Mycobacterium avium is an opportunistic bacterium associated with pathogenic behavior in both humans and animals. M. avium has evolved as a pathogen by having an environmental component in its life style. Prophages ar...Mycobacterium avium is an opportunistic bacterium associated with pathogenic behavior in both humans and animals. M. avium has evolved as a pathogen by having an environmental component in its life style. Prophages are the integrated viral forms in bacterium genome. They constitute about 10% - 20% of genome of many bacteria and they contribute to pathogenicity of microbes. We investigated whether the M. avium 104 genome contained prophages and evaluated the genes/proteins for putative functions. Three prophage genes were identified in the M. avium 104 database, and sequences were analyzed for specific motifs. The prophage sequences were then cloned in Mycobacterium smegmatis and the bacterial phenotype was evaluated in gain of function assays for environmental stresses, such as tolerance to extreme temperatures, UV light, biofilm formation and resistance to acid as well as macrophage survival. The results indicate that two of the prophage genes, MAV_0696 and MAV_2265, confer M. smegmatis with enhanced ability to produce biofilm. Using a Real-Time PCR, it was determined that MAV_0696 and MAV_2265 transcripts were upregulated upon biofilm formation by M. avium. The expression of MAV_2265 gene was significantly higher at all selected time points. In addition, the expression of MAV_2265 in M. smegmatis also led to significantly greater survival rate at pH 5.0 compared to the wild-type control. None of the other physical abilities were altered by overexpressing the prophage genes in M. smegmatis. In summary, we identified three prophage sequences in M. avium 104, from which two of them were found to be associated with biofilm formation and one with resistance to the acidic environment. Future studies will identify the mechanisms involved in the prophages function.展开更多
Abundant virus-like particles were concentrated from large-volume samples from two hot springs. Both addition of viral concentrates and addition of samples induced by addition of mitomycin-C changed patterns of carbon...Abundant virus-like particles were concentrated from large-volume samples from two hot springs. Both addition of viral concentrates and addition of samples induced by addition of mitomycin-C changed patterns of carbon source utilization by hot spring microbial communities. Specific effects of the two treatments depended upon both temperature and incubation period. Increased metabolic capability with greater exposure to free phages, consistent with the view that phages are major lateral transporters of metabolic genes, was observed most clearly in microbes incubated at a temperature lower than that encountered in situ. On the other hand, decreases in the diversity of utilizable C sources upon exposure to phages may have been due to lytic activity in which susceptible bacterial populations were differentially reduced by infective viruses, consistent with the “killing the winner” hypothesis. Treatment of cultures with MC-treated culture extracts, assumed to increase exposure to excised prophages, resulted in higher average metabolic rates after 18 h, but lower rates after 48 h of incubation. With incubation at in situ temperature, this same treatment led to an initial increase in the number of readily utilized C sources, followed by a decrease in community metabolic diversity relative to controls in samples from both hot springs. Thus, treatments designed to increase the interaction between hot spring microbes and either free or newly-excised phages had observable time- and temperature-dependent effects on community metabolism, demonstrating an important, yet complex, ecological role for phages in hot spring waters.展开更多
Phage-microbe interactions are appealing systems to study coevolution,and have also been increasingly emphasized due to their roles in human health,disease,and the development of novel therapeutics.Phage-microbe inter...Phage-microbe interactions are appealing systems to study coevolution,and have also been increasingly emphasized due to their roles in human health,disease,and the development of novel therapeutics.Phage-microbe interactions leave diverse signals in bacterial and phage genomic sequences,defined as phage-host interaction signals(PHISs),which include clustered regularly interspaced short palindromic repeats(CRISPR)targeting,prophage,and protein-protein interaction signals.In the present study,we developed a novel tool phage-host interaction signal detector(PHISDetector)to predict phage-host interactions by detecting and integrating diverse in silico PHISs,and scoring the probability of phage-host interactions using machine learning models based on PHIS features.We evaluated the performance of PHISDetector on multiple benchmark datasets and application cases.When tested on a dataset of 758 annotated phage-host pairs,PHISDetector yields the prediction accuracies of 0.51 and 0.73 at the species and genus levels,respectively,outperforming other phage-host prediction tools.When applied to 125,842 metagenomic viral contigs(mVCs)derived from 3042 geographically diverse samples,a detection rate of 54.54% could be achieved.Furthermore,PHISDetector could predict infecting phages for 85.6% of 368 multidrug-resistant(MDR)bacteria and 30% of 454 human gut bacteria obtained from the National Institutes of Health(NIH)Human Microbiome Project(HMP).The PHISDetector can be run either as a web server(http://www.microbiome-bigdata.com/PHISDetector/)for general users to study individual inputs or as a stand-alone version(https://github.com/HITImmunologyLab/PHISDetector)to process massive phage contigs from virome studies.展开更多
文摘Mycobacterium avium is an opportunistic bacterium associated with pathogenic behavior in both humans and animals. M. avium has evolved as a pathogen by having an environmental component in its life style. Prophages are the integrated viral forms in bacterium genome. They constitute about 10% - 20% of genome of many bacteria and they contribute to pathogenicity of microbes. We investigated whether the M. avium 104 genome contained prophages and evaluated the genes/proteins for putative functions. Three prophage genes were identified in the M. avium 104 database, and sequences were analyzed for specific motifs. The prophage sequences were then cloned in Mycobacterium smegmatis and the bacterial phenotype was evaluated in gain of function assays for environmental stresses, such as tolerance to extreme temperatures, UV light, biofilm formation and resistance to acid as well as macrophage survival. The results indicate that two of the prophage genes, MAV_0696 and MAV_2265, confer M. smegmatis with enhanced ability to produce biofilm. Using a Real-Time PCR, it was determined that MAV_0696 and MAV_2265 transcripts were upregulated upon biofilm formation by M. avium. The expression of MAV_2265 gene was significantly higher at all selected time points. In addition, the expression of MAV_2265 in M. smegmatis also led to significantly greater survival rate at pH 5.0 compared to the wild-type control. None of the other physical abilities were altered by overexpressing the prophage genes in M. smegmatis. In summary, we identified three prophage sequences in M. avium 104, from which two of them were found to be associated with biofilm formation and one with resistance to the acidic environment. Future studies will identify the mechanisms involved in the prophages function.
文摘Abundant virus-like particles were concentrated from large-volume samples from two hot springs. Both addition of viral concentrates and addition of samples induced by addition of mitomycin-C changed patterns of carbon source utilization by hot spring microbial communities. Specific effects of the two treatments depended upon both temperature and incubation period. Increased metabolic capability with greater exposure to free phages, consistent with the view that phages are major lateral transporters of metabolic genes, was observed most clearly in microbes incubated at a temperature lower than that encountered in situ. On the other hand, decreases in the diversity of utilizable C sources upon exposure to phages may have been due to lytic activity in which susceptible bacterial populations were differentially reduced by infective viruses, consistent with the “killing the winner” hypothesis. Treatment of cultures with MC-treated culture extracts, assumed to increase exposure to excised prophages, resulted in higher average metabolic rates after 18 h, but lower rates after 48 h of incubation. With incubation at in situ temperature, this same treatment led to an initial increase in the number of readily utilized C sources, followed by a decrease in community metabolic diversity relative to controls in samples from both hot springs. Thus, treatments designed to increase the interaction between hot spring microbes and either free or newly-excised phages had observable time- and temperature-dependent effects on community metabolism, demonstrating an important, yet complex, ecological role for phages in hot spring waters.
基金supported by the National Natural Science Foundation of China(Grant Nos.31825008,31422014,and 61872117).
文摘Phage-microbe interactions are appealing systems to study coevolution,and have also been increasingly emphasized due to their roles in human health,disease,and the development of novel therapeutics.Phage-microbe interactions leave diverse signals in bacterial and phage genomic sequences,defined as phage-host interaction signals(PHISs),which include clustered regularly interspaced short palindromic repeats(CRISPR)targeting,prophage,and protein-protein interaction signals.In the present study,we developed a novel tool phage-host interaction signal detector(PHISDetector)to predict phage-host interactions by detecting and integrating diverse in silico PHISs,and scoring the probability of phage-host interactions using machine learning models based on PHIS features.We evaluated the performance of PHISDetector on multiple benchmark datasets and application cases.When tested on a dataset of 758 annotated phage-host pairs,PHISDetector yields the prediction accuracies of 0.51 and 0.73 at the species and genus levels,respectively,outperforming other phage-host prediction tools.When applied to 125,842 metagenomic viral contigs(mVCs)derived from 3042 geographically diverse samples,a detection rate of 54.54% could be achieved.Furthermore,PHISDetector could predict infecting phages for 85.6% of 368 multidrug-resistant(MDR)bacteria and 30% of 454 human gut bacteria obtained from the National Institutes of Health(NIH)Human Microbiome Project(HMP).The PHISDetector can be run either as a web server(http://www.microbiome-bigdata.com/PHISDetector/)for general users to study individual inputs or as a stand-alone version(https://github.com/HITImmunologyLab/PHISDetector)to process massive phage contigs from virome studies.
