Genomic insights and comparative analysis of Flavobacterium bizetiae HJ-32-4 isolated from soil.

In the late 1970s, Flavobacterium bizetiae was first isolated from diseased fish in Canada. After four decades of preservation, it was reported as a novel species in 2020. Here, we report the first complete genome sequence of HJ-32-4, a novel strain of F. bizetiae. Interestingly, HJ-32-4 was isolated from soil in Gangwon-do, Republic of Korea, unlike the other two previously reported F. bizetiae strains which were isolated from fish. We generated a single circular chromosome of HJ-32-4, comprising 5,745,280 bp with a GC content of 34.2%. The average nucleotide identity (ANI) value of 96.2% indicated that HJ-32-4 belongs to F. bizetiae CIP 105534T. The virulence factor was not detected in the genome. Comparative genomic analysis of F. bizetiae and major flavobacterial pathogens revealed that F. bizetiae had a larger genome size and the ratio of peptidases (PEP) and glycoside hydrolase (GH) genes of F. bizetiae were lower than those of the rest strains, implying that F. bizetiae exhibits similar characteristics with non-pathogenic strains from a genomic point of view. However, further experimental verification is required to ensure these in silico predictions. This study will provide insight into the overall characteristics of HJ-32-4 compared to other strains.

The Tetracycline Resistance Gene, tet(W) in Bifidobacterium animalis subsp. lactis Follows Phylogeny and Differs From tet(W) in Other Species.

The tetracycline resistance gene tet(W) encodes a ribosomal protection protein that confers a low level of tetracycline resistance in the probiotic bacterium Bifidobacterium animalis subsp. lactis. With the aim of assessing its phylogenetic origin and potential mobility, we have performed phylogenetic and in silico genome analysis of tet(W) and its flanking genes. tet(W) was found in 41 out of 44 examined B. animalis subsp. lactis strains. In 38 strains, tet(W) was flanked by an IS5-like element and an open reading frame encoding a hypothetical protein, which exhibited a similar GC content (51-53%). These genes were positioned in the same genomic context within the examined genomes. Phylogenetically, the B. animalis subsp. lactis tet(W) cluster in a clade separate from tet(W) of other species and genera. This is not the case for tet(W) encoded by other bifidobacteria and other species where tet(W) is often found in association with transferable elements or in different genomic regions. An IS5-like element identical to the one flanking the B. animalis subsp. lactis tet(W) has been found in a human gut related bacterium, but it was not associated with any tet(W) genes. This suggests that the IS5-like element is not associated with genetic mobility. tet(W) and the IS5 element have previously been shown to be co-transcribed, indicating that co-localization may be associated with tet(W) expression. Here, we present a method where phylogenetic and in silico genome analysis can be used to determine whether antibiotic resistance genes should be considered innate (intrinsic) or acquired. We find that B. animalis subsp. lactis encoded tet(W) is part of the ancient resistome and thereby possess a negligible risk of transfer.

Advances in aggregation induced emission (AIE) materials in biosensing and imaging of bacteria.

With their ubiquitous nature, bacteria have had a significant impact on human health and evolution. Though as commensals residing in/on our bodies several bacterial communities support our health in many ways, bacteria remain one of the major causes of infectious diseases that plague the human world. Adding to this, emergence of antibiotic resistant strains limited the use of available antibiotics. The current available techniques to prevent and control such infections remain insufficient. This has been proven during one of greatest pandemic of our generation, COVID-19. It has been observed that bacterial coinfections were predominantly observed in COVID-19 patients, despite antibiotic treatment. Such higher rates of coinfections in critical patients even after antibiotic treatment is a matter of concern. Owing to many reasons across the world drug resistance in bacteria is posing a major problem i. According to Center for Disease control (CDC) antibiotic report threats (AR), 2019 more than 2.8 million antibiotic resistant cases were reported, and more than 35,000 were dead among them in USA alone. In both normal and pandemic conditions, failure of identifying infectious agent has played a major role. This strongly prompts the need to improve upon the existing techniques to not just effective identification of an unknown bacterium, but also to discriminate normal Vs drug resistant strains. New techniques based on Aggregation Induced Emission (AIE) are not only simple and rapid but also have high accuracy to visualize infection and differentiate many strains of bacteria based on biomolecular variations which has been discussed in this chapter.

Microbiota of semen from stallions in Sweden identified by MALDI-TOF.

Stallion semen is known to contain environmental bacteria and normal commensals, and in some cases may contain opportunistic pathogens. These bacteria may negatively influence sperm quality during storage before artificial insemination. The bacteria isolated depend on the culture conditions and method of identification; therefore, the aim of this study was to identify as many of the bacteria present in stallion semen as possible by culturing aliquots of semen under a variety of conditions. Eleven semen samples were available: five extended semen samples from one stud together with a sample of the extender, and six raw semen samples from another stud. Aliquots of semen samples were cultured on different agars and under specialized conditions; individual bacterial colonies were identified using Matrix-assisted laser desorption ionization time of flight mass spectrometry. Approximately 55% of the bacteria could be identified, with 20 bacterial taxa being isolated from semen samples from the five stallions on the first stud and 11 taxa from the semen samples from six stallions on the second stud. Staphylococcus spp. were present in all samples, and Micrococcus spp. were present in all of the extended semen samples although they were also isolated from the extender. The number of bacteria in colony forming units per mL varied considerably among samples. Only one microbe known to be associated with equine infertility, Pseudomonas spp., was isolated from three samples, albeit in low numbers. In conclusion, bacterial culture followed by MALDI-TOF does not identify all bacteria present in stallion semen samples. In-depth knowledge of which microbes are likely to be present is useful in determining their effects on sperm quality and, where appropriate, developing protocols for effectively controlling microbial growth.

Contributions of protein microenvironment in tannase industrial applicability: An in-silico comparative study of pathogenic and non-pathogenic bacterial tannase.

Tannase is an inducible industrially important enzyme, produced by several microorganisms. A large number of bacteria have reported as tannase producers; however, some of them are pathogenic in nature. Therefore, it is quite uncertain whether the application of these tannase enzymes from such pathogenic bacteria is suitable for industries and human welfare. Till date, there is no clear evidence regarding which group of bacteria (non-pathogenic or pathogenic) is better suited for their application in the edge of industries with particular reference to the food industry. The present study is following the findings of the above queries. In this study, a large number of tannase protein sequences have been retrieved from the databases, including both non-pathogenic and pathogenic bacterial species. Physiochemical and evolutionary properties of those sequences have been evaluated. Results have shown that non-pathogenic bacterial tannase possesses a high number of acidic and basic amino acid residues as compared to their pathogenic counterparts. The acidic and basic amino acid residues of tannase provide unique microenvironment to it. In the other hand, the numbers of disorder forming residues are higher in tannase sequences of pathogenic bacteria. The study of tannase microenvironment leads in the formation of salt bridges, which finally favoring the stability and proper functioning of tannase. This is the first report of such observation on tannase enzyme using in silico approach. Study of the microenvironment concept will be helpful in protein engineering.

The Quality of Sputum Specimens as a Predictor of Isolated Bacteria From Patients With Lower Respiratory Tract Infections at a Tertiary Referral Hospital, Denpasar, Bali-Indonesia.

Sputum quality is crucial in finding infectious bacteria that will be used to guide definitive antibiotic therapy. Errors in reporting isolated bacteria will affect the rate of patients' morbidity, mortality, and increase patient care costs. This study aims to find out the relationship between sputum quality and isolated bacteria at a Tertiary Referral Hospital, Denpasar, Bali-Indonesia. The study was conducted for 6 months in the Sanglah Hospital Clinical Microbiology laboratory. There were 726 sputum specimens examined and categorized based on Murray Washington criteria. After Gram examination, all specimens were inoculated on aerobic culture media. We classified 41.4% of poor-quality sputum specimens, and non-pathogenic bacteria were isolated from 70.2% of that specimen dominated by Streptococcus mitis (42.53%). Whereas, isolated pathogens were obtained from 54.4% of good-quality sputum specimens dominated by Klebsiella pneumonia (30.86%). Statistical analyses showed that there is a relationship between isolated bacteria and the sputum quality (OR = 3.844; p < 0.001). Good-quality sputum is 3.8 times more likely to isolate pathogenic bacteria than poor-quality sputum. In the Pearson Chi-Square test, the likelihood of isolating pathogenic bacteria from good-quality specimens was significant too (p < 0.001). The results of this study indicate that poor-quality sputum specimens are still found. Therefore, the capacity of good sputum collection must be improved. Supervision of the application of standard sputum culture operational procedures must be more rigorously carried out.

Burkholderia thailandensis as a microbial cell factory for the bioconversion of used cooking oil to polyhydroxyalkanoates and rhamnolipids.

The present work assessed the feasibility of used cooking oil as a low cost carbon source for rhamnolipid biosurfactant production employing the strain Burkholderia thailandensis. According to the results, B. thailandensis was able to produce rhamnolipids up to 2.2 g/L, with the dominant congener being the di-rhamnolipid Rha-Rha-C14-C14. Rhamnolipids had the ability to reduce the surface tension to 37.7 mN/m and the interfacial tension against benzene and oleic acid to 4.2 and 1.5 mN/m, while emulsification index against kerosene reached up to 64%. The ability of B. thailandensis to accumulate intracellular biopolymers, in the form of polyhydroxyalkanoates (PHA), was also monitored. Polyhydroxybutyrate (PHB) was accumulated simultaneously and consisted of up to 60% of the cell dry weight. PHB was further characterized in terms of its molecular weight and thermal properties. This is the first study reporting the simultaneous production of polyhydroxyalkanoates and rhamnolipids by the non-pathogen rhamnolipid producer B. thailandensis.

Rhamnolipids from non-pathogenic Burkholderia thailandensis E264: Physicochemical characterization, antimicrobial and antibiofilm efficacy against oral hygiene related pathogens.

Biosurfactants are naturally occurring surface active compounds that have mainly been exploited for environmental applications and consumer products, with their biomedical efficacy an emerging area of research. Rhamnolipids area major group of biosurfactants that have been reported for their antimicrobial and antibiofilm efficacy. One of the main limiting factors for scaled up production and downstream applications of rhamnolipids is the fact that they are predominantly produced from the opportunistic pathogen Pseudomonas aeruginosa. In this article, we have reported the production and characterisation of long chain rhamnolipids from non-pathogenic Burkholderia thailandensis E264 (ATCC 700388). We have also investigated the antibacterial and antibiofilm properties of these rhamnolipids against some oral pathogens (Streptococcus oralis, Actinomyces naeslundii, Neisseria mucosa and Streptococcus sanguinis), important for oral health and hygiene. Treating these bacteria with different concentrations of long chain rhamnolipids resulted in a reduction of 3-4 log of bacterial viability, placing these rhamnolipids close to being classified as biocidal. Investigating long chain rhamnolipid efficacy as antibiofilm agents for prospective oral-related applications revealed good potency against oral-bacteria biofilms in a co-incubation experiments, in a pre-coated surface format, in disrupting immature biofilms and has shown excellent combination effect with Lauryl Sodium Sulphate which resulted in a drastic decrease in its minimal inhibitory concentration against different bacteria. Investigating the rhamnolipid permeabilization effect along with their ability to induce the formation of reactive oxygen species has shed light on the mechanism through which inhibition/killing of bacteria may occur.

Surfaces Presenting α-Phenyl Mannoside Derivatives Enable Formation of Stable, High Coverage, Non-pathogenic Escherichia coli Biofilms against Pathogen Colonization.

Prevention of pathogenic colonization on medical devices over a long period of time remains a great challenge, especially in a high-nutrient environment that accelerates production of biomass leading to biofouling of the device. Since biofouling and the subsequent pathogen colonization is eventually inevitable, a new strategy using non-pathogenic bacteria as living guards against pathogenic colonization on medical devices has attracted increasing interest. Crucial to the success of this strategy is to pre-establish a high coverage and stable biofilm of benign bacteria on the surface. Silicone elastomers are one of the most widely used materials in biomedical devices. In this work, we modified silicone surfaces to promote formation of high coverage and stable biofilms by a non-pathogenic Escherichia coli strain 83972 with type 1 fimbriae (fim+) to interfere the colonization of an aggressive biofilm-forming, uropathogenic Enterococcus faecalis. Although it is well known that mannoside surfaces promote the initial adherence of fim+ E. coli through binding to the FimH receptor at the tip of the type 1 fimbriae, it is not clear whether the fast initial adherence could lead to a high coverage and stable protective biofilm. To explore the role of mannoside ligands, we synthesized a series of alkyl and aryl mannosides varied in structure and immobilized them on silicone surfaces pre-coated with poly(amidoamine) (PAMAM) dendrimer. We found that stable and densely packed benign E. coli biofilms were formed on the surfaces presenting biphenyl mannoside with the highest initial adherence of fim+ E. coli. These non-pathogenic biofilms prevented the colonization of E. faecalis for 11 days at a high concentration (108 CFU mL-1, 100,000 times above the diagnostic threshold for urinary tract infection) in the nutrient-rich Lysogeny Broth (LB) media. The result shows a correlation among the initial adherence of fim+ E. coli 83972, the coverage and long-term stability of the resultant biofilms, as well as their efficiency for preventing the pathogen colonization.