Antibiotic resistance genes (ARGs) as emerging contaminants, often co-occur with mobile genetic elements (MGEs) and are prevalent in drinking water treatment plants (DWTPs). In this study, the characteristics of free-living (FL) and particle-associated (PA) ARGs associated with bacterial communities were investigated along two processes within a full-scale DWTP. A total of 13 ARGs and two MGEs were detected. FL-ARGs with diverse subtypes and PA-ARGs with high abundances displayed significantly different structures. PA-MGEs showed a strong positive correlation with PA-ARGs. Chlorine dioxide disinfection achieved 1.47-log reduction of FL-MGEs in process A and 0.24-log reduction of PA-MGEs in process B. Notably, PA-fraction virtually disappeared after treatment, while blaTEM, sul2, mexE, mexF and IntI1 of FL-fraction remained in the finished water. Moreover, Acinetobacter lwoffii (0.04 % ∼ 45.58 %) and Acinetobacter schindleri (0.00 % ∼ 18.54 %) dominated the 16 pathogens, which were more abundant in FL than PA bacterial communities. PA bacteria exhibited a more complex structure with more keystone species than FL bacteria. MGEs contributed 20.23 % and 19.31 % to the changes of FL-ARGs and PA-ARGs respectively, and water quality was a key driver (21.73 %) for PA-ARGs variation. This study provides novel insights into microbial risk control associated with size-fractionated ARGs in drinking water.

UNASSIGNED: To date, more than 770 million individuals have become coronavirus disease 2019 (COVID-19) convalescents worldwide. Emerging evidence highlights the influence of COVID-19 on the oral microbiome during both acute and convalescent disease phases. Front-line healthcare workers are at an elevated risk of exposure to viral infections, and the effects of COVID-19 on their oral microbiome remain relatively unexplored.
UNASSIGNED: Oropharyngeal swab specimens, collected one month after a negative COVID-19 test from a cohort comprising 55 healthcare workers, underwent 16S rRNA sequencing. We conducted a comparative analysis between this post-COVID-19 cohort and the pre-infection dataset from the same participants. Community composition analysis, indicator species analysis, alpha diversity assessment, beta diversity exploration, and functional prediction were evaluated.
UNASSIGNED: The Shannon and Simpson indexes of the oral microbial community declined significantly in the post-COVID-19 group when compared with the pre-infection cohort. Moreover, there was clear intergroup clustering between the two groups. In the post-COVID-19 group, the phylum Firmicutes showed a significant increase. Further, there were clear differences in relative abundance of several bacterial genera in contrast with the pre-infection group, including Streptococcus, Gemella, Granulicatella, Capnocytophaga, Leptotrichia, Fusobacterium, and Prevotella. We identified Gemella enrichment in the post-COVID-19 group, potentially serving as a recovery period performance indicator. Functional prediction revealed lipopolysaccharide biosynthesis downregulation in the post-COVID-19 group, an outcome with host inflammatory response modulation and innate defence mechanism implications.
UNASSIGNED: During the recovery phase of COVID-19, the oral microbiome diversity of front-line healthcare workers failed to fully return to its pre-infection state. Despite the negative COVID-19 test result one month later, notable disparities persisted in the composition and functional attributes of the oral microbiota.

Biofilm formation in dental unit waterlines and the resulting microbial contamination of the water in the system has become a significant problem. Contaminated water in the dental units is a major concern in dental clinics due to potential risk of causing infections particularly in elderly and immunocompromised patients. The aim of this study was at first to determine microbial contamination of the dental unit waterlines and then to study the efficacy of a comprehensive disinfection protocol on decreasing the microbial load. Water samples were collected before and after disinfection procedure from handpieces and water storage bottles from the dental units, a small 1-cm tubing was cut from each unit and subjected to microbiological culture on different growth media. Identification of the predominant species was achieved by 16S rRNA gene sequencing. Microbial growth was observed in samples collected from all dental units. Upon disinfection procedure, microbial contamination in the water samples and in the tubing surfaces was significantly reduced (P > 0.05). 16S rRNA gene sequencing revealed the presence of several species belonging to the genera Staphylococcus, Corynebacterium and Roseomonas, some of which are implicated in human infections. Aggravation of the biofilm growth on the tubing surfaces and the microbial contamination in the water can be effectively controlled by implementing appropriate and routine disinfection protocols. This may help protect the dental unit staff and the patients being exposed to the risk of infections.

Bats have attracted global attention because of their zoonotic association with severe acute respiratory syndrome coronavirus (SARS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Previous and ongoing studies have predominantly focused on bat-borne viruses; however, the prevalence or abundance of bat-borne pathogenic bacteria and their potential public health significance have largely been neglected. For the first time, this study used both metataxonomics (16S rRNA marker gene sequencing) and culturomics (traditional culture methods) to systematically evaluate the potential public health significance of bat fecal pathogenic bacteria. To this end, fecal samples were obtained from five bat species across different locations in China, and their microbiota composition was analyzed. The results revealed that the bat microbiome was most commonly dominated by Proteobacteria, while the strictly anaerobic phylum Bacteroidetes occupied 35.3% of the relative abundance in Rousettus spp. and 36.3% in Hipposideros spp., but less than 2.7% in the other three bat species (Taphozous spp., Rhinolophus spp., and Myotis spp.). We detected 480 species-level phylotypes (SLPs) with PacBio sequencing, including 89 known species, 330 potentially new species, and 61 potentially higher taxa. In addition, a total of 325 species were identified by culturomics, and these were classified into 242 named species and 83 potentially novel species. Of note, 32 of the 89 (36.0%) known species revealed by PacBio sequencing were found to be pathogenic bacteria, and 69 of the 242 (28.5%) known species isolated by culturomics were harmful to people, animals, or plants. Additionally, nearly 40 potential novel species which may be potential bacterial pathogens were identified. IMPORTANCE Bats are one of the most diverse and widely distributed groups of mammals living in close proximity to humans. In recent years, bat-borne viruses and the viral zoonotic diseases associated with bats have been studied in great detail. However, the prevalence and abundance of pathogenic bacteria in bats have been largely ignored. This study used high-throughput sequencing techniques (metataxonomics) in combination with traditional culture methods (culturomics) to analyze the bacterial flora in bat feces from different species of bats in China, revealing that bats are natural hosts of pathogenic bacteria and carry many unknown bacteria. The results of this study can be used as guidance for future investigations of bacterial pathogens in bats.

BACKGROUND: Citrus are among the most important crops in the world. However, there are many diseases that affect Citrus caused by different pathogens. Citrus also hosts many symbiotic microorganisms in a relationship that may be advantageous for both organisms. The fungi Phyllosticta citricarpa, responsible for citrus black spot, and Phyllosticta capitalensis, an endophytic species, are examples of closely related species with different behavior in citrus. Both species are always biologically associated and are morphologically very similar, and comparing their genomes could help understanding the different lifestyles. In this study, a comparison was carried to identify genetic differences that could help us to understand the biology of P. citricarpa and P. capitalensis.
RESULTS: Drafts genomes were assembled with sizes close to 33 Mb for both fungi, carrying 15,206 and 14,797 coding sequences for P. citricarpa and P. capitalensis, respectively. Even though the functional categories of these coding sequences is similar, enrichment analysis showed that the pathogenic species presents growth and development genes that may be necessary for the pathogenicity of P. citricarpa. On the other hand, family expansion analyses showed the plasticity of the genome of these species. Particular families are expanded in the genome of an ancestor of P. capitalensis and a recent expansion can also be detected among this species. Additionally, evolution could be driven by environmental cues in P. citricarpa.
CONCLUSIONS: This work demonstrated genomic differences between P. citricarpa and P. capitalensis. Although the idea that these differences could explain the different lifestyles of these fungi, we were not able to confirm this hypothesis. Genome evolution seems to be of real importance among the Phyllosticta isolates and it is leading to different biological characteristics of these species.

Indian biodiversity is a hub for medicinal plants. Extensive research has been carried out to select plants with numerous properties which can be used for human welfare. Present research is about Cymbopogon citratus, an economically valuable medicinal plant. In this study Cymbopogon citratus was elected as a subject plant over the five selected plants (Azadirachta indica, Plumeria obtuse, Sapindus mukorossi, Capsicum annuum and Phyllanthus emblica) on the basis of antibacterial effect against dominating pathogenic species of gram positive (Bacillus cereus, Bacillus licheniformis) and gram negative (Pseudomonas aeruginosa, Escherichia coli) bacteria. Further, bioactive agents behind antibacterial potential of Cymbopogon citratus was analyzed using analytical method (Phyto-chemical, FTIR, NMR and GC-MS). Due to the broad antimicrobial spectrum, silver nanoparticles have turned into a noteworthy decision for the improvement of new medication. Therefore, this investigation further elaborated in the development of Cymbopogon citratus silver nano-particles (CNPs). Antibacterial potential of CNPs examine in a range of C25-C150 (μg/ml) through minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) where, C25 (μg/ml) concentration of CNPs were recorded as the MIC for all bacterial species and C25 (μg/ml) and C50 (μg/ml) noted as the MBC for Pseudomonas aeruginosa, Escherichia coli and Bacillus cereus, Bacillus licheniformis, respectively. In agar disk diffusion assay of CNPs, maximum diameter of zone of inhibition was observed for C150 (μg/ml) concentration Bacillus cereus (20.12 ± 0.42), Bacillus licheniformis (22.34 ± 0.4), Pseudomonas aeruginosa (35.23 ± 0.46) and Escherichia coli (31.87 ± 0.24). Involvement of bioactive component as a reducing and capping agent can be confirmed through FTIR spectrum of CNPs. Moreover XRD, EDXRF and SEM showed crystalline and cuboidal nature of CNPs with ∼35 nm sizes. Prominently, cytotoxic analysis was conducted to understand the toxic effect of CNPs. This research highlights the potential of CNPs due to the bioactive components present in Cymbopogon citratus extract: Polyphenols (phenol; 1584.56 ± 16.32 mg/L, Flavanoids) and mixture of terpenoids (Citral, Myrcene, Farnesol, β-myrcene and β -Pinene).

Preclinical Research Approximately 2,500 years ago, Hippocrates used the word herpes as a medical term to describe lesions that appeared to creep or crawl on the skin, advocating heat as a possible treatment. During the last 50 years, pharmaceutical research has made great strides, and therapeutic options have expanded to include small molecule antiviral agents, protease inhibitors, preventive vaccines for a handful of the papillomaviruses, and even cures for hepatitis C virus infections. However, effective treatments for persistent and recurrent viral infections, particularly the highly prevalent herpesviruses, continue to represent a significant unmet medical need, affecting the majority of the world\'s population. Exploring the population diversity of the human microbiome and the effects its compositional variances have on the immune system, health, and disease are the subjects of intense investigational research and study. Among the collection of viruses, bacteria, fungi, and single-cell eukaryotes that comprise the human microbiome, the virome has been grossly understudied relative to the influence it exerts on human pathophysiology, much as mitochondria have until recently failed to receive the attention they deserve, given their critical biomedical importance. Fortunately, cellular epigenetic machinery offers a wealth of druggable targets for therapeutic intervention in numerous disease indications, including those outlined above. With advances in synthetic biology, engineering our body\'s commensal microorganisms to seek out and destroy pathogenic species is clearly on the horizon. This is especially the case given recent breakthroughs in genetic manipulation with tools such as the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) gene-editing platforms. Tying these concepts together with our previous work on the microbiome and neurodegenerative and neuropsychiatric diseases, we suggest that, because mammalian cells respond to a viral infection by triggering a cascade of antiviral innate immune responses governed substantially by the cell\'s mitochondria, small molecule carnitinoids represent a new class of therapeutics with potential widespread utility against many infectious insults. Drug Dev Res 78 : 24-36, 2017.   © 2016 Wiley Periodicals, Inc.

Traditionally, the shelf-life and safety of foods have been achieved by thermal processing. Low temperature long time and high temperature short time treatments are the most commonly used hurdles for the pasteurization of fluid foods and raw materials. However, the thermal treatments can reduce the product quality and freshness. Consequently, some non-thermal pasteurization process have been proposed during the last decades, including high hydrostatic pressure, pulsed electric field, ultrasound (US), and high pressure homogenization (HPH). This last technique has been demonstrated to have a great potential to provide \"fresh-like\" products with prolonged shelf-life. Moreover, the recent developments in high-pressure-homogenization technology and the design of new homogenization valves able to withstand pressures up to 350-400 MPa have opened new opportunities to homogenization processing in the food industries and, consequently, permitted the development of new products differentiated from traditional ones by sensory and structural characteristics or functional properties. For this, this review deals with the principal mechanisms of action of HPH against microorganisms of food concern in relation to the adopted homogenizer and process parameters. In addition, the effects of homogenization on foodborne pathogenic species inactivation in relation to the food matrix and food chemico-physical and process variables will be reviewed. Also the combined use of this alternative technology with other non-thermal technologies will be considered.

The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position.