Optimization of single plate-serial dilution spotting (SP-SDS) with sample anchoring as an assured method for bacterial and yeast cfu enumeration and single colony isolation from diverse samples

Bacteriophage treatment is effective against carbapenem-resistant Klebsiella pneumoniae (KPC) in a neutropenic murine model of gastrointestinal translocation and renal infection

Carbapenemase-producing Klebsiella pneumoniae (KPC) are globally emerging pathogens that cause life-threatening infections. Novel treatment alternatives are urgently needed. We therefore investigated the effectiveness of three novel bacteriophages (Spivey, Pharr, and Soft) in a neutropenic murine model of KPC gastrointestinal colonization, translocation, and disseminated infection. Bacteriophage efficacy was determined by residual bacterial burden of KPC (CFU/g) in kidneys. Parallel studies were conducted of bacteriophage pharmacokinetics and resistance. Treatment of mice with 5 × 109 PFU of phage cocktail via intraperitoneal injection was effective in significantly reducing renal KPC CFU by 100-fold (P < 0.01) when administered every 24 h and 1000-fold (P < 0.01) every 12 h. Moreover, a combination of bacteriophage and ceftazidime-avibactam produced a synergistic effect, resulting in a 105-fold reduction in bacterial burden in cecum and kidney (P < 0.001 in both tissues). Prophylactic administration of bacteriophages via oral gavage did not prevent KPC translocation to the kidneys. Bacteriophage decay determined by linear regression of the ln of mean concentrations demonstrated R2 values in plasma of 0.941, kidney 0.976, and cecum 0.918, with half-lives of t1/2 = 2.5 h. Furthermore, a phage-resistant mutant displayed increased sensitivity to serum killing in vitro, but did not show significant defects in renal infection in vivo. A combination of bacteriophages demonstrated significant efficacy alone and synergy with ceftazidime/avibactam in the treatment of experimental disseminated KPC infection in neutropenic mice.

Pseudomonas aeruginosa kills Staphylococcus aureus in a polyphosphate-dependent manner

Due to their frequent coexistence in many polymicrobial infections, including in patients with cystic fibrosis or burn/chronic wounds, many studies have investigated the mechanistic details of the interaction between the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus. P. aeruginosa rapidly outcompetes S. aureus under in vitro cocultivation conditions, which is mediated by several of P. aeruginosa's virulence factors. Here, we report that polyphosphate (polyP), an efficient stress defense system and virulence factor in P. aeruginosa, plays a role in the pathogen's ability to inhibit and kill S. aureus in a contact-independent manner. We show that P. aeruginosa cells characterized by low polyP levels are less detrimental to S. aureus growth and survival while the Gram-positive pathogen is significantly more compromised by the presence of P. aeruginosa cells that produce high levels of polyP. The polyP-dependent phenotype of P. aeruginosa-mediated killing of S. aureus could at least in part be direct, as polyP was detected in the spent media and causes significant damage to the S. aureus cell envelope. However, more likely is that polyP's effects are indirect through modulating the production of one of P. aeruginosa's virulence factors, pyocyanin. We show that pyocyanin production in P. aeruginosa occurs polyP-dependently and harms S. aureus through membrane damage and potentially the generation of reactive oxygen species, resulting in the increased expression of antioxidant enzymes. In summary, our study adds a new component to the list of biomolecules that the Gram-negative pathogen P. aeruginosa generates to compete with S. aureus for resources.IMPORTANCEHow do interactions between microorganisms shape the course of polymicrobial infections? Previous studies have provided evidence that the two opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus generate molecules that modulate their interaction with potentially significant impact on disease outcomes. Our study identified the biopolymer polyphosphate (polyP) as a new effector molecule that impacts P. aeruginosa's interaction with S. aureus. We show that P. aeruginosa kills S. aureus in a polyP-dependent manner, which occurs primarily through the polyP-dependent production of the P. aeruginosa virulence factor pyocyanin. Our findings add a new role for polyP to an already extensive list of functions. A more in-depth understanding of how polyP influences interspecies interactions is critical, as targeting polyP synthesis in bacteria such as P. aeruginosa may have a significant impact on other microorganisms and potentially result in dynamic changes in the microbial composition.

The influence of pH on the efficacy of oxidation-reduction potential (ORP) to predict chlorine disinfection of surrogate bacteria, Escherichia coli O157:H7 and Listeria monocytogenes in oxidant demand free conditions and fresh produce wash water

Oxidation-reduction potential (ORP) is commonly used as a rapid measurement of the antimicrobial potential of free chlorine during industrial fresh produce washing. The current study tested the hypothesis that ORP can act as a "single variable" measurement of bacterial (vegetative and endospores) inactivation effectiveness with free chlorine irrespective of the water pH value. This situation has on occasion been assumed but never confirmed nor disproven. Chlorine-dosed pH 6.5 and 8.5 phosphate buffer solutions were inoculated with Escherichia coli (E. coli), Listeria innocua (L. innocua), or Bacillus subtilis (B. subtilis) endospores. ORP, free chlorine (FC), and log reduction were monitored after 5 s (for E. coli and L. innocua) and up to 30 min (for B. subtilis spores) of disinfection. Logistic and exponential models were developed to describe how bacteria reduction varied as a function of ORP at different pH levels. Validation tests were performed in phosphate buffered pH 6.5 and 8.5 cabbage wash water periodically dosed with FC, cabbage extract and a cocktail of Escherichia coli O157:H7 (E. coli O157:H7) and Listeria monocytogenes (L. monocytogenes). The built logistic and exponential models confirmed that at equal ORP values, the inactivation of the surrogate strains was not consistent across pH 6.5 and pH 8.5, with higher reductions at higher pH. This is the opposite of the well-known free chlorine-controlled bacterial inactivation, where the antibacterial effect is higher at lower pH. The validation test results indicated that in the cabbage wash water, the relationship between disinfection efficiency and ORP was consistent with the oxidant demand free systems. The study suggests that ORP cannot serve as a reliable single variable measurement to predict bacterial disinfection in buffered systems. When using ORP to monitor and control the antibacterial effectiveness of the chlorinated wash water, it is crucial to take into account (and control) the pH.

Potential of using an engineered indole lactic acid producing Escherichia coli Nissle 1917 in a murine model of colitis

The gut microbiome is a significant factor in the pathophysiology of ulcerative colitis (UC), prompting investigations into the use of probiotic therapies to counter gastrointestinal inflammation. However, while much attention has been given to the therapeutic potential of microbes at the species and strain level, the discovery and application of their metabolic products may offer more precise and controlled solutions in battling disease. In this work, we examined the therapeutic potential of indole lactic acid (ILA) to alleviate inflammation in a murine model of colitis. A previously constructed ILA-producing Escherichia coli Nissle 1917 strain (EcN aldh) and its isogenic non-ILA producing counterpart (EcN) were studied in a murine model of Dextran Sodium Sulfate (DSS) induced colitis. The colitic animals suffered from severe colitic symptoms, with no differentiation between the groups in body weight loss and disease activity index. However, three days after cessation of DSS treatment the EcN aldh-treated mice showed signs of reduced intestinal inflammation, as manifested by lower concentrations of fecal lipocalin-2. Additionally, expression analysis of the inflamed tissue revealed distinct effects of the EcN aldh strain on proteins associated with intestinal health, such as TFF3, occludin and IL-1β expression. These results show no impact of EcN or EcN aldh on acute DSS-induced colitis, but suggest that in particular EcN aldh may assist recovery from intestinal inflammation.

Effects of Commercial Probiotics on the Growth Performance, Intestinal Microbiota and Intestinal Histomorphology of Nile Tilapia (Oreochromis niloticus) Reared in Biofloc Technology (BFT)

Though different types of commercial probiotics are supplemented in biofloc technology (BFT), very little information is available on their effects on the farmed fish. Therefore, this study focused on evaluating the effects of three most commonly used commercial probiotics on the growth performance, intestinal histomorphology, and intestinal microbiota of Nile tilapia (Oreochromis niloticus) reared in BFT. Tilapia fry, with an average weight of 3.02 ± 0.50 g, were stocked at a density of 60 fry/0.2 m3, and cultured for 90 days. Three commercial probiotics were administered, with three replications for each: a single-genus multi-species probiotic (Bacillus spp.) (T1), a multi-genus multi-species probiotic (Bacillus sp., Lactobacillus sp., Nitrosomonas sp., Nitrobacter sp.) (T2), and a multi-species probiotic (Bacillus spp.) combined with enzymes including amylase, protease, cellulase, and xylanase (T3). The results showed significant variations in growth and feed utilization, with T3 outperforming other treatments in terms of weight gain, liver weight, and intestine weight. Adding Bacillus spp. with enzymes (T3) to water significantly increased the histomorphological parameters (villi length, villi depth, crypt depth, muscle thickness, intestinal thickness) as well as microbes (total viable count and total lactic acid bacteria) of intestine of fish compared to T1 and T2, leading to improved digestion and absorption responses. It is concluded that the supplementation of commercial probiotics has potential benefits on farmed fish species in BFT.

Life on Earth can grow on extraterrestrial organic carbon

The universe is a vast store of organic abiotic carbon that could potentially drive heterotrophy on habitable planets. Meteorites are one of the transporters of this carbon to planetary surfaces. Meteoritic material was accumulating on early Earth when life emerged and proliferated. Yet it is not known if this organic carbon from space was accessible to life. In this research, an anaerobic microbial community was grown with the CM2 carbonaceous chondrite Aguas Zarcas as the sole carbon, energy and nutrient source. Using a reversed 13C-stable isotope labelling experiment in combination with optical photothermal infrared (O-PTIR) spectroscopy of single cells, this paper demonstrates the direct transfer of carbon from meteorite into microbial biomass. This implies that meteoritic organics could have been used as a carbon source on early Earth and other habitable planets, and supports the potential for a heterotrophic metabolism in early living systems.

Beneficial effects of bioinspired silver nanoparticles on zebrafish embryos including a gene expression study

Background and purpose

Many sectors use nanoparticles and dispose of them in the aquatic environment without deciding the fate of these particles.

Experimental approach

To identify a benign species of nanoparticles which can cause minimum harm to the aquatic environment, a comparative study was done with chemically synthesized silver nanoparticles (AgNPs) and green tea mediated synthesis (GT/AgNP) in both in vitro using human alveolar cancer cell line (A549) and normal cell line (L132), and in in vivo with zebrafish embryos.

Key results

The in vitro studies revealed that GT/AgNPs were less toxic to normal cells than cancer cells. The GT/AgNPs showed high biocompatibility for zebrafish embryos monitored microscopically for their developmental stages and by cumulative hatchability studies. The reduced hatchability found in the AgNPs-treated group was correlated by differential gene expression of zebrafish hatching enzymes (ZHE) (ZHE1 and ZHE2).

Conclusion

The results indicated that nanoparticles can affect the hatching of zebrafish embryos and elicit toxicity at the gene level.

Quantitative Analysis of the Inactivation Process of Internalized Bacteria in Dictyostelium Cells

The understanding of the inactivation process of ingested bacteria by phagocytes is a key focus in the field of host-pathogen interactions. Dictyostelium is a model organism that has been at the forefront of uncovering the mechanisms underlying this type of interaction. In this study, we describe an assay designed to measure the inactivation of Klebsiella aerogenes in the phagosomes of Dictyostelium discoideum.

Mitigating the attachment of Salmonella Infantis on isolated poultry skin with cetylpyridinium chloride

To provide the poultry industry with effective mitigation strategies, the effects of cetylpyridinium chloride (CPC) on the reduction of Salmonella Infantis, hilA expression, and chicken skin microbiota were evaluated. Chicken breast skins (4×4 cm; N = 100, n = 10, k = 5) were inoculated with Salmonella (Typhimurium or Infantis) at 4°C (30min) to obtain 108 CFU/g attachment. Skins were shaken (30s), with remaining bacteria being considered firmly attached. Treatments were applied as 30s dips in 50 mL: no inocula-no-treatment control (NINTC), no treatment control (NTC), tap water (TW), TW+600 ppm PAA (PAA), or TW+0.5% CPC (CPC). Excess fluid was shaken off (30s). Samples were homogenized in nBPW (1 min). Samples were discarded. Salmonella was enumerated and Log10 transformed. Reverse transcriptase-qPCR (rt-qPCR) was performed targeting hilA gene and normalized using the 2-ΔΔCt method. Data were analyzed using one-way ANOVA in RStudio with means separated by Tukey's HSD (P≤0.05). Genomic DNA of rinsates was extracted, 16S rRNA gene (V4) was sequenced (MiSeq), and data analyzed in QIIME2 (P≤0.05 and Q≤0.05). CPC and PAA affected Salmonella levels differently with CPC being effective against S. Infantis compared to TW (P<0.05). Treatment with CPC on S. Infantis-infected skin altered the hilA expression compared to TW (P<0.05). When inoculated with S. Typhimurium, there was no difference between the microbiota diversity of skins treated with PAA and CPC; however, when inoculated with S. Infantis, there was a difference in the Shannon's Entropy and Jaccard Dissimilarity between the two treatments (P<0.05). Using ANCOM at the genus level, Brochothrix was significant (W = 118) among skin inoculated with S. Typhimurium. Among S. Infantis inoculated, Yersiniaceae, Enterobacterales, Lachnospiraceae CHKCI001, Clostridia vadinBB60 group, Leuconostoc, Campylobacter, and bacteria were significant (408). CPC and PAA-treated skins had lowest relative abundance of the genera. In conclusion, CPC mitigated Salmonella Infantis, altered hilA expression, and influenced the chicken skin microbiota.

Therapeutic effects of orally administration of viable and inactivated probiotic strains against murine urinary tract infection

Urinary tract infections (UTIs) are highly prevalent bacterial infections that pose significant health risks. Specific probiotic strains have been recommended for UTI control and management of antibiotic resistance. Otherwise, para-probiotics, defined as inactivated probiotic cells, offer potential advantages by minimizing risks associated with live microorganisms. However, the effectiveness of heat-killed probiotic strains against UTIs remains uncertain. Additionally, lactoferrin (LF), an iron-binding glycoprotein, exhibits immunomodulatory, antimicrobial, and anti-inflammatory properties. Recently, we had developed recombinant LF-expression probiotics, which can display considerate antibacterial activities against select food-borne pathogens in vitro. Thus, the present study aimed to evaluate the antibacterial activities of heat-killed natural and recombinant LF-expressing probiotics against UTIs in vitro and in vivo. Firstly, using in vitro assays, we assessed the antibacterial activity of heat-killed natural and recombinant LF-expressing probiotics against uropathogenic Escherichia coli and Klebsiella pneumoniae. Among the tested probiotics, 10 heat-killed LF-expressing strains displayed superior antibacterial efficacy compared to 12 natural probiotics. Based on their potent in vitro activity, selected probiotics were formulated into three probiotic mixtures: viable probiotic mixture (LAB), heat-killed probiotic mixture (HK-LAB), and heat-killed LF-expressing probiotic mixture (HK-LAB/LF). To further evaluate the therapeutic potential of these probiotic mixtures in vivo, we established a murine model of UTIs by intraurethral administration of E. coli to 40 female C57BL/6JNarl mice on day 0. Subsequently, mice received oral gavage of placebo, LAB, HK-LAB, or HK-LAB/LF for 21 consecutive days (n = 8 per group). An additional control group (n = 8) received ampicillin treatment for 7 days. To assess protective effects against re-infection or UTI relapse, all mice were challenged with E. coli on day 22 and E. coli plus K. pneumoniae on day 25. Results from the murine UTI model demonstrated that placebo administration did not reduce bacteriuria throughout the experiment. Conversely, supplementation with ampicillin, HK-LAB/LF, HK-LAB, or LAB significantly (p < 0.05) reduced daily bacteriuria by 103 to 104-fold on days 1, 3, 5, and 14, respectively. Furthermore, all four therapeutic treatments improved the bacteriological cure rate (BCR) with varying levels of efficacy. For the 7-day treatment course, the BCR was 25% (placebo), 62.5% (ampicillin), 37.5% (LAB), 37.5% (HK-LAB), and 62.5% (HK-LAB/LF). For the 21-day treatment course, the BCR was 25% (placebo), 75% (ampicillin), 37.5% (LAB), 37.5% (HK-LAB), and 75% (HK-LAB/LF). Notably, HK-LAB and HK-LAB/LF demonstrated superior therapeutic efficacy compared to viable LAB in treating UTIs. Overall, regarding BCR, the three probiotic mixtures can provide benefits against UTI in mice, but ampicillin therapy remains the most efficient among the four treatments. Furthermore, there was no significant difference between pre- and post-challenge courses for the two instances of re-challenging uropathogens in all mice groups, as bacteriuria levels remained below 103 CFU/mL, implying that adaptive responses of mice may help reduce the risk of recurrent UTIs. In conclusion, our results provide new evidence that oral administration of heat-killed probiotic mixtures can confer significant therapeutic efficacy against UTIs in a murine model.

Pseudomonas aeruginosa kills Staphylococcus aureus in a polyphosphate-dependent manner

Due to their frequent coexistence in many polymicrobial infections, including in patients with burn or chronic wounds or cystic fibrosis, recent studies have started to investigate the mechanistic details of the interaction between the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus. P. aeruginosa rapidly outcompetes S. aureus under in vitro co-cultivation conditions, which is mediated by several of P. aeruginosa's virulence factors. Here, we report that polyphosphate (polyP), an efficient stress defense system and virulence factor in P. aeruginosa, plays a role for the pathogen's ability to inhibit and kill S. aureus in a contact-independent manner. We show that P. aeruginosa cells characterized by low polyP level are less detrimental to S. aureus growth and survival while the gram-positive pathogen is significantly more compromised by the presence of P. aeruginosa cells that produce high level of polyP. We show that the polyP-dependent phenotype could be a direct effect by the biopolymer, as polyP is present in the spent media and causes significant damage to the S. aureus cell envelope. However, more likely is that polyP's effects are indirect through the regulation of one of P. aeruginosa's virulence factors, pyocyanin. We show that pyocyanin production in P. aeruginosa occurs polyP-dependent and harms S. aureus through membrane damage and the generation of reactive oxygen species, resulting in increased expression of antioxidant enzymes. In summary, our study adds a new component to the list of biomolecules that the gram-negative pathogen P. aeruginosa generates to compete with S. aureus for resources.

Enhancement of Electricity Production in Microbial Fuel Cells Using a Biosurfactant-Producing Co-Culture

Microbial fuel cells are bio-electrochemical devices that enable the conversion of chemical energy into bioelectricity. In this manuscript, the use of biosurfactants (Tween 80 and surfactin) and the effect of coculturing E. coli and L. plantarum were used to investigate the generation of bioelectricity coming from an H-type microbial fuel cell. In this setup, E. coli acts as an electron donor while L. plantarum acts as an in situ biosurfactant producer. It was observed that the use of exogenous surfactants enhanced electricity production compared to conventional E. coli cultures. The utilization of Tween 80 and surfactin increased the power generation from 204 µW m-2 to 506 µW m-2 and 577 µW m-2, respectively. Furthermore, co-culturing E. coli and L. plantarum also resulted in a higher power output compared to pure cultures (132.8% more when compared to using E. coli alone and 68.1% more when compared to using L. plantarum alone). Due to the presence of surfactants, the internal resistance of the cell was reduced. The experimental evidence collected here clearly indicates that the production of endogenous surfactants, as well as the addition of exogenous surfactants, will enhance MFC electricity production.

Engineered lytic phage of Bacillus cereus and its application in milk

Phages have been approved for use in the food industry to control bacterial contamination in some countries. However, their broader adoption is hindered by some limitations. For instance, the persistence of infectious phages in the food industry can lead to the emergence of resistant bacteria, which negatively impacts the long-term effectiveness of phages. Additionally, the narrow host range of phages limits their effectiveness against various strains. To address these deficiencies, phage engineering has been proposed as a rational approach for modifying phages. In this study, we developed a simple and efficient engineering method for Bacillus cereus phage, using DK1 as an example, to reduce the number of residual phages and expand its range of hosts. Specifically, we knocked out the appendage gene, which codes for the receptor-binding protein, to produce phage progeny with structural defects in their appendages, resulting in the loss of infectivity after host elimination. Furthermore, we used plasmid-mediated means to express different appendage proteins during phage preparation, which allowed altering the host spectrum of the engineered phages without gene insertion. In practical applications, our engineered phages effectively reduced the number of B. cereus in milk and prevented the amplification of active progeny. Our strategy transformed phages from active viruses into more controllable antibacterial agents, making them safer and more efficient for the prevention and control of B. cereus. Moreover, we believe this strategy will help drive the use of engineered phages in the food industry.

The mosquito Aedes aegypti requires a gut microbiota for normal fecundity, longevity and vector competence

Mosquitoes shift from detritus-feeding larvae to blood-feeding adults that can vector pathogens to humans and other vertebrates. The sugar and blood meals adults consume are rich in carbohydrates and protein but are deficient in other nutrients including B vitamins. Facultatively hematophagous insects like mosquitoes have been hypothesized to avoid B vitamin deficiencies by carryover of resources from the larval stage. However, prior experimental studies have also used adults with a gut microbiota that could provision B vitamins. Here, we used Aedes aegypti, which is the primary vector of dengue virus (DENV), to ask if carryover effects enable normal function in adults with no microbiota. We show that adults with no gut microbiota produce fewer eggs, live longer with lower metabolic rates, and exhibit reduced DENV vector competence but are rescued by provisioning B vitamins or recolonizing the gut with B vitamin autotrophs. We conclude carryover effects do not enable normal function.

Unlocking the Power of Onion Peel Extracts: Antimicrobial and Anti-Inflammatory Effects Improve Wound Healing through Repressing Notch-1/NLRP3/Caspase-1 Signaling

Onion peels are often discarded, representing an unlimited amount of food by-products; however, they are a valuable source of bioactive phenolics. Thus, we utilized UPLC-MS/MS to analyze the metabolomic profiles of red (RO) and yellow (YO) onion peel extracts. The cytotoxic (SRB assay), anti-inflammatory (Griess assay), and antimicrobial (sensitivity test, MIC, antibiofilm, and SP-SDS tests) properties were assessed in vitro. Additionally, histological analysis, immunohistochemistry, and ELISA tests were conducted to investigate the healing potential in excisional skin wound injury and Candida albicans infection in vivo. RO extract demonstrated antibacterial activity, limited skin infection with C. albicans, and improved the skin's appearance due to the abundance of quercetin and anthocyanin derivatives. Both extracts reduced lipopolysaccharide-induced nitric oxide release in vitro and showed a negligible cytotoxic effect on MCF-7 and HT29 cells. When extracts were tested in vivo for their ability to promote tissue regeneration, it was found that YO peel extract had the greatest impact. Further biochemical analysis revealed that YO extract suppressed NLRP3/caspase-1 signaling and decreased inflammatory cytokines. Furthermore, YO extract decreased Notch-1 levels and boosted VEGF-mediated angiogenesis. Our findings imply that onion peel extract can effectively treat wounds by reducing microbial infection, reducing inflammation, and promoting tissue regeneration.

Exploring the potential immunomodulatory effects of gallic acid on milk phagocytes in bovine mastitis caused by Staphylococcus aureus

Bovine mastitis caused by Staphylococcus aureus may exacerbate by resulting in significant economic losses and impacting milk quality. To date, the use of gallic acid, a phenolic compound naturally occurring in various plants, holds promise due to its potent anti-oxidant and anti-inflammatory effects in many pieces of literature, thus, making it a subject of interest in bovine innate immunity research. Here we used gallic acid to assess its potential immunomodulation on milk phagocytes in vitro challenges with mastitis-causing bacteria. Our findings indicated that cells exposed to gallic acid showed no harm to cell viability but might maintain the longevity of cells during the bacterial infection. Gallic acid-treated cells displayed reduced cell migration, phagocytosis, and bacterial killing ability, while showing an increase in ROS production, all of which are undoubtedly linked to the intracellular killing abilities of the cells. Nonetheless, the extracellular structure called neutrophil extracellular traps (NETs) was significantly released after receiving gallic acid, representing extracellular killing. We also reported that gallic acid neutralizes inflammation by regulating specific pro-inflammatory genes (IL1B, IL6, TNF) and ROS-generating genes (CYBA, LAMP1, RAC1), subsequently preventing tissue damage. Regarding apoptosis-related genes and proteins, the increased production of caspase-3 and Bcl-2 family proteins could potentially promote the longevity of cells, implicated in the mechanism of combating bacterial invasion during udder inflammation and infection. The novel role of gallic acid on milk phagocytes highlights its potential immunomodulatory properties and contributes to our understanding of its effects on bacterial-host interactions, and provides valuable molecular insights.

Combined benefits of fermented washed rice water and NPK mineral fertilizer on plant growth and soil fertility over three field planting cycles

Washed rice water (WRW) is the leftover water after washing rice grains and is usually discarded. However, WRW contains nutrients leached from rice, making it a potential plant fertilizer. Reusing WRW promotes better water governance, particularly in the face of increased freshwater needs due to population expansion and climate change. Recent experiments in rain shelters have demonstrated the advantages of using WRW as fertilizer. Building on this, our study assessed WRW's efficacy in an open field against NPK fertilizer, both individually and in combination. The treatments were: R3 (3-day fermented WRW), N1 (full recommended NPK rate), N0.5R3 (half NPK rate and R3), and CON (tap water only). These treatments were tested over three consecutive planting cycles of choy sum (Brassica chinensis var. parachinensis) vegetable. At the end of each planting cycle, measurements were taken for the plant's growth, nutrient content and uptake, as well as various soil chemical properties and bacterial population. Plants were watered daily with 5 mm WRW (R3 and N0.5R3) or tap water (N1 and CON). N0.5R3 showed the best results in terms of plant growth, nutrient content, uptake, and soil nutrient levels. N0.5R3 supplied the most nutrients, especially N, P, and K. Increased plant growth also led to increased plant uptake of nutrients, including micronutrients. Macronutrients had a greater impact on plant biomass than micronutrients, as R3 and N1 had similar results. R3 soils had higher bacterial populations but were more acidic than N1 soils. The negative effect of NPK on bacteria was partially offset by combining NPK with WRW as N0.5R3. No carryover effects were observed, likely because of the high nutrient leaching from heavy rains. These findings confirm WRW's is an effective fertilizer in open fields, but measures like surface mulching are crucial to minimize nutrient leaching prior to its use.

Catheter-Based Medical Device Biofilm Ablation Using Histotripsy: A Parameter Study

OBJECTIVE

Biofilm formation in medical catheters is a major source of hospital-acquired infections which can produce increased morbidity and mortality for patients. Histotripsy is a non-invasive, non-thermal focused ultrasound therapy and recently has been found to be effective at removal of biofilm from medical catheters. Previously established histotripsy methods for biofilm removal, however, would require several hours of use to effectively treat a full-length medical catheter. Here, we investigate the potential to increase the speed and efficiency with which biofilms can be ablated from catheters using histotripsy.

METHODS

Pseudomonas aeruginosa (PA14) biofilms were cultured in in vitro Tygon catheter mimics and treated with histotripsy using a 1 MHz histotripsy transducer and a variety of histotripsy pulsing rates and scanning methods. The improved parameters identified in these studies were then used to explore the bactericidal effect of histotripsy on planktonic PA14 suspended in a catheter mimic.

RESULTS

Histotripsy can be used to remove biofilm and kill bacteria at substantially increased speeds compared with previously established methods. Near-complete biofilm removal was achieved at treatment speeds up to 1 cm/s, while a 4.241 log reduction in planktonic bacteria was achieved with 2.4 cm/min treatment.

CONCLUSION

These results represent a 500-fold increase in biofilm removal speeds and a 6.2-fold increase in bacterial killing speeds compared with previously published methods. These findings indicate that histotripsy shows promise for the treatment of catheter-associated biofilms and planktonic bacteria in a clinically relevant time frame.

Algae drive convergent bacterial community assembly at low dilution frequency

Microbial community assembly is a complex dynamical process that determines community structure and function. The interdependence of inter-species interactions and nutrient availability presents a challenge for understanding community assembly. We sought to understand how external nutrient supply rate modulated interactions to affect the assembly process. A statistical decomposition of taxonomic structures of bacterial communities assembled with and without algae and at varying dilution frequencies allowed the separation of the effects of biotic (presence of algae) and abiotic (dilution frequency) factors on community assembly. For infrequent dilutions, the algae strongly impact community assembly, driving initially diverse bacterial consortia to converge to a common structure. Analyzing sequencing data revealed that this convergence is largely mediated by a decline in the relative abundance of specific taxa in the presence of algae. This study shows that complex phototroph-heterotroph communities can be powerful model systems for understanding assembly processes relevant to the global ecosystem functioning.

Microliter spotting and micro-colony observation: A rapid and simple approach for counting bacterial colony forming units

For enumerating viable bacteria, traditional dilution plating to count colony forming units (CFUs) has always been the preferred method in microbiology owing to its simplicity, albeit being laborious and time-consuming. Similar CFU counts can be obtained by quantifying growing micro-colonies in conjunction with the benefits of a microscope. Here, we employed a simple method of five to ten microliter spotting of a diluted bacterial culture multiple times on a single Petri dish followed by determining CFU by counting micro-colonies using a phase-contrast microscope. In this method, the CFU of an Escherichia coli culture can be estimated within a four-hour period after spotting. Further, within a ten-hour period after spotting, CFU in a culture of Ralstonia solanacearum, a bacterium with a generation time of around 2 h, can be estimated. The CFU number determined by micro-colonies observed for 10⁶-fold dilutions or lower is similar to that obtained by the dilution plating method for 10⁷-fold dilutions or lower. Micro-colony numbers observed in the early hours of growth (2 h in case of E. coli and 8 h in case of R. solanacearum) were found to remain consistent at later hours (4 h in case of E. coli and 10 h in case of R. solanacearum), where the visibility of the colonies was better due to a noticeable increase in the size of the colonies. This suggested that micro-colonies observed in the early hours indeed represent the bacterial number in the culture. Practical applications to this counting method were employed in studying the rifampicin-resistant mutation rate as well as performing a fluctuation test in E. coli. The spotting method described here to enumerate bacterial CFU results in reduction of labour, time and resources.

Effect of Different Vat Polymerization Techniques on Mechanical and Biological Properties of 3D-Printed Denture Base

Three-dimensional printing is increasingly applied in dentistry to fabricate denture bases. Several 3D-printing technologies and materials are available to fabricate denture bases, but there is data scarcity on the effect of printability, mechanical, and biological properties of the 3D-printed denture base upon fabricating with different vat polymerization techniques. In this study, the NextDent denture base resin was printed with the stereolithography (SLA), digital light processing (DLP), and light-crystal display (LCD) technique and underwent the same post-processing procedure. The mechanical and biological properties of the denture bases were characterized in terms of flexural strength and modulus, fracture toughness, water sorption and solubility, and fungal adhesion. One-way ANOVA and Tukey’s post hoc were used to statistically analyze the data. The results showed that the greatest flexural strength was exhibited by the SLA (150.8±7.93 MPa), followed by the DLP and LCD. Water sorption and solubility of the DLP are significantly higher than other groups (31.51±0.92 μgmm3) and 5.32±0.61 μgmm3, respectively. Subsequently, the most fungal adhesion was found in SLA (221.94±65.80 CFU/mL). This study confirmed that the NextDent denture base resin designed for DLP can be printed with different vat polymerization techniques. All of the tested groups met the ISO requirement aside from the water solubility, and the SLA exhibited the greatest mechanical strength.

Prospects of Using Gum Arabic Silver Nanoparticles in Toothpaste to Prevent Dental Caries

There is growing interest in the use of green synthesized silver nanoparticles (AgNPs) to control and prevent dental diseases. The incorporation of green synthesized AgNPs into dentifrices to reduce pathogenic oral microbes is motivated by their presumed biocompatibility and broad-spectrum antimicrobial activity. In the present study, gum arabic AgNPs (GA-AgNPs) were formulated into a toothpaste (TP) using a commercial TP at a non-active concentration, to produce GA-AgNPs_TP. The TP was selected after evaluating the antimicrobial activity of four commercial TPs 1-4 on selected oral microbes using agar disc diffusion and microdilution assays. The less active TP-1 was then used in the formulation of GA-AgNPs_TP-1; thereafter, the antimicrobial activity of GA-AgNPs_0.4g was compared to GA-AgNPs_TP-1. The cytotoxicity of GA-AgNPs_0.4g and GA-AgNPs_TP-1 was also assessed on the buccal mucosa fibroblast (BMF) cells using the MTT assay. The study demonstrated that antimicrobial activity of GA-AgNPs_0.4g was retained after being combined with a sub-lethal or inactive concentration of TP-1. The non-selective antimicrobial activity and cytotoxicity of both GA-AgNPs_0.4g and GA-AgNPs_TP-1 was demonstrated to be time and concentration dependent. These activities were instant, reducing microbial and BMF cell growth in less than one hour of exposure. However, the use of dentifrice commonly takes 2 min and rinsed off thereafter, which could prevent damage to the oral mucosa. Although, GA-AgNPs_TP-1 has a good prospect as a TP or oral healthcare product, more studies are required to further improve the biocompatibility of this formulation.

Intracellular Experimental Evolution of Francisella tularensis Subsp. holarctica Live Vaccine Strain (LVS) to Antimicrobial Resistance

In vitro experimental evolution has complemented clinical studies as an excellent tool to identify genetic changes responsible for the de novo evolution of antimicrobial resistance. However, the in vivo context for adaptation contributes to the success of particular evolutionary trajectories, especially in intracellular niches where the adaptive landscape of virulence and resistance are strongly coupled. In this work, we designed an ex vivo evolution approach to identify evolutionary trajectories responsible for antibiotic resistance in the Live Vaccine Strain (LVS) of Francisella tularensis subsp. holarctica while being passaged to increasing ciprofloxacin (CIP) and doxycycline (DOX) concentrations within macrophages. Overall, adaptation within macrophages advanced much slower when compared to previous in vitro evolution studies reflecting a limiting capacity for the expansion of adaptive mutations within the macrophage. Longitudinal genomic analysis identified resistance conferring gyrase mutations outside the Quinolone Resistance Determining Region. Strikingly, FupA/B mutations that are uniquely associated with in vitro CIP resistance in Francisella were not observed ex vivo, reflecting the coupling of intracellular survival and resistance during intracellular adaptation. To our knowledge, this is the first experimental study demonstrating the ability to conduct experimental evolution to antimicrobial resistance within macrophages. The results provide evidence of differences in mutational profiles of populations adapted to the same antibiotic in different environments/cellular compartments and underscore the significance of host mediated stress during resistance evolution.

Towards the Understanding of the Function of Lanthipeptide and TOMM-Related Genes in Haloferax mediterranei

Research on secondary metabolites produced by Archaea such as ribosomally synthesized and post-translationally modified peptides (RiPPs) is limited. The genome of Haloferax mediterranei ATCC 33500 encodes lanthipeptide synthetases (medM1, medM2, and medM3) and a thiazole-forming cyclodehydratase (ycaO), possibly involved in the biosynthesis of lanthipeptides and the TOMMs haloazolisins, respectively. Lanthipeptides and TOMMs often have antimicrobial activity, and H. mediterranei has antagonistic activity towards haloarchaea shown to be independent of medM genes. This study investigated (i) the transcription of ycaO and medM genes, (ii) the involvement of YcaO in bioactivity, and (iii) the impact of YcaO and MedM-encoding genes' absence in the biomolecular profile of H. mediterranei. The assays were performed with biomass grown in agar and included RT-qPCR, the generation of knockout mutants, bioassays, and FTIR analysis. Results suggest that ycaO and medM genes are transcriptionally active, with the highest number of transcripts observed for medM2. The deletion of ycaO gene had no effect on H. mediterranei antihaloarchaea activity. FTIR analysis of medM and ycaO knockout mutants suggest that MedMs and YcaO activity might be directly or indirectly related t lipids, a novel perspective that deserves further investigation.

Growth and inactivation of Listeria monocytogenes in sterile extracts of fruits and vegetables: Impact of the intrinsic factors pH, sugar and organic acid content

Intrinsic characteristics of fresh produce, such as pH, water activity, acid content and nutrient availability are critical factors in determining the survival and growth of Listeria monocytogenes (Lm). In this study, sterile fresh produce juice was used to analyze Lm growth potential among 14 different commodities and to identify physicochemical characteristics in those juices that affect Lm growth. Significant growth of Lm was observed in juices with pH ≥5.6 and low acidity (0.04-0.07 % titratable acidity (TA)) (cantaloupe, carrot, celery, green pepper, parsley, and romaine lettuce), slight reduction of Lm was observed in juices with pH 4.1 (tomato) and pH 3.9 (mango), and no Lm counts were recovered from juices with pH ≤3.8 and high acidity (0.28-1.17 % TA) (apple, blueberry, grape, peach, and pineapple). Although these acidic fruit juices possessed a high sugar content, the pH and acidity of produce juice seemed to be the primary determinants for Lm growth. The neutralization of acidic juices (i.e., Fuji and Gala apple, blueberry, grape, mango, pineapple, peach, and tomato) enabled Lm growth at 37 °C in all juices except for Gala apple and peach. Strong decline in Lm populations in Gala apple, grape and peach juices might be linked to sensitivity to organic acids, such as malic acid. Furthermore, Lm populations significantly decreased in pH-neutral (7.6) cauliflower juice, suggesting that potential antilisterial substances may play a role in Lm decline in cauliflower juice.

Linking Pedobacter lusitanus NL19 volatile exometabolome with growth medium composition: what can we learn using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry?

Microbial metabolomics allows understanding and to comprehensively analyse metabolites, and their related cellular and metabolic processes, that are produced and released to the extracellular environment under specific conditions. In that regard, the main objective of this research is to understand the impact of culture media changes in the metabolic profile of Pedobacter lusitanus NL19 (NL19) and Pedobacter himalayensis MTCC 6384 (MTCC6384) and respective influence on the production of biotechnologically relevant compounds. Solid-phase microextraction combined with comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry with time-of-flight analyser (GC × GC-ToFMS) was applied to comprehensively study the metabolites produced by NL19 and MTCC6384 both in tryptic soy broth 100% (TSB100) and tryptic soy broth with 25% casein peptone (PC25). A total of 320 metabolites were putatively identified, which belong to different chemical families: alcohols, aldehydes, esters, ethers, hydrocarbons, ketones, nitrogen compounds, sulphur compounds, monoterpenes, and sesquiterpenes. Metabolites that were statistically different from the control (sterile medium) were selected allowing for the construction of the metabolic profile of both strains. A set of 80 metabolites was tentatively associated to the metabolic pathways such as the metabolism of fatty acids, branched-chain aminoacids, phenylalanine, methionine, aromatic compounds, and monoterpene and sesquiterpene biosynthesis. This study allowed to better understand how slight changes of the culture media and thus the composition of nutrients impair the metabolic profile of bacteria, which may be further explored for metabolomics pipeline construction or biotechnological applications.

Phage Therapy for Mosquito Larval Control: a Proof-of-Principle Study

The mosquito microbiota has a profound impact on multiple biological processes ranging from reproduction to disease transmission. Interestingly, the adult mosquito microbiota is largely derived from the larval microbiota, which in turn is dependent on the microbiota of their water habitat. The larval microbiota not only plays a crucial role in larval development but also has a significant impact on the adult stage of the mosquito. By precisely engineering the larval microbiota, it is feasible to alter larval development and other life history traits of the mosquitoes. Bacteriophages, given their host specificity, can serve as a tool for modulating the microbiota. For this proof-of-principle study, we selected representative strains of five common Anopheles mosquito-associated bacterial genera, namely, Enterobacter, Serratia, Pseudomonas, Elizabethkingia, and Asaia. Our results with monoaxenic cultures showed that Anopheles larvae with Enterobacter and Pseudomonas displayed normal larval development with no significant mortality. However, monoaxenic Anopheles larvae with Elizabethkingia showed delayed larval development and higher mortality. Serratia and Asaia gnotobiotic larvae failed to develop past the first instar. We isolated and characterized three novel bacteriophages (EP1, SP1, and EKP1) targeting Enterobacter, Serratia, and Elizabethkingia, respectively, and utilized a previously characterized bacteriophage (GH1) targeting Pseudomonas to modulate larval water microbiota. Gnotobiotic Anopheles larvae with all five bacterial genera showed reduced survival and larval development with the addition of bacteriophages EP1 and GH1, targeting Enterobacter and Pseudomonas, respectively. The effect was synergistic when both EP1 and GH1 were added together. Our results demonstrate a novel application of bacteriophages for mosquito control. IMPORTANCE Mosquitoes are efficient vectors of multiple human and animal pathogens. The biology of mosquitoes is strongly affected by their associated microbiota. Because of the important role of the larval microbiota in mosquito biology, the microbiota can potentially serve as a target for altering mosquito life-history traits. Our study provides proof of principle that bacteriophages can be used as tools to modulate the mosquito larval habitat microbiota and can, in turn, affect larval development and survival. These results highlight the utility of bacteriophages in mosquito microbiota research and also provide a new potential mosquito control tool.

Antimicrobial Effects of Gum Arabic-Silver Nanoparticles against Oral Pathogens

Dental caries is considered one of the most prevalent oral diseases worldwide, with a high rate of morbidity among populations. It is a chronic infectious disease with a multifactorial etiology that leads to the destruction of the dental tissues. Due to their antimicrobial, anti-inflammatory, antifungal, and antioxidant properties; silver nanoparticles (AgNPs) are incorporated in dental products to help prevent infectious oral diseases. In this study, the antimicrobial effects of AgNPs synthesized using Gum Arabic extracts (GAE) were examined. The GA-AgNPs were synthesized and characterized using ultraviolet-visible (UV-Vis) spectrophotometer, dynamic light scattering (DLS), transmission electron microscopy (TEM), and Fourier transform infrared (FTIR) spectroscopy. The antimicrobial activity of the GA-AgNPs was evaluated on Streptococcus sanguinis (S. sanguinis), Streptococcus mutans (S. mutans), Lactobacillus acidophilus (L. acidophilus), and Candida albicans (C. albicans) using agar disc diffusion and microdilution assays. The antibiofilm of GA-AgNPs was evaluated on the surface of human tooth enamel that had been exposed to S. mutans with and without the GA-AgNPs using scanning electron microscopy (SEM). GA-AgNPs were spherical in shape with a particle size distribution between 4 and 26 nm. The GA-AgNPs exhibited antimicrobial activity against all the tested oral microbes, with GA-AgNPs_0.4g having higher antimicrobial activity. The GA-AgNPs_0.4g inhibited S. mutans adhesion and biofilm formation on the surface of the tooth enamel. Therefore, this study supports the prospective implementation of the plant extract-mediated AgNPs in dental healthcare.

Isolation of multidrug-resistant Escherichia coli and Salmonella spp. from sulfonamide-treated diarrheic calves

Background and Aim

The bovine industry is threatened by one of the most serious and deadly enteric diseases, calf diarrhea, particularly in developing nations like Bangladesh. In this context, bacterial resistance to antimicrobial drugs and its detrimental consequences have become a critical public health issue that is difficult to address globally. This study aimed to isolate and identify Escherichia coli and Salmonella spp. with their antibiogram and antibiotic resistance gene detection from sulfonamide-treated diarrheic calves.

Materials and Methods

Twelve diarrheic calves suffering from calf diarrhea in a dairy farm were selected and a total of 36 fecal samples were aseptically collected directly from rectum before, during, and at the end of treatment for each calf to determine the total viable count, total E. coli count and total Salmonella count. A polymerase chain reaction was used for the specific detection of E. coli and Salmonella genus targeting fliC and invA genes, respectively. Antibiotic sensitivity test of the isolated E. coli and Salmonella spp. were performed by the disk diffusion method for eight commonly used antibiotics.

Results

A total of 36 E. coli (100%) and 12 Salmonella spp. (33%) were isolated from the samples and were confirmed by polymerase chain reaction. Total viable count was found to be ranged from 35 × 10⁷ to 99 × 10¹⁰ colony-forming unit (CFU)/g fecal sample before starting sulfonamide treatment, 34 × 10⁵ to 25 × 10¹⁰ CFU/g during treatment with sulfonamide, and 48 × 10³ to 69 × 10¹⁰ CFU/g immediately after completion of sulfonamide treatment. Total E. coli count was found to be ranged from 4 × 10⁴ to 36 × 10¹⁰ CFU/g, 24 × 10⁴ to 23 × 10⁸ CFU/g, and 13 × 10⁴ to 85 × 10¹⁰ CFU/g, whereas total Salmonella count was found to be ranged from 16 × 10⁶ to 18.5 × 10¹¹ CFU/g, 15 × 10⁴ to 44 × 10⁷ CFU/g, and 13.2 × 10⁵ to 21 × 10¹⁰ CFU/g fecal sample before starting sulfonamide treatment, during treatment with sulfonamide immediately after completion of sulfonamide treatment, respectively. The in vitro antibiotic sensitivity test showed that all the E. coli and Salmonella spp. isolated from diarrheic calves (100%) contained multidrug-resistant (MDR) phenotypes. Escherichia coli isolates were found 100% resistant to amoxicillin (AMX), cefuroxime, cephalexin (CN), erythromycin (ERY), and tetracycline (TET); whereas 94.4%, 86.1%, and 77.8% isolates were resistant to doxycycline (DOX), moxifloxacin (MOF), and gentamycin (GEN), respectively. In case of Salmonella isolates, all were found 100% resistant to AMX, CN, and ERY; whereas 91.7% of resistance was observed for DOX, MOF, cefuroxime, GEN, and TET. Based on the molecular screening of the antibiotic resistance genes, tetA gene was present in 83.3% of the isolated E. coli and 75% of the isolated Salmonella strains, whereas 83.3% E. coli and 79.2% Salmonella isolates contained blaTEM gene.

Conclusion

These findings suggest that MDR E. coli and Salmonella spp. might be responsible for calf scouring, which is challenging to treat with antibiotics or sulfonamide drugs alone. Therefore, it is important to check the antibiotic sensitivity pattern to select a suitable antibiotic for the treatment of calf scoring. A suitable antibiotic or combination of an antibiotic and sulfonamide could be effective against E. coli and Salmonella spp. responsible for calf scouring.

Automation of yeast spot assays using an affordable liquid handling robot

The spot assay of the budding yeast Saccharomyces cerevisiae is an experimental method that is used to evaluate the effect of genotypes, medium conditions, and environmental stresses on cell growth and survival. Automation of the spot assay experiments from preparing a dilution series to spotting to observing spots continuously has been implemented based on large laboratory automation devices and robots, especially for high-throughput functional screening assays. However, there has yet to be an affordable solution for the automated spot assays suited to researchers in average laboratories and with high customizability for end-users. To make reproducible spot assay experiments widely available, we have automated the plate-based yeast spot assay of budding yeast using Opentrons OT-2 (OT-2), an affordable liquid-handling robot, and a flatbed scanner. We prepared a 3D-printed mount for the Petri dish to allow for precise placement of the Petri dish inside the OT-2. To account for the uneven height of the agar plates, which were made by human hands, we devised a method to adjust the z-position of the pipette tips based on the weight of each agar plate. During the incubation of the agar plates, a flatbed scanner was used to automatically take images of the agar plates over time, allowing researchers to quantify and compare the cell density within the spots at optimal time points a posteriori. Furthermore, the accuracy of the newly developed automated spot assay was verified by performing spot assays with human experimenters and the OT-2 and quantifying the yeast-grown area of the spots. This study will contribute to the introduction of automated spot assays and the automated acquisition of growth processes in conventional laboratories that are not adapted for high-throughput laboratory automation.

Bioformulation Containing Cohorts of Ensifer adhaerens MSN12 and Bacillus cereus MEN8 for the Nutrient Enhancement of Cicer arietinum L

Here we examine the effects of different carrier based bioinoculants on the growth, yield and nutritional value of chickpea and on associated soil nutrients. A consortium of two taxonomically distinct endophytic bacteria-Ensifer adhaerens MSN12 and Bacillus cereus MEN8-have promising plant growth promoting (PGP) attributes. We demonstrate their delivery from the laboratory to the field via the formulation of an effective bioinoculant with economic and accessible carriers. Sugarcane straw ash (SCSA) was found to be an efficient carrier and bioformulation for enhancing viability and shelf-life of strains up to 12 months. A bioformulation containing an SCSA-based consortium (MSN12 + MEN8) increased seed germination by 7%, plant weight by 29%, length by 17%, seed-yield by 12%, harvesting index by 14% and proximate nutritional constituents by 20% over consortium treatment without SCSA. In addition, the bioformulation of post-harvest treated soil improved the physico-chemical properties of the soil in comparison to a pre-sowing SCSA-based bioformulation treated crop, being fortified in different proximate nutritional constituents including dry matter (30%), crude protein (45%), crude fiber (35%), and ether extract (40%) in comparison to the control. Principal component analysis and scattered matrix plots showed a positive correlation among the treatments, which also validates improvement in the soil nutrient components and proximate constituents by T6 treatment (MSN12 + MEN8 + SCSA). The above results suggest efficiency of SCSA not only as a carrier material but also to support microbial growth for adequate delivery of lab strains as a substitute for chemi-fertilizers.

Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis

BACKGROUND

The extreme conditions of thermal springs constitute a unique aquatic habitat characterized by low nutrient contents and the absence of human impacts on the microbial community composition. Thus, these springs may host phylogenetically novel microorganisms with potential use in biotechnology. With this hypothesis in mind, we examined the microbial composition of four thermal springs of the world-renowned spa town of Karlovy Vary (Carlsbad), Czechia, which differ in their temperature and chemical composition.

RESULTS

Microbial profiling using 16S rRNA gene sequencing revealed the presence of phylogenetically novel taxa at various taxonomic levels, spanning from genera to phyla. Many sequences belonged to novel classes within the phyla Hydrothermae, Altiarchaeota, Verrucomicrobia, and TA06. Cultivation-based methods employing oligotrophic media resulted in the isolation of 44 unique bacterial isolates. These include strains that withstand concentrations of up to 12% NaCl_w/v in cultivation media or survive a temperature of 100 °C, as well as hitherto uncultured bacterial species belonging to the genera Thermomonas, Paenibacillus, and Cellulomonas. These isolates harbored stress response genes that allow them to thrive in the extreme environment of thermal springs.

CONCLUSIONS

Our study is the first to analyze the overall microbial community composition of the renowned Karlovy Vary thermal springs. We provide insight into yet another level of uniqueness of these springs. In addition to their unique health benefits and cultural significance, we demonstrate that these springs harbor phylogenetically distinct microorganisms with unusual life strategies. Our findings open up avenues for future research with the promise of a deeper understanding of the metabolic potential of these microorganisms.

Evaluation of the biofilm life cycle between Candida albicans and Candida tropicalis

Candida tropicalis is an emergent pathogen with a high rate of mortality associated with its biofilm formation. Biofilm formation has important repercussions on the public health system. However, little is still known about its biofilm life cycle. The present study analyzed the biofilm life cycle of Candida albicans and C. tropicalis during various timepoints (24, 48, 72, and 96 h) through biomass assays, colony-forming unit (CFU) counting, and epifluorescence and scanning electron microscopies. Our results showed a significant difference between C. albicans and C. tropicalis biofilms in each biomass and viability assay. All-time samples in the biomass and viability assays confirmed statistical differences between the Candida species through pairwise Wilcoxon tests (p < 0.05). C. albicans demonstrated a lower biomass growth but reached nearly the same level of C. tropicalis biomass at 96 h, while the CFU counting assays exhibited a superior number of viable cells within the C. tropicalis biofilm. Statistical differences were also found between C. albicans and C. tropicalis biofilms from 48- and 72-h microscopies, demonstrating C. tropicalis with a higher number of total cells within biofilms and C. albicans cells with a superior cell area and higher matrix production. Therefore, the present study proved the higher biofilm production of C. tropicalis.

Self-locomotive, antimicrobial microrobot (SLAM) swarm for enhanced biofilm elimination

Biofilm is a major cause of infections and infrastructure deterioration, largely due to molecular diffusion restrictions that hamper the antimicrobial activity of traditional antibiotics and disinfectants. Here, we present a self-locomotive, antimicrobial microrobot (SLAM) swarm that can penetrate, fracture, and detach biofilm and, in turn, nullify bacterial resistance to antibiotics. The SLAM is assembled by loading a controlled mass of manganese oxide nanosheets on diatoms with the polydopamine binder. In hydrogen peroxide solution, SLAMs produce oxygen bubbles that generate thrust to penetrate the rigid and dense Pseudomonas aeruginosa biofilm and self-assemble into a swarm that repeatedly surrounds, expands, and bursts oxygen bubbles. The resulting cavities continue to deform and fracture extracellular polymeric substances from microgrooved silicone substrates and wounded skin explants while decreasing the number of viable bacterial cells. Additionally, SLAM allows irrigating water or antibiotics to access the residual biofilm better, thus enhancing the synergistic efficacy in killing up to 99.9% of bacterial cells.

Inhibition of Candida glabrata Biofilm by Combined Effect of Dendritic Compounds and Amphotericin

In the last decade, Candida glabrata has become an important emerging opportunistic pathogen not only because of the increase in nosocomial infections frequency but also because of its ability to form biofilms and its innate resistance to commercial antifungals. These characteristics make this pathogen a major problem in hospital settings, including problems regarding equipment, and in immunosuppressed patients, who are at high risk for candidemia. Therefore, there is an urgent need for the development of and search for new antifungal drugs. In this study, the efficacy of two dendritic wedges with 4-phenyl butyric acid (PBA) at the focal point and cationic charges on the surface ArCO₂G₂(SNMe₃I)₄ (1) and ArCO₂G₃(SNMe₃I)₈ (2) was studied against C. glabrata strain to inhibit the formation of biofilms and eliminate established biofilm. For this, MBIC (minimum biofilm inhibitory concentration), MBDC (minimum biofilm damaging concentrations), as well as MFCB (minimum fungicidal concentration in biofilm) and MBEC (minimum biofilm eradicating concentration) were determined. In addition, different combinations of dendrons and amphotericin B were tested to study possible synergistic effects. On the other hand, cytotoxicity studies were performed. C. glabrata cells and biofilm structure were visualized by confocal microscopy. ArCO₂G₂(SNMe₃I)₄ (1) and ArCO₂G₃(SNMe₃I)₈ (2) dendrons showed both an MBIC of 8 mg/L and a MBDC of 32 mg/L and 64 mg/L, respectively. These dendrons managed to eradicate the entirety of an established biofilm. In combination with the antifungal amphotericin, it was possible to prevent the generation of biofilms and eradicate established biofilms at lower concentrations than those required individually for each compound at these conditions.

Ultra-/Small Angle X-ray Scattering (USAXS/SAXS) and Static Light Scattering (SLS) Modeling as a Tool to Determine Structural Changes and Effect on Growth in S. epidermidis

Usually, to characterize bacterial cells' susceptibility to antimicrobials, basic microbiology techniques such as serial dilutions or disk assays are used. In this work, we present an approach focused on combining static light scattering (SLS) and ultra-/small angle X-ray scattering (USAXS/SAXS). This approach was used to support microbiology techniques, with the aim of understanding the structural changes caused to bacteria when they are exposed to different stresses like pH, oxidation, and surfactants. Using USAXS/SAXS and SLS data, we developed a detailed multiscale model for a Gram-positive bacterium, S. epidermidis, and we extracted information regarding changes in the overall size and cell thickness induced by different stresses (i.e., pH and hydrogen peroxide). Increasing the concentration of hydrogen peroxide leads to a progressive reduction in cell wall thickness. Moreover, the concomitant use of pH and hydrogen peroxide provides evidence for a synergy in inhibiting the S. epidermidis growth. These promising results will be used as a starting base to further investigate more complex formulations and improve/refine the data modeling of bacteria in the small angle scattering regime.

Electrically Conductive and Antimicrobial Agro-Food Waste Biochar Functionalized with Zinc Oxide Particles

Carbonaceous materials derived from biomass have been used as sustainable platforms for the growth of ZnO particles aiming the production of functional composite fillers. Kidney-bean pods were pyrolyzed by applying an experimental design that demonstrates that the specific surface area (S_BET) of biochar is improved with increasing pyrolysis temperature combined with a short air-oxidation time. Meanwhile, the graphitization degree and the electrical conductivity (EC) of biochars were negatively affected by increasing the air-oxidation time. The biochar sample with the higher EC and the one with the higher S_BET were selected to be functionalized with ZnO particles by a solvothermal methodology, obtaining composites with an EC and S_BET properties superior to the ZnO-rGO composite, in addition to a similar antibacterial activity. The developed ZnO-biochar composite structures, which are more ecological and biocompatible than the ZnO composites derived from graphene sheets, can be applied as electrically conductive and active fillers.

Particle-Mediated Histotripsy for the Targeted Treatment of Intraluminal Biofilms in Catheter-Based Medical Devices

Objective. This paper is an initial work towards developing particle-mediated histotripsy (PMH) as a novel method of treating catheter-based medical device (CBMD) intraluminal biofilms. Impact Statement. CBMDs commonly become infected with bacterial biofilms leading to medical device failure, infection, and adverse patient outcomes. Introduction. Histotripsy is a noninvasive focused ultrasound ablation method that was recently proposed as a novel method to remove intraluminal biofilms. Here, we explore the potential of combining histotripsy with acoustically active particles to develop a PMH approach that can noninvasively remove biofilms without the need for high acoustic pressures or real-time image guidance for targeting. Methods. Histotripsy cavitation thresholds in catheters containing either gas-filled microbubbles (MBs) or fluid-filled nanocones (NCs) were determined. The ability of these particles to sustain cavitation over multiple ultrasound pulses was tested after a series of histotripsy exposures. Next, the ability of PMH to generate selective intraluminal cavitation without generating extraluminal cavitation was tested. Finally, the biofilm ablation and bactericidal capabilities of PMH were tested using both MBs and NCs. Results. PMH significantly reduced the histotripsy cavitation threshold, allowing for selective luminal cavitation for both MBs and NCs. Results further showed PMH successfully removed intraluminal biofilms in Tygon catheters. Finally, results from bactericidal experiments showed minimal reduction in bacteria viability. Conclusion. The results of this study demonstrate the potential for PMH to provide a new modality for removing bacterial biofilms from CBMDs and suggest that additional work is warranted to develop histotripsy and PMH for treatment of CBMD intraluminal biofilms.

Decreased efficacy of antimicrobial agents in a polymicrobial environment

The airways of people with cystic fibrosis (CF) often harbour diverse polymicrobial communities. These airway infections can be impossible to resolve through antibiotic intervention, even though isolates of the individual species present are susceptible to the treatment when tested in vitro. In this work, we investigate how polymicrobial cultures comprised of key CF-associated pathogens respond to challenge with species-specific antimicrobial agents; colistin (targets Pseudomonas aeruginosa), fusidic acid (targets Staphylococcus aureus), and fluconazole (targets Candida albicans). We found that growth in a polymicrobial environment protects the target microorganism (sometimes by several orders of magnitude) from the effect(s) of the antimicrobial agent. This decreased antimicrobial efficacy was found to have both non-heritable (physiological) and heritable (genetic) components. Whole-genome sequencing of the colistin-resistant P. aeruginosa isolates revealed single nucleotide polymorphisms and indels in genes encoding lipopolysaccharide (LPS) biosynthesis and/or pilus biogenesis, indicating that a previously undescribed colistin resistance mechanism was in operation. This was subsequently confirmed through further genetic analyses. Our findings indicate that the polymicrobial nature of the CF airways is likely to have a significant impact on the clinical response to antimicrobial therapy.

The Old Yellow Enzyme OfrA Fosters Staphylococcus aureus Survival via Affecting Thiol-Dependent Redox Homeostasis

Old yellow enzymes (OYEs) are widely found in the bacterial, fungal, and plant kingdoms but absent in humans and have been used as biocatalysts for decades. However, OYEs’ physiological function in bacterial stress response and infection situations remained enigmatic. As a pathogen, the Gram-positive bacterium Staphylococcus aureus adapts to numerous stress conditions during pathogenesis. Here, we show that in S. aureus genome, two paralogous genes (ofrA and ofrB) encode for two OYEs. We conducted a bioinformatic analysis and found that ofrA is conserved among all publicly available representative staphylococcal genomes and some Firmicutes. Expression of ofrA is induced by electrophilic, oxidative, and hypochlorite stress in S. aureus. Furthermore, ofrA contributes to S. aureus survival against reactive electrophilic, oxygen, and chlorine species (RES, ROS, and RCS) via thiol-dependent redox homeostasis. At the host–pathogen interface, S. aureusΔofrA has defective survival in macrophages and whole human blood and decreased staphyloxanthin production. Overall, our results shed the light onto a novel stress response strategy in the important human pathogen S. aureus.

Resazurin-based high-throughput screening method for the discovery of dietary phytochemicals to target microbial transformation of L-carnitine into trimethylamine, a gut metabolite associated with cardiovascular disease

Nowadays, there is great interest in the discovery of food compounds that might inhibit gut microbial TMA production from its methylamine precursors. In this work, an innovative novel screening strategy capable of rapidly determining the differences in the metabolic response of Klebsiella pneumoniae, a bacteria producing TMA under aerobic conditions, to a library of extracts obtained from food and natural sources was developed. The proposed high-throughput screening (HTS) method combines resazurin reduction assay in 384-well plates and Gaussian Processes as a machine learning tool for data processing, allowing for a fast, cheap and highly standardized evaluation of any interfering effect of a given compound or extract on the microbial metabolism sustained by L-carnitine utilization. As a proof-of-concept of this strategy, a pilot screening of 39 extracts and 6 pure compounds was performed to search for potential candidates that could inhibit in vitro TMA formation from L-carnitine. Among all the extracts tested, three of them were selected as candidates to interfere with TMA formation. Subsequent in vitro assays confirmed the potential of oregano and red thyme hexane extracts (at 1 mg mL^-1) to inhibit TMA formation in bacterial lysates. In such in vitro assay, the red thyme extract exerted comparable effects on TMA reduction (∼40%) as 7.5 mM meldonium (∼50% TMA decrease), a reported L-carnitine analogue. Our results show that metabolic activity could be used as a proxy of the capacity to produce TMA under controlled culture conditions using L-carnitine to sustain metabolism.

Meteorites as Food Source on Early Earth: Growth, Selection, and Inhibition of a Microbial Community on a Carbonaceous Chondrite

Meteoritic material accumulated on the surface of the anoxic early Earth during the Late Heavy Bombardment around 4.0 Gya and may have provided Earth's surface with extraterrestrial nutrients and energy sources. This research investigates the growth of an anaerobic microbial community from pond sediment on native and pyrolyzed (heat-treated) carbonaceous chondrite Cold Bokkeveld. The community was grown anaerobically in liquid media. Native Cold Bokkeveld supported the growth of a phylogenetically clustered subset of the original pond community by habitat filtering. The anaerobic community on meteorite was dominated by the Deltaproteobacteria Geobacteraceae and Desulfuromonadaceae. Members of these taxa are known to use elemental sulfur and ferric iron as electron acceptors, and organic compounds as electron donors. Pyrolyzed Cold Bokkeveld, however, was inhibitory to the growth of the microbial community. These results show that carbonaceous chondrites can support and select for a specific anaerobic microbial community, but that pyrolysis, for example by geothermal activity, could inhibit microbial growth and toxify the material. This research shows that extraterrestrial meteoritic material can shape the abundance and composition of anaerobic microbial ecosystems with implications for early Earth. These results also provide a basis to design anaerobic material processing of asteroidal material for future human settlement.

Cytobacts: Abundant and Diverse Vertically Seed-Transmitted Cultivation-Recalcitrant Intracellular Bacteria Ubiquitous to Vascular Plants

We have recently described ‘Cytobacts’ as abundant intracellular endophytic bacteria inhabiting live plant cells based on the observations with callus and cell suspension cultures of grapevine and other plant species with the origin ascribable to field explants. In this study, we investigated the prevalence of such cytoplasmic bacterial associations in field plants across different taxa, their cultivability, and the extent of taxonomic diversity and explored the possibility of their embryo-mediated vertical transmission. Over 100 genera of field plants were surveyed for ‘Cytobacts’ through bright-field live-cell imaging as per our previous experience using fresh tissue sections from surface-sterilized shoot-tissues with parallel cultivation-based assessments. This revealed widespread cellular bacterial associations visualized as copious motile micro-particles in the cytoplasm with no or sparse colony forming units (CFU) from the tissue-homogenates indicating their general non-cultivability. Based on the ease of detection and the abundance of ‘Cytobacts’ in fresh tissue sections, the surveyed plants were empirically classified into three groups: (i) motile bacteria detected instantly in most cells; (ii) motility not so widely observed, but seen in some cells; and (iii) only occasional motile units observed, but abundant non-motile bacterial cells present. Microscopy versus 16S-rRNA V3–V4 amplicon profiling on shoot-tip tissues of four representative plants—tomato, watermelon, periwinkle, and maize—showed high bacterial abundance and taxonomic diversity (11–15 phyla) with the dominance of Proteobacteria followed by Firmicutes/Actinobacteria, and several other phyla in minor shares. The low CFU/absence of bacterial CFU from the tissue homogenates on standard bacteriological media endorsed their cultivation-recalcitrance. Intracellular bacterial colonization implied that the associated organisms are able to transmit vertically to the next generation through the seed-embryos. Microscopy and 16S-rRNA V3–V4 amplicon/metagenome profiling of mature embryos excised from fresh watermelon seeds revealed heavy embryo colonization by diverse bacteria with sparse or no CFU. Observations with grapevine fresh fruit-derived seeds and seed-embryos endorsed the vertical transmission by diverse cultivation-recalcitrant endophytic bacteria (CREB). By and large, Proteobacteria formed the major phylum in fresh seed-embryos with varying shares of diverse phyla. Thus, we document ‘Cytobacts’ comprising diverse and vertically transmissible CREBs as a ubiquitous phenomenon in vascular plants.

An Evaluation of Aluminum Tolerant Pseudomonas aeruginosa A7 for In Vivo Suppression of Fusarium Wilt of Chickpea Caused by Fusarium oxysporum f. sp. ciceris and Growth Promotion of Chickpea

Chickpea wilt, caused by Fusarium oxysporum f. sp. ciceris, is a disease that decreases chickpea productivity and quality and can reduce its yield by as much as 15%. A newly isolated, moss rhizoid-associated Pseudomonas aeruginosa strain A7, demonstrated strong inhibition of Fusarium oxysporum f. sp. ciceris growth. An in vitro antimicrobial assay revealed A7 to suppress the growth of several fungal and bacterial plant pathogens by secreting secondary metabolites and by producing volatile compounds. In an in vivo pot experiment with Fusarium wilt infection in chickpea, the antagonist A7 exhibited a disease reduction by 77 ± 1.5%, and significantly reduced the disease incidence and severity indexes. Furthermore, A7 promoted chickpea growth in terms of root and shoot length and dry biomass during pot assay. The strain exhibited several traits associated with plant growth promotion, extracellular enzymatic production, and stress tolerance. Under aluminum stress conditions, in vitro growth of chickpea plants by A7 resulted in a significant increase in root length and plant biomass production. Additionally, hallmark genes for antibiotics production were identified in A7. The methanol extract of strain A7 demonstrated antimicrobial activity, leading to the identification of various antimicrobial compounds based on retention time and molecular weight. These findings strongly suggest that the strain’s significant biocontrol potential and plant growth enhancement could be a potential environmentally friendly process in agricultural crop production.

Photobiomodulation and Antimicrobial Photodynamic Influence of a 650 nm Wavelength on Staphylocoagulase and Viability of Staphylococcus aurous

Introduction: Staphylococcus aureus is one of the critical pathological bacteria. This bacterium had developed a variety of genetic mutations that made it resistant to drugs and more harmful to humans. In addition, all attempts to design a specific vaccine against S. aureus have failed. Therefore, this experiment was designed as a trial for vaccine production, by using a photodynamic treatment (PDT) through partial biological inhibition. The PDT of bacteria mainly focused on reducing the activity of staphylocoagulase (SC), which has a protective feature for bacteria. This study aimed to examine the photodynamic effect of combining a specific wavelength of a laser and a certain dilution photosensitizer, methylene blue (MB) dye. The possible PDT effect on the inhibition of pathogenic enzymatic activity was predicted. This study also aimed to evaluate the inhibitory effect of PDT on the total bacterial account (viability) simultaneously with SC assay. Methods: A 650nm wavelength diode laser was used with 100 mW output power and 2 minutes of exposure time. Dye dilutions were 50, 100, 150 and 200 μg/mL. The viability of bacteria after and before laser treatment was calculated using single plate-serial dilution spotting methods. The activity of SC was detected by using human plasma for 4 hours incubation of crude-substrate interaction. Results: The results revealed a significant decrease in enzyme activity and colony-forming units (CFU) after irradiating bacterial suspension with 150 g/mL MB, as well as a decline in CFU. However, irradiation with a laser alone showed a significant increase in SC activity and CFU for the same exposure time. Conclusion: Besides reducing the production of SC activity, PDT significantly inhibited the viability of S. aureus. The application of MB photosensitizer at a concentration of 150 g/mL in combination with a laser wavelength of 650 nm resulted in a complete decrease in the SC activity value as well as the viability of bacteria.