Induction of amylase and protease as antibiofilm agents by starch, casein, and yeast extract in Arthrobacter sp. CW01

Biorefinery-inspired, two-step valorization strategy to manage plant-based recalcitrant organic waste, involving solvent extraction, and fermentation with Bacillus clausii-a proof of concept study

Approximately 40-50% of municipal solid waste is organic and causing biogenic malodor and infections, due to inefficient treatment methods. Biorefinery-based bioremediation and valorization is in vogue against these conventional strategies since it combines unit operations for better efficiency and productivity. Deriving inspiration, the proposed strategy puts together a unique and compatible combination of processes. This novel two-step valorization workflow involves the extraction of small molecules using organic solvents, and fermentation of resulting denatured residues (increased biodegradability or decreased recalcitrance) of reduced microbial load. The extraction step also doubles up as a sterilization event, with different solvents (petroleum ether, chloroform, ethyl methyl ketone and methanol) exhibiting varied efficiency, methanol and ethyl methyl ketone being the most effective. Different recalcitrant plant organic wastes resulting from four plants (Cocos nucifera, Allium cepa, Artocarpus hirsutus and Swietenia mahagoni) were used as feedstocks in the preliminary exploratory study using chosen pathogenic bacteria. Onion peel (Allium cepa) ethyl methyl ketone extract was chosen for further studies, as it inhibits Salmonella enterica, which is associated with infection and malodour (due to biogenic H2S) in wastewater. Further, fractionation of the extract yielded quercetin and its glycoside. The onion peel residue, after solvent extraction was fortified with peptone and essential minerals to promote the growth of Bacillus clausii. Fortified post-extraction residue supported the growth better than the pre-extraction residue. The residue resultant after solvent extraction was fermented with Bacillus clausii and with release of bioactive supernatants. The concentrated supernatant showed significant inhibition of Salmonella enterica and Shigella dysenteriae. Additionally, all the exudates showed considerable inhibition in H2S production, respectively.

Purification and biochemical characterization of novel α-amylase and cellulase from Bacillus sp. PM06

Bacillus sp. PM06, previously isolated from sugarcane waste pressmud, could produce dual enzymes α-amylase and cellulase. The isolate's crude enzymes were purified homogeneously using ammonium sulfate precipitation followed by High Quaternary amine anion exchange chromatography. Purified enzymes revealed the molecular weights of α-amylase and cellulase as 55 and 52 kDa, with a purification fold of 15.4 and 11.5, respectively. The specific activity of purified α-amylase and cellulase were 740.7 and 555.6 U/mg, respectively. It demonstrated a wide range of activity from pH 5.0 to 8.5, with an optimum pH of 5.5 and 6.4 for α-amylase and cellulase. The optimum temperature was 50 °C for α-amylase and 60 °C for cellulase. The kinetic parameters of purified α-amylase were 741.5 ± 3.75 µmol/min/mg, 1.154 ± 0.1 mM, and 589 ± 3.5/(s mM), using starch as a substrate. Whereas cellulase showed 556.3 ± 1.3 µmol/min/mg, 1.78 ± 0.1 mM, and 270.9 ± 3.8/(s mM) of Vmax, Km, Kcat/Km, respectively, using carboxymethyl cellulose (CMC) as substrate. Among the various substrates tested, α-amylase had a higher specificity for amylose and CMC for cellulase. Different inhibitors and activators were also examined. Ca2+ Mg2+, Co2+, and Mn2+ boosted α-amylase and cellulase activities. Cu2+ and Ni2+ both inhibited the enzyme activities. Enzymatic saccharification of wheat bran yielded 253.61 ± 1.7 and 147.5 ± 1.0 mg/g of reducing sugar within 12 and 24 h of incubation when treated with purified α-amylase and cellulase. A more significant amount of 397.7 ± 1.9 mg/g reducing sugars was released from wheat bran due to the synergetic effect of two enzymes. According to scanning electron micrograph analysis, wheat bran was effectively broken down by both enzymes.

Microbial anti-biofilms: types and mechanism of action

Biofilms have been recognized as a serious threat to public health as it protects microbes from antimicrobials, immune defence mechanisms, chemical treatments and nutritional stress. Biofilms are also a source of concern in industries and water treatment because their presence compromises the integrity of equipment. To overcome these problems, it is necessary to identify novel anti-biofilm compounds. Products of microorganisms have been identified as promising broad-spectrum anti-biofilm agents. These natural products include biosurfactants, antimicrobial peptides, enzymes and bioactive compounds. Anti-biofilm products of microbial origin are chemically diverse and possess a broad spectrum of activities against biofilms. The objective of this review is to give an overview of the different types of microbial anti-biofilm products and their mechanisms of action.

α-Amylase purified and characterized from fenugreek (Trigonella foenum-graecum) showed substantial anti-biofilm activity against Staphylococcus aureus MTCC740

Starch hydrolyzing α-amylase from germinated fenugreek (Trigonella foenum-graecum) has been purified 104-fold to apparent electrophoretic homogeneity with a final specific activity of 297.5 units/mg. SDS-PAGE of the final preparation revealed a single protein band of 47.5 kDa, supported by LC/MS analysis and size-exclusion chromatography on the Superdex 200 (ÄKTA-FPLC). α-Amylase exhibited maximum activity at pH 5.5. An activation energy (Ea) of 9.12 kcal/mol was found to exist in the temperature range of 20 to 90 °C. When substrate concentrations were evaluated between 0.5 and 10 mg/mL, the Km and Vmax values for starch were observed to be 1.12 mg/mL and 384.14 μmol/min/mg, respectively. The major substrate starch exhibited high specificity for fenugreek α-amylase. In the presence of EDTA (5 mM), the activity was lost, however, it could be largely reversed with the addition of calcium. Furthermore, an effort was made to assess the ability of fenugreek seed-derived partially purified (DEAE-cellulose enzyme) and purified α-amylase to disperse inside 48 h-old biofilms of Staphylococcus aureus MTCC740. The outcomes clearly demonstrated that the purified and partially purified α-amylase both exhibited strong biofilm dispersion activity.

The Inhibitory Effects of Amylase and Streptokinase on Minimum Inhibitory Concentration of Antibiotics Used to Treat Gram Negative Bacteria Biofilm Infection on Indwelling Devices

The study evaluated and compared the effect of adding streptokinase and amylase to antibiotics that are already used in clinical practice to treat Gram negative bacteria biofilm infection on indwelling devices on the antibiotics' minimum inhibitory concentration (MIC). 24 h-old biofilms were developed on 96-well plate with eight clinical isolates. MIC of amikacin, cefepime, ceftazidime, colistin, meropenem, and piperacillin-tazobactam, on biofilms were measured before and after the addition of 25 U/ml streptokinase and 25 μg/ml amylase with microplate reader. The addition of streptokinase reduces the MICs of cefepime, ceftazidime, colistin, meropenem from (16, 16, 8, 4 μg/ml) to (8, 1, 1, 0.5 μg/ml) in Escherichia coli (isolate 1). While the addition of amylase reduces the MICs of only cefepime, ceftazidime from (16, 16 μg/ml) to (2, 4 μg/ml) in E. coli (isolate 1). In Pseudomonas aeruginosa (isolate 4), the MICs of amikacin, cefepime, ceftazidime, colistin and meropenem (64, 16, 32, 4, 32 μg/ml) reduced to (2, 1, 0.5, 0.25, 0.5 μg/ml) with streptokinase and (4, 4, 4, 2, 0.5 μg/ml) with amylase respectively. Similar inhibitions were seen in Pseudomonas putida, Proteus mirabilis. We can conclude that the addition of streptokinase and amylase were effective in reducing the MICs of antibiotics that are commonly used to treat Gram negative bacteria biofilm infection on indwelling devices, thereby increasing susceptibility of bacteria to antibiotics. Streptokinase obviously had a greater effect than amylase, implying that it should be prioritized in future in vivo and clinical studies to obtain successful therapy with antibiotics on biofilm infections.

Modulating the Microbiome for Crohn's Disease Treatment

The central role of the gut microbiota in the regulation of health and disease has been convincingly demonstrated. Polymicrobial interkingdom interactions between bacterial (the bacteriome) and fungal (the mycobiome) communities of the gut have become a prominent focus for development of potential therapeutic approaches. In addition to polymicrobial interactions, the complex gut ecosystem also mediates interactions between the host and the microbiota. These interactions are complex and bidirectional; microbiota composition can be influenced by host immune response, disease-specific therapeutics, antimicrobial drugs, and overall ecosystems. However, the gut microbiota also influences host immune response to a drug or therapy by potentially transforming the drug's structure and altering bioavailability, activity, or toxicity. This is especially true in cases where the gut microbiota has produced a biofilm. The negative ramifications of biofilm formation include alteration of gut permeability, enhanced antimicrobial resistance, and alteration of host immune response effectiveness. Natural modulation of the gut microbiota, using probiotic and prebiotic approaches, may also be used to affect the host microbiome, a type of "natural" modulation of the host microbiota composition. In this review, we discuss potential bidirectional interactions between microbes and host, and we describe the changes in gut microbiota induced by probiotic and prebiotic approaches as well as their potential clinical consequences, including biofilm formation. We outline a systematic approach to designing probiotics capable of altering the host microbiota in disease states, using Crohn's disease as a model chronic disease. Understanding how the effective changes in the microbiome may enhance treatment efficacy may unlock the possibility of modulating the gut microbiome to improve treatment using a natural approach.

Discovery of Novel Resistance Mechanisms of Vibrio parahaemolyticus Biofilm against Aminoglycoside Antibiotics

Inappropriate use of antibiotics eventually leads to the emergence of antibiotic-resistant strains and invalidates the treatment of infectious diseases. Aminoglycoside antibiotics (AGAs) are a class of broad-spectrum cationic antibiotics widely used for the treatment of Gram-negative bacterial infections. Understanding the AGA resistance mechanism of bacteria would increase the efficacy of treating these infections. This study demonstrates a significant correlation between AGA resistance and the adaptation of biofilms by Vibrio parahaemolyticus (VP). These adaptations were the result of challenges against the aminoglycosides (amikacin and gentamicin). Confocal laser scanning microscope (CLSM) analysis revealed an enclosure type mechanism where the biological volume (BV) and average thickness (AT) of V. parahaemolyticus biofilm were significantly positively correlated with amikacin resistance (BIC) (p < 0.01). A neutralization type mechanism was mediated by anionic extracellular polymeric substances (EPSs). The biofilm minimum inhibitory concentrations of amikacin and gentamicin were reduced from 32 µg/mL to 16 µg/mL and from 16 µg/mL to 4 µg/mL, respectively, after anionic EPS treatment with DNase I and proteinase K. Here, anionic EPSs bind cationic AGAs to develop antibiotic resistance. Transcriptomic sequencing revealed a regulatory type mechanism, where antibiotic resistance associated genes were significantly upregulated in biofilm producing V. parahaemolyticus when compared with planktonic cells. The three mechanistic strategies of developing resistance demonstrate that selective and judicious use of new antibiotics are needed to win the battle against infectious disease.

Involvement of Versatile Bacteria Belonging to the Genus Arthrobacter in Milk and Dairy Products

Milk is naturally a rich source of many essential nutrients; therefore, it is quite a suitable medium for bacterial growth and serves as a reservoir for bacterial contamination. The genus Arthrobacter is a food-related bacterial group commonly present as a contaminant in milk and dairy products as primary and secondary microflora. Arthrobacter bacteria frequently demonstrate the nutritional versatility to degrade different compounds even in extreme environments. As a result of their metabolic diversity, Arthrobacter species have long been of interest to scientists for application in various industry and biotechnology sectors. In the dairy industry, strains from the Arthrobacter genus are part of the microflora of raw milk known as an indicator of hygiene quality. Although they cause spoilage, they are also regarded as important strains responsible for producing fermented milk products, especially cheeses. Several Arthrobacter spp. have reported their significance in the development of cheese color and flavor. Furthermore, based on the data obtained from previous studies about its thermostability, and thermoacidophilic and thermoresistant properties, the genus Arthrobacter promisingly provides advantages for use as a potential producer of β-galactosidases to fulfill commercial requirements as its enzymes allow dairy products to be treated under mild conditions. In light of these beneficial aspects derived from Arthrobacter spp. including pigmentation, flavor formation, and enzyme production, this bacterial genus is potentially important for the dairy industry.

Combined Anti-Biofilm Enzymes Strengthen the EradicateEffect of Vibrio parahaemolyticus Biofilm: Mechanism on cpsA-J Expression and Application on Different Carriers

Vibrio parahaemolyticus is a human foodborne pathogen, and it can form a mature biofilm on food and food contact surfaces to enhance their resistance to antibacterial agents. In this study, the effect of anti-biofilm enzymes (combined lipase, cellulase and proteinase K) on the inhibition and eradication of pathogen biofilm was evaluated. The biofilm content of V. parahaemolyticus showed the highest level at the incubation time of 24 h, and the combined enzymes significantly inhibited the biofilm’s development. The biofilm’s inhibition and eradication rate at an incubation time of 24 h was 89.7% and 66.9%, respectively. The confocal laser scanning microscopic images confirmed that the microcolonies’ aggregation and the adhesion of biofilm were inhibited with the combined enzyme treatment. Furthermore, combined enzymes also decreased the concentration of exopolysaccharide (EPS) and disrupted the EPS matrix network, wherein the expression of the EPS-related gene, cpsA-J, was likewise suppressed. The combined enzymes showed an excellent inhibition effect of V. parahaemolyticus biofilm on different carriers, with the highest inhibition rate of 59.35% on nonrust steel plate. This study demonstrates that the combined enzyme of lipase, cellulase and proteinase K could be a novel candidate to overcome biofilm’s problem of foodborne pathogens in the food industry.

Purification and Characterization of Strong Simultaneous Enzyme Production of Protease and α-Amylase from an Extremophile-Bacillus sp. FW2 and Its Possibility in Food Waste Degradation

Microbial enzymes such as protease and amylase are valuable enzymes with various applications, widely investigated for their applications in degradation of organic waste, biofuel industries, agricultural, pharmaceuticals, chemistry, and biotechnology. In particular, extremophiles play an important role in biorefinery due to their novel metabolic products such as high value catalytic enzymes that are active even under harsh environmental conditions. Due to their potentials and very broad activities, this study isolated, investigated, and characterized the protease- and amylase-producing bacterial strain FW2 that was isolated from food waste. Strain FW2 belongs to the genus Bacillus and was found to be closest to Bacillus amyloliquefaciens DSM 7T with a similarity of 99.86%. This strain was able to degrade organic compounds at temperatures from −6 °C to 75 °C (but weak at 80 °C) under a wide pH range (4.5–12) and high-salinity conditions up to 35% NaCl. Maximum enzyme production was obtained at 1200 ± 23.4 U/mL for protease and 2400 ± 45.8 U/mL for amylase for 4 days at pH 7–7.5, 40–45 °C, and 0–10% NaCl. SDS-PAGE analysis showed that the molecular weights of purified protease were 28 kDa and 44 kDa, corresponding to alkaline protease (AprM) and neutral protease (NprM), respectively, and molecular weight of α-amylase was 55 kDa. Degradation food waste was determined after 15 days, observing a 69% of volume decrease. A potential commercial extremozyme-producing bacteria such as strain FW2 may be a promising contributor to waste degradation under extreme environmental conditions.