bacillus subtilis enzymologie genetika MeSH
- bakteriální geny MeSH
- delece genu MeSH
- DNA řízené RNA-polymerasy chemie genetika metabolismus MeSH
- duplikace genu MeSH
- endoribonukleasy genetika fyziologie MeSH
- genetická transkripce MeSH
- homeostáza MeSH
- messenger RNA metabolismus MeSH
- molekulární evoluce MeSH
- mutace MeSH
- suprese genetická MeSH
- transkriptom MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
