Nocardia spp., which belongs to one of the Nocardio-form filamentous bacteria, is usually surface hydrophobic and when overproduced attaches to the surface of bubbles under the action of surfactants, allowing the stable presence of foam on the surface of aeration tanks, leading to the occurrence of sludge-foaming events. Two novel phages, P69 and KYD2, were isolated from the environment, and their hosts were Nocardia transvalensis and Nocardia carnea, respectively. These two phages are Siphophages-like with long tails. An aeration tank pilot plant was constructed in the laboratory to simulate sludge foaming, and these two strains of phage were applied. Compared with the reactor not dosed with phage, the application of phage could reduce the host level in the reactor, resulting in the highest decrease in turbidity by more than 68% and sludge volume index by more than 25%. The time for surface foam disappearance was 9 h earlier than that of the control group (the group with the same concentration of Nocardia carnea but no bacteriophage applied), significantly improving water quality. The phage can effectively inhibit the propagation of Nocardia in the actual sludge-foaming event, control the sludge foaming, and improve the effluent quality. It provides a novel and relatively economical solution for controlling sludge foaming in sewage treatment plants in the future, shows that the phages have potential application value in the prevention and control of Nocardia, and provides another way to control the sludge-foaming event caused by the excessive reproduction of Nocardia in the future.
- MeSH
- antibiotická rezistence * účinky léků MeSH
- bakteriální infekce farmakoterapie MeSH
- bakteriofágy izolace a purifikace klasifikace růst a vývoj MeSH
- fágová terapie * dějiny metody MeSH
- lidé MeSH
- profágy patogenita MeSH
- průmyslová mikrobiologie trendy MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
Klebsiella pneumoniae (family Enterobacteriaceae) is a gram-negative bacterium that has strong pathogenicity to humans and can cause sepsis, pneumonia, and urinary tract infection. In recent years, the unreasonable use of antibacterial drugs has led to an increase in drug-resistant strains of K. pneumoniae, a serious threat to public health. Bacteriophages, viruses that infect bacteria, are ubiquitous in the natural environment. They are considered to be the most promising substitute for antibiotics because of their high specificity, high efficiency, high safety, low cost, and short development cycle. In this study, a novel phage designated vB_KpnP_IME279 was successfully isolated from hospital sewage using a multidrug-resistant strain of K. pneumoniae as an indicator. A one-step growth curve showed that vB_KpnP_IME279 has a burst size of 140 plaque-forming units/cell and a latent period of 20 min at its optimal multiplicity of infection (MOI = 0.1). Phage vB_KpnP_IME279 survives in a wide pH range between 3 and 11 and is stable at temperatures ranging from 40 to 60 °C. Ten of the 20 strains of K. pneumoniae including the host bacteria were lysed by the phage vB_KpnP_IME279, and the multilocus sequence typing and wzi typing of the 10 strains were ST11, ST37, ST375, wzi209, wzi52, and wzi72, respectively. The genome of vB_KpnP_IME279 is 42,518 bp long with a G + C content of 59.3%. Electron microscopic observation showed that the phage belongs to the family Podoviridae. BLASTN alignment showed that the genome of the phage has low similarity with currently known phages. The evolutionary relationship between phage vB_KpnP_IME279 and other Podoviridae was analyzed using a phylogenetic tree based on sequences of phage major capsid protein and indicates that the phage vB_KpnP_IME279 belongs to the Podoviridae subfamily. These data enhance understanding of K. pneumoniae phages and will help in development of treatments for multidrug-resistant bacteria using phages.
- MeSH
- antibakteriální látky farmakologie MeSH
- bakteriofágy klasifikace genetika izolace a purifikace fyziologie MeSH
- fylogeneze MeSH
- genom virový MeSH
- hostitelská specificita MeSH
- Klebsiella pneumoniae účinky léků izolace a purifikace virologie MeSH
- lidé MeSH
- mikrobiologické techniky MeSH
- mnohočetná bakteriální léková rezistence MeSH
- multilokusová sekvenční typizace MeSH
- nemocnice MeSH
- odpadní vody mikrobiologie virologie MeSH
- Podoviridae klasifikace genetika izolace a purifikace MeSH
- RNA ribozomální 16S MeSH
- sekvenování celého genomu MeSH
- techniky typizace bakterií MeSH
- teplota MeSH
- zastoupení bazí MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
- MeSH
- Bacteroidetes klasifikace genetika virologie MeSH
- bakteriofágy klasifikace genetika MeSH
- DNA virů genetika MeSH
- feces virologie MeSH
- fylogeneze MeSH
- fylogeografie MeSH
- genetická variace MeSH
- koevoluce * MeSH
- lidé MeSH
- primáti virologie MeSH
- střevní mikroflóra * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Phage tail fibres are elongated protein assemblies capable of specific recognition of bacterial surfaces during the first step of viral infection1-4. The folding of these complex trimeric structures often requires a phage-encoded tail fibre assembly (Tfa) protein5-7. Despite the wide occurrence of Tfa proteins, their functional mechanism has not been elucidated. Here, we investigate the tail fibre and Tfa of Escherichia coli phage Mu. We demonstrate that Tfa forms a stable complex with the tail fibre, and present a 2.1 Å resolution X-ray crystal structure of this complex. We find that Tfa proteins are comprised of two domains: a non-conserved N-terminal domain that binds to the C-terminal region of the fibre and a conserved C-terminal domain that probably mediates fibre oligomerization and assembly. Tfa forms rapidly exchanging multimers on its own, but not a stable trimer, implying that Tfa does not specify the trimeric state of the fibre. We propose that the key conserved role of Tfa is to ensure that fibre assembly and multimerization initiates at the C terminus, ensuring that the intertwined and repetitive structural elements of fibres come together in the correct sequence. The universal importance of correctly aligning the C termini of phage fibres is highlighted by our work.
- MeSH
- bakteriofágy klasifikace fyziologie MeSH
- Escherichia coli metabolismus virologie MeSH
- krystalografie rentgenová MeSH
- molekulární modely MeSH
- multimerizace proteinu MeSH
- proteiny virových bičíků chemie genetika metabolismus MeSH
- sbalování proteinů MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- vazba proteinů MeSH
- virové proteiny chemie genetika metabolismus MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Next-generation sequencing has opened avenues to studying complex populations such as the bacteriome (all bacteria), mycobiome (all fungi), and virome (all viruses in a given sample). Viromes are less often investigated as compared to bacteriomes. The reasons are mostly methodological: because no common pan-viral sequence signature exists, metagenomic sequencing remains the only option. This brings about the need of laborious virus enrichment, multiple signal amplification steps with virtually no possibility of interim quality control, and complicated bioinformatic analysis of the ensuing sequence data. Nevertheless, over the past decade virome sequencing has been enormously successful in identifying new agents in human and animal diseases, and in characterizing viruses in various ecological niches. Recently, virome sequencing has been also employed in studies of non-infectious diseases, which has brought about new challenges of sensitivity, costs, and reproducibility in testing of large sets of samples. Here, we present a detailed protocol that has been utilized in virome studies where hundreds of samples had to be reliably tested in order to assess the association of the stool virome with susceptibility to type 1 diabetes, a non-infectious autoimmune disease.
- MeSH
- bakteriofágy klasifikace genetika izolace a purifikace MeSH
- DNA virů genetika izolace a purifikace MeSH
- feces virologie MeSH
- genová knihovna MeSH
- metagenom * MeSH
- metagenomika * metody MeSH
- polymerázová řetězová reakce MeSH
- RNA virová genetika izolace a purifikace MeSH
- střevní mikroflóra * MeSH
- ultracentrifugace MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
In this study, a method combining Raman spectroscopy with chemometric analysis was developed for detection of phage presence in raw milk and discrimination of Streptococcus thermophilus and Lactobacillus bulgaricus phages which are among the main phages causing problems in dairy industry. For this purpose, S. thermophilus and L. bulgaricus phages were added into raw milk separately, and then some pretreatments such as fat separation, removal of casein, and filtration were applied to the raw milk samples. Raman spectra of the samples were collected and then analyzed using principal component analysis in order to discriminate these phages in raw milk. In the next step, dilutions of S. thermophilus phages in pretreated raw milk were prepared, and Raman spectra were collected. These spectra were analyzed by using partial least squares method to quantify phages in low titer. Consequently, it has been demonstrated that S. thermophilus and L. bulgaricus phages, which have titers sufficient to fail the fermentation (~ 107 pfu/mL) and have lower titers (102-103 pfu/mL), could be discriminated from antibiotic and each other. Additionally, low concentrations of S. thermophilus phages (102 pfu/mL) could be detected through Raman spectroscopy with a short analysis time (60 min) and high coefficient of determination (R2) values for both calibration (0.985) and validation (0.906) with a root mean square error of calibration of 70.54 and root mean square error of prediction of 165.47. However, a lower success was achieved with L. bulgaricus phages and the obtained coefficient of determination values were not sufficiently high (0.649).
- MeSH
- analýza hlavních komponent MeSH
- bakteriofágy klasifikace fyziologie MeSH
- fermentace MeSH
- Lactobacillus delbrueckii virologie MeSH
- mlékárenství metody MeSH
- mléko mikrobiologie virologie MeSH
- Ramanova spektroskopie * MeSH
- Streptococcus thermophilus virologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- technické zprávy MeSH
BACKGROUND: We set out to explore associations between the stool bacteriome profiles and early-onset islet autoimmunity, taking into account the interactions with the virus component of the microbiome. METHODS: Serial stool samples were longitudinally collected from 18 infants and toddlers with early-onset islet autoimmunity (median age 17.4 months) followed by type 1 diabetes, and 18 tightly matched controls from the Finnish Diabetes Prediction and Prevention (DIPP) cohort. Three stool samples were analyzed, taken 3, 6, and 9 months before the first detection of serum autoantibodies in the case child. The risk of islet autoimmunity was evaluated in relation to the composition of the bacteriome 16S rDNA profiles assessed by mass sequencing, and to the composition of DNA and RNA viromes. RESULTS: Four operational taxonomic units were significantly less abundant in children who later on developed islet autoimmunity as compared to controls-most markedly the species of Bacteroides vulgatus and Bifidobacterium bifidum. The alpha or beta diversity, or the taxonomic levels of bacterial phyla, classes or genera, showed no differences between cases and controls. A correlation analysis suggested a possible relation between CrAssphage signals and quantities of Bacteroides dorei. No apparent associations were seen between development of islet autoimmunity and sequences of yet unknown origin. CONCLUSIONS: The results confirm previous findings that an imbalance within the prevalent Bacteroides genus is associated with islet autoimmunity. The detected quantitative relation of the novel "orphan" bacteriophage CrAssphage with a prevalent species of the Bacteroides genus may exemplify possible modifiers of the bacteriome.
- MeSH
- autoimunita * MeSH
- autoimunitní nemoci krev epidemiologie etiologie imunologie MeSH
- Bacteroides klasifikace imunologie izolace a purifikace virologie MeSH
- bakteriální RNA chemie metabolismus MeSH
- bakteriofágy klasifikace imunologie izolace a purifikace MeSH
- diabetes mellitus 1. typu krev epidemiologie etiologie imunologie MeSH
- dítě MeSH
- dysbióza imunologie mikrobiologie patofyziologie virologie MeSH
- feces mikrobiologie virologie MeSH
- fylogeneze MeSH
- kohortové studie MeSH
- Langerhansovy ostrůvky imunologie MeSH
- lidé MeSH
- longitudinální studie MeSH
- molekulární typizace MeSH
- nemocnice univerzitní MeSH
- prospektivní studie MeSH
- riziko MeSH
- RNA ribozomální 16S chemie metabolismus MeSH
- RNA virová chemie metabolismus MeSH
- střevní mikroflóra imunologie MeSH
- studie případů a kontrol MeSH
- výpočetní biologie MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- multicentrická studie MeSH
- Geografické názvy
- Finsko epidemiologie MeSH
Bacteriophages (or phages), the most abundant viral entity of the planet, are omni-present in all the ecosystems. On the basis of their unique characteristics and anti-bacterial property, phages are being freshly evaluated taxonomically. Phages replicate inside the host either by lytic or lysogenic mode after infecting and using the cellular machinery of a bacterium. Since their discovery by Twort and d'Herelle in the early 1900s, phage became an important agent for combating pathogenic bacteria in clinical treatments and its related research gained momentum. However, due to recent emergence of bacterial resistance on antibiotics, applications of phage (phage therapy) become an inevitable option of research. Phage particles become popular as a biotechnological tool and treatment of pathogenic bacteria in a range of applied areas. However, there are few concerns over the application of phage-based solutions. This review deals with the updated phage taxonomy (ICTV 2015 Release and subsequent revision) and phage biology and the recent development of its application in the areas of biotechnology, biosensor, therapeutic medicine, food preservation, aquaculture diseases, pollution remediation, and wastewater treatment and issues related with limitations of phage-based remedy.
- MeSH
- bakteriální infekce terapie MeSH
- bakteriofágy klasifikace fyziologie MeSH
- biomedicínský výzkum trendy MeSH
- biotechnologie metody MeSH
- fágová terapie metody MeSH
- lidé MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Low-GC Actinobacteria are among the most abundant and widespread microbes in freshwaters and have largely resisted all cultivation efforts. Consequently, their phages have remained totally unknown. In this work, we have used deep metagenomic sequencing to assemble eight complete genomes of the first tailed phages that infect freshwater Actinobacteria. Their genomes encode the actinobacterial-specific transcription factor whiB, frequently found in mycobacteriophages and also in phages infecting marine pelagic Actinobacteria. Its presence suggests a common and widespread strategy of modulation of host transcriptional machinery upon infection via this transcriptional switch. We present evidence that some whiB-carrying phages infect the acI lineage of Actinobacteria. At least one of them encodes the ADP-ribosylating component of the widespread bacterial AB toxins family (for example, clostridial toxin). We posit that the presence of this toxin reflects a 'trojan horse' strategy, providing protection at the population level to the abundant host microbes against eukaryotic predators.
- MeSH
- Actinobacteria klasifikace genetika virologie MeSH
- bakteriofágy klasifikace genetika izolace a purifikace MeSH
- fylogeneze MeSH
- genom virový MeSH
- metagenomika MeSH
- sladká voda mikrobiologie virologie MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
