Similarities and specificities of fungal keratinolytic proteases: comparison of keratinases of Paecilomyces marquandii and Doratomyces microsporus to some known proteases

Proteases, a powerful biochemical tool in the service of medicine, clinical and pharmaceutical

Proteases, enzymes that hydrolyze peptide bonds, have various applications in medicine, clinical applications, and pharmaceutical development. They are used in cancer treatment, wound debridement, contact lens cleaning, prion degradation, biofilm removal, and fibrinolytic agents. Proteases are also crucial in cardiovascular disease treatment, emphasizing the need for safe, affordable, and effective fibrinolytic drugs. Proteolytic enzymes and protease biosensors are increasingly used in diagnostic and therapeutic applications. Advanced technologies, such as nanomaterials-based sensors, are being developed to enhance the sensitivity, specificity, and versatility of protease biosensors. These biosensors are becoming effective tools for disease detection due to their precision and rapidity. They can detect extracellular and intracellular proteases, as well as fluorescence-based methods for real-time and label-free detection of virus-related proteases. The active utilization of proteolytic enzymatic biosensors is expected to expand significantly in biomedical research, in-vitro model systems, and drug development. We focused on journal articles and books published in English between 1982 and 2024 for this study.

Effects of various substances on the binding of keratin monomers to S. maltophilia DHHJ cells for the induction of keratinase production

Biodegradation effectiveness of S. maltophilia DHHJ is determined by its ability to attach to the hydrolyzed feather keratin monomers. This binding capacity can be influenced by many components in the culture medium. Keratin monomers from feathers or those produced by gene overexpression can induce keratinase production in S. maltophilia DHHJ, and several proteases lack the ability to degrade keratin fragments and cysteines. In this study, we co-incubated FITC-labelled keratin monomers with S. maltophilia DHHJ cells in the presence of BSA, DNA, ATP, and several metal ions, and measured fluorescence values and keratinase activity. BSA was found to compete with keratins for cell binding sites, resulting in less keratinase production. DNA did not interfere with cellular binding to keratins revealing unchanged keratinase level. ATP, along with metal ions, enhanced the cellular binding capacity to keratins and increased the production of keratinase by S. maltophilia DHHJ. Fragments of keratin monomers degraded by proteases reduced the ability of cells to bind to keratin and affected enzyme production. Cysteine, a characteristic amino acid of feather keratin, did not have an effect on cellular binding to keratin monomer or on keratinase production. This study will facilitate the tweaking of catalytic parameters to improve feather biodegradation by S. maltophilia DHHJ.

An eco-friendly, water-saving and cost-effective approach to manufacturing machine-washable wool fabric using a broad-temperature-range proteinase (BTRP) and an innovative "pad-steam-pad-cold batch" technique

Nowadays, the Chlorination-Hercosett process dominates the production of machine-washable wool fabric. However, absorbable organic halogens (AOX) generated during the treatment are highly detrimental to human health and the environment. Herein, we developed an innovative pad-steam-pad-cold batch enzymatic treatment with the merit of being eco-friendly, water-saving, and cost-effective to replace traditional high pollution chlorination technique. With the assistance of sodium sulfite or L-cysteine, a broad-temperature-range proteinase (BTRP) can efficiently hydrolyze wool scales during the steaming and cold batch processes. The results indicate that BTRP treatment endows the wool fabric with excellent dimensional stability, acceptable strength loss, and improved wearability properties such as drapability, and air and moisture permeability. This non-chlorination treatment achieves a felting shrinkage of 4.33 % ± 0.28 %, and a tensile strength loss of 12.36 % ± 1.46 %. Furthermore, colored wool samples treated with BTRP were shown to maintain their original color performance, including K/S value and various color fastness properties. Pilot plant tests indicates that this technique remarkably decreased the cost of chemical materials and water usage during enzymatic treatment. As an ideal alternative substitute for the Chlorination-Hercosett treatment, the "pad-steam-pad-cold batch" approach based on BTRP treatment can be utilized for commercial production of pristine and colored machine-washable wool garments.

Transcriptomics Reveals the Mechanism of Purpureocillium lilacinum GZAC18-2JMP in Degrading Keratin Material

Microbial degradation of keratin is characterized by its inherent safety, remarkable efficiency, and the production of copious degradation products. All these attributes contribute to the effective management of waste materials at high value-added and in a sustainable manner. Microbial degradation of keratin materials remains unclear, however, with variations observed in the degradation genes and pathways among different microorganisms. In this study, we sequenced the transcriptome of Purpureocillium lilacinum GZAC18-2JMP mycelia on control medium and the medium containing 1% feather powder, analyzed the differentially expressed genes, and revealed the degradation mechanism of chicken feathers by P. lilacinum GZAC18-2JMP. The results showed that the chicken feather degradation rate of P. lilacinum GZAC18-2JMP reached 64% after 216 h of incubation in the fermentation medium, reaching a peak value of 148.9 μg·mL-1 at 192 h, and the keratinase enzyme activity reached a peak value of 211 U·mL-1 at 168 h, which revealed that P. lilacinum GZAC18-2JMP had a better keratin degradation effect. A total of 1001 differentially expressed genes (DEGs) were identified from the transcriptome database, including 475 upregulated genes and 577 downregulated genes. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis of the DEGs revealed that the metabolic pathways related to keratin degradation were mainly sulfur metabolism, ABC transporters, and amino acid metabolism. Therefore, the results of this study provide an opportunity to gain further insight into keratin degradation and promote the biotransformation of feather wastes.

Enzymes for dermatological use

Skin is the ultimate barrier between body and environment and prevents water loss and penetration of pathogens and toxins. Internal and external stressors, such as ultraviolet radiation (UVR), can damage skin integrity and lead to disorders. Therefore, skin health and skin ageing are important concerns and increased research from cosmetic and pharmaceutical sectors aims to improve skin conditions and provide new anti-ageing treatments. Biomolecules, compared to low molecular weight drugs and cosmetic ingredients, can offer high levels of specificity. Topically applied enzymes have been investigated to treat the adverse effects of sunlight, pollution and other external agents. Enzymes, with a diverse range of targets, present potential for dermatological use such as antioxidant enzymes, proteases and repairing enzymes. In this review, we discuss enzymes for dermatological applications and the challenges associated in this growing field.

On the interactions involving serine proteases obtained from Monacrosporium thaumasium (Ascomycota: Orbiliomycetes) and deoxyribonucleic acid (DNA): biological macromolecules in action

The use of force spectroscopy approaches performed with optical tweezers can be very useful in determining the binding modes and the physical chemistry of DNA interactions with ligands, from small drugs to proteins. Helminthophagous fungi, on the other hand, have important enzyme secretion mechanisms for various purposes, and the interactions between such enzymes and nucleic acids are very poorly studied. Therefore, the main goal of the present work was to investigate, at the molecular level, the mechanisms of interaction between fungal serine proteases and the double-stranded (ds) DNA molecule. Experimental assays performed with this single molecule technique consist in exposing different concentrations of the protease of this fungus to dsDNA until saturation while monitoring the changes on the mechanical properties of the macromolecular complexes formed, from where the physical chemistry of the interaction can be deduced. It was found that the protease binds strongly to the double-helix, forming aggregates and changing the persistence length of the DNA molecule. The present work thus allowed us to infer information at the molecular level on the pathogenicity of these proteins, an important class of biological macromolecules, when applied to a target specimen.

Research progress on the degradation mechanism and modification of keratinase

Keratin is regarded as the main component of feathers and is difficult to be degraded by conventional proteases, leading to substantial abandonment. Keratinase is the only enzyme with the most formidable potential for degrading feathers. Although there have been in-depth studies in recent years, the large-scale application of keratinase is still associated with many problems. It is relatively challenging to find keratinase not only with high activity but could also meet the industrial application environment, so it is urgent to exploit keratinase with high acid and temperature resistance, strong activity, and low price. Therefore, researchers have been keen to explore the degradation mechanism of keratinases and the modification of existing keratinases for decades. This review critically introduces the basic properties and mechanism of keratinase, and focuses on the current situation of keratinase modification and the direction and strategy of its future application and modification. KEY POINTS: •The research status and mechanism of keratinase were reviewed. •The new direction of keratinase application and modification is discussed. •The existing modification methods and future modification strategies of keratinases are reviewed.

Isolation, Identification and Characterization of Keratin-Degrading Streptomyces rochei AM8

Keratinolytic microorganisms are highly valuable for decomposition of poultry waste. This study aimed to isolate keratin-decomposing actinobacteria from poultry farm soils and examine their capacity to decompose feathers. Soil samples were placed in a basal medium with feather meal, which is a deposit of carbon and nitrogen. Nine actinobacterial strains were isolated. Actinobacteria were cultured in the media to show clear feather-decomposing potential. Actinobacterial strains were identified using 16S ribosomal RNA (rRNA) sequencing as being related to Streptomyces rochei AM8. Thus, the supernatant of S. rochei AM8 exhibited keratinolytic enzyme activity. Increased biodecomposition of feathers was recorded in a keratinase assay (0.782 U/mL) for separated cultures. The ability of the selected microorganisms to decompose feathers may be an effective biotechnological solution for managing feather waste from poultry.

Chicken Feather Waste Valorization Into Nutritive Protein Hydrolysate: Role of Novel Thermostable Keratinase From Bacillus pacificus RSA27

Microbial keratinases exhibit a momentous role in converting keratin biowastes into exceedingly valuable protein supplements. This study reports a novel, highly stable keratinase from Bacillus pacificus RSA27 for the production of pure peptides rich in essential amino acids from chicken feathers. Purified keratinase showed a specific activity of 38.73 U/mg, 2.58-fold purification, and molecular weight of 36 kDa. Kinetic studies using a chicken feather as substrate report K_m and V_max values of 5.69 mg/ml and 142.40 μg/ml/min, respectively, suggesting significant enzyme-substrate affinity/biocatalysis. Identification and in silico structural-functional analysis of keratinase discovered the presence of distinct amino acid residues and their positions. Besides, keratinase possesses a high-affinity calcium-binding site (Asp¹²⁸, Leu¹⁶², Asn¹⁶⁴, Ile¹⁶⁶, and Val¹⁶⁸) and a catalytic triad of Asp¹¹⁹, His¹⁵¹, and Ser³⁰⁸, known attributes of serine protease (subtilisin family). Furthermore, a scale-up to 5 L fermenter revealed complete feather hydrolysis (94.5%) within 24 h with high activity (789 U/ml) and total amino acid of 153.97 μmol/ml. Finally, cytotoxicity evaluation of protein hydrolysate resulted in negligible cytotoxic effects (1.02%) on the mammalian hepatoblastoma cell line, signifying its potential biotechnological applications.

A Newly Isolated Strain Lysobacter brunescens YQ20 and Its Performance on Wool Waste Biodegradation

Wool keratin is difficult to degrade as comparing to feathers because of its tough secondary structure. In order to develop an approach for high-value utilization of wool fiber waste by keratinolytic microorganisms, which is produced from shearing, weaving, and industrial processing of wool, screening of wool-degrading bacterium with high degradation efficiency were performed in this study. To this end, Lysobacter brunescens YQ20 was identified and characterized. The optimized conditions for wool degradation were pH 9.0 and 37°C with 20% liquid volume of Erlenmeyer flask. After fermentation, 15 essential amino acids were detected when wool fiber waste was fermented. The total amino acids produced from 1% wool per hour were 13.7 mg/L. The concentration was 8.6-fold higher than that produced by the strain Stenotrophomonas maltophilia BBE11-1, which had previously been reported to have the highest wool-degrading capacity. Our study reports the first Lysobacter strain that exhibits efficient wool degradation and yields higher concentrations of amino acids than previously reported strains. Whole-genome sequencing indicated that there were 18 keratinase-like genes in the genome of YQ20, which exhibited a long evolutionary distance from those of Bacillus. Therefore, L. brunescens YQ20 may have applications in the environmentally friendly management of wool waste as fertilizer in agriculture.

Keratinase improves the growth performance, meat quality and redox status of broiler chickens fed a diet containing feather meal

The objective of this study was to assess the effects of dietary supplementation of keratinase on the production of broilers fed a diet containing feather meal. A total of 162 1-d-old Cobb 500 male broiler (n = 9 cages/diet with 6 chicks/cage) were randomly allocated to 3 dietary treatments. The broilers were fed a corn-soybean-feather meal based diet (BD), or BD supplemented with keratinase at 100,000 or 200,000 U/kg for 6 weeks. Compared to the control, dietary supplementation with 200,000 U/kg keratinase increased (P < 0.05) body weight gain (3.6–4.3%) and reduced feed conversion ratio (2.4–5.6%) during the various experimental periods, and also improved (P < 0.05) apparent total tract digestibility of ash and calcium by 45.0% and 8.8%, respectively. Meanwhile, dietary supplementation of keratinase at 100,000 U/kg reduced (P < 0.05) the drip loss (29.2%), while 200,000 U/kg keratinase supplementation increased (P < 0.05) the pH value (1.6%) at 45 min and decreased (P < 0.05) the lightness (L* value; 13.6%) and drip loss (22.1%) of pectoral muscle. Moreover, dietary supplementation of keratinase at both levels of 100,000 and 200,000 U/kg increased (P < 0.05) Glutathione peroxidase activity (82.5–87.5%) and decreased the Malondialdehyde concentration (14.5–18.3%) in the pectoral muscle. In conclusion, dietary supplementation of keratinase at 200,000 U/kg can improve the performance, meat quality, apparent total tract digestibility of nutrients, and redox status of broiler chickens fed a diet containing feather meal.

Exoproduction and Biochemical Characterization of a Novel Serine Protease from Ornithinibacillus caprae L9T with Hide-Dehairing Activity

This study is the first report on production and characterization of the enzyme from an Ornithinibacillus species. A 4.2-fold increase in the extracellular protease (called L9^T) production from Ornithinibacillus caprae L9^T was achieved through the one-factor-at-a-time approach and response surface methodological optimization. L9^T protease exhibited a unique protein band with a mass of 25.9 kDa upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This novel protease was active over a range of pH (4-13), temperatures (30-80°C) and salt concentrations (0-220 g/l), with the maximal activity observed at pH 7, 70°C and 20 g/l NaCl. Proteolytic activity was upgraded in the presence of Ag⁺, Ca²⁺ and Sr²⁺, but was totally suppressed by 5 mM phenylmethylsulfonyl fluoride, which suggests that this enzyme belongs to the serine protease family. L9^T protease was resistant to certain common organic solvents and surfactants; particularly, 5 mM Tween 20 and Tween 80 improved the activity by 63 and 15%, respectively. More importantly, L9^T protease was found to be effective in dehairing of goatskins, cowhides and rabbit-skins without damaging the collagen fibers. These properties confirm the feasibility of L9^T protease in industrial applications, especially in leather processing.

Fungal Proteases as Emerging Biocatalysts to Meet the Current Challenges and Recent Developments in Biomedical Therapies: An Updated Review

With the increasing world population, demand for industrialization has also increased to fulfill humans' living standards. Fungi are considered a source of essential constituents to produce the biocatalytic enzymes, including amylases, proteases, lipases, and cellulases that contain broad-spectrum industrial and emerging applications. The present review discussed the origin, nature, mechanism of action, emerging aspects of genetic engineering for designing novel proteases, genome editing of fungal strains through CRISPR technology, present challenges and future recommendations of fungal proteases. The emerging evidence revealed that fungal proteases show a protective role to many environmental exposures and discovered that an imbalance of protease inhibitors and proteases in the epithelial barriers leads to the protection of chronic eosinophilic airway inflammation. Moreover, mitoproteases recently were found to execute intense proteolytic processes that are crucial for mitochondrial integrity and homeostasis function, including mitochondrial biogenesis, protein synthesis, and apoptosis. The emerging evidence revealed that CRISPR/Cas9 technology had been successfully developed in various filamentous fungi and higher fungi for editing of specific genes. In addition to medical importance, fungal proteases are extensively used in different industries such as foods to prepare butter, fruits, juices, and cheese, and to increase their shelf life. It is concluded that hydrolysis of proteins in industries is one of the most significant applications of fungal enzymes that led to massive usage of proteomics.

An overview of the use of proteolytic enzymes as exfoliating agents

BACKGROUND

Proteolytic enzymes are biological catalysts that can compose cosmetic formulations: These enzymes are capable of mimicking the desquamation process of the skin, acting as exfoliants. Although enzymatic exfoliation is not new and commercial products were easily found, there is a lack of scientific literature about this topic.

METHODS

A search was carried out until 2021 in different scientific databases (Web of Science, Scopus, Scielo, PubMed, etc.). In vitro and in vivo studies that evaluated the application of enzymes aiming to exfoliate the skin or with a similar cosmetic or dermatological application were selected.

RESULTS

Only 11 articles were found, and, among them, few studies applied enzymes as exfoliants in clinical trials. Nevertheless, the results demonstrate that the enzymes can exfoliate the skin and improve some desired characteristics of the organ. Papain, bromelain, keratinases, and microbial proteases are some enzymes already applied as exfoliants. The study of pH, temperature, and stabilization of the enzymes in cosmetic formulations were also demonstrated to be important aspects to be evaluated, principally in preventing loss of enzyme activity and possible allergens/irritations on the skin.

CONCLUSION

This literature review showed the main aspects that should be evaluated before considering producing or applying proteolytic enzymes in exfoliation products/procedures. The use of enzymatic exfoliation has potential in the cosmetic industry. Hence, further robust in vivo studies are needed before the enzymatic exfoliation can be recommended with safety as a treatment modality in the current conditions.

Fungal decomposition of chicken-feather waste in submerged and solid-state fermentation

Poultry industry is expanding rapidly and producing million tons of feather waste annually. Massive production of keratinaceous byproducts in the form of industrial wastes throughout the world necessitates its justified utilization. Chemical treatment of keratin waste is proclaimed as an eco-destructive approach by various researchers since it generates secondary pollutants. Keratinase released by a variety of microbes (bacteria and fungi) can be used for the effective treatment of keratin waste. Microbial degradation of keratin waste is an emerging and eco-friendly approach and offers dual benefits, i.e., treatment of recalcitrant pollutant (keratin) and procurement of a commercially important enzyme (keratinase). This study involves the isolation, characterization, and potential utility of fungal species for the degradation of chicken-feather waste through submerged and solid-state fermentation. The isolated fungus was identified and characterized as Aspergillus (A.) flavus. In a trial of 30 days, it was appeared that 74 and 8% feather weight was reduced through sub-merged and solid-state fermentation, respectively by A. flavus. The pH of the growth media in submerged fermentation was changed from 4.8 to 8.35. The exploited application of keratinolytic microbes is, therefore, recommended for the treatment of keratinaceous wastes to achieve dual benefits of remediation.

Keratinases Produced by Aspergillus stelliformis, Aspergillus sydowii, and Fusarium brachygibbosum Isolated from Human Hair: Yield and Activity

Twenty fungal strains belonging to 17 species and isolated from male scalp hair were tested for their capacity to hydrolyze keratinous material from chicken feather. The identification of the three most efficient species was confirmed by sequencing of the internal transcribed spacer (ITS) region of rDNA. Activities of fungal keratinases produced by Aspergillus stelliformis (strain AUMC 10920), A. sydowii (AUMC 10935), and Fusarium brachygibbosum (AUMC 10937) were 113, 120, and 130 IU mg⁻¹ enzymes, respectively. The most favorable conditions were at pH 8.0 and 50 °C. Keratinase activity was markedly inhibited by EDTA and metal ions Ca⁺², Co⁺², Ni⁺², Cu⁺², Fe⁺², Mg⁺², and Zn⁺², with differences between the fungal species. To the best of our knowledge, this is the first study on the activity of keratinase produced by A. stelliformis, A. sydowii, and F. brachygibbosum. F. brachygibbosum keratinase was the most active, but the species is not recommended because of its known phytopathogenicty. Aspergillus sydowii has many known biotechnological solutions and here we add another application of the species, as producer of keratinases. We introduce A. stelliformis as new producer of active fungal keratinases for biotechnological solutions, such as in the management of keratinous waste in poultry industry.

Chicken Feather Waste Hydrolysate as a Superior Biofertilizer in Agroindustry

Billions of tons of keratinous waste in the form of feathers, antlers, bristles, claws, hair, hoofs, horns, and wool are generated by different industries and their demolition causes environmental deterioration. Chicken feathers have 92% keratin that can be a good source of peptides, amino acids, and minerals. Traditional methods of feather hydrolysis require large energy inputs, and also reduce the content of amino acids and net protein utilization values. Biological treatment of feathers with keratinolytic microbes is a feasible and environmental favorable preference for the formulation of hydrolysate that can be used as bioactive peptides, protein supplement, livestock feed, biofertilizer, etc. The presence of amino acids, soluble proteins, and peptides in hydrolysate facilitates the growth of microbes in rhizosphere that promotes the uptake and utilization of nutrients from soil. Application of hydrolysate enhances water holding capacity, C/N ratio, and mineral content of soil. The plant growth promoting activities of hydrolysate potentiates its possible use in organic farming, and improves soil ecosystem and microbiota. This paper reviews the current scenario on the methods available for management of keratinous waste, nutritional quality of hydrolysate generated using keratinolytic microbes, and its possible application as plant growth promoter in agroindustry.

Metabolomic analysis of Trichophyton rubrum and Microsporum canis during keratin degradation

Keratin is important and needed for the growth of dermatophytes in the host tissue. In turn, the ability to invade keratinised tissues is defined as a pivotal virulence attribute of this group of medically important fungi. The host–dermatophyte interaction is accompanied by an adaptation of fungal metabolism that allows them to adhere to the host tissue as well as utilize the available nutrients necessary for their survival and growth. Dermatophyte infections pose a significant epidemiological and clinical problem. Trichophyton rubrum is the most common anthropophilic dermatophyte worldwide and its typical infection areas include skin of hands or feet and nail plate. In turn, Microsporum canis is a zoophilic pathogen, and mostly well known for ringworm in pets, it is also known to infect humans. The aim of the study was to compare the intracellular metabolite content in the T. rubrum and M. canis during keratin degradation using liquid chromatography system coupled with tandem mass spectrometer (LC-MS/MS). The metabolite “fingerprints” revealed compounds associated with amino acids metabolism, carbohydrate metabolism related to the glycolysis and the tricarboxylic acid cycle (TCA), as well as nucleotide and energy metabolism. The metabolites such as kynurenic acid, l-alanine and cysteine in case of T. rubrum as well as cysteine and riboflavin in case of M. canis were detected only during keratin degradation what may suggest that these compounds may play a key role in the interactions of T. rubrum and M. canis with the host tissue. The metabolomic results were completed by qPCR gene expression assay. Our findings suggest that metabolomic analysis of T. rubrum and M. canis growing in culture media that mimic the dermatophyte infection could allow the understanding of processes involved in the pathogenesis of dermatophytes.

Bio-degradation of Feathers Waste by the Staphylococcus epidermidis P3A

Development of industrialization is directly proportional to the development of nations. Rising industrializations also increase the pollutions. One of them is poultry industry which discharges a huge amount of keratinous waste. The present study focused on the selection of feather degrading bacteria from Barshi region of Maharashtra. Bacterial strains were grown in whole feather broth medium. Out of 16 proteolytic bacterial isolates, 9 feather degrading isolates were selected from the Parande road side feather waste dumping area. Among these isolates, P3A was selected and classified on the basis of morphological and biochemical analysis. 16S rRNA studies confirmed that the isolated strain was Staphylococcus epidermidis. Staphylococcus epidermidis P3A shows 84% feather degradation and 72 U/ml maximum keratinase activity after 96 hrs. The isolate shows potential use in feather waste disposal methods which are safe and environment friendly.

Microbial Keratinase: Next Generation Green Catalyst and Prospective Applications

The search for novel renewable products over synthetics hallmarked this decade and those of the recent past. Most economies that are prospecting on biodiversity for improved bio-economy favor renewable resources over synthetics for the potential opportunity they hold. However, this field is still nascent as the bulk of the available resources are non-renewable based. Microbial metabolites, emphasis on secondary metabolites, are viable alternatives; nonetheless, vast microbial resources remain under-exploited; thus, the need for a continuum in the search for new products or bio-modifying existing products for novel functions through an efficient approach. Environmental distress syndrome has been identified as a factor that influences the emergence of genetic diversity in prokaryotes. Still, the process of how the change comes about is poorly understood. The emergence of new traits may present a high prospect for the industrially viable organism. Microbial enzymes have prominence in the bio-economic space, and proteases account for about sixty percent of all enzyme market. Microbial keratinases are versatile proteases which are continuously gaining momentum in biotechnology owing to their effective bio-conversion of recalcitrant keratin-rich wastes and sustainable implementation of cleaner production. Keratinase-assisted biodegradation of keratinous materials has revitalized the prospects for the utilization of cost-effective agro-industrial wastes, as readily available substrates, for the production of high-value products including amino acids and bioactive peptides. This review presented an overview of keratin structural complexity, the potential mechanism of keratin biodegradation, and the environmental impact of keratinous wastes. Equally, it discussed microbial keratinase; vis-à-vis sources, production, and functional properties with considerable emphasis on the ecological implication of microbial producers and catalytic tendency improvement strategies. Keratinase applications and prospective high-end use, including animal hide processing, detergent formulation, cosmetics, livestock feed, and organic fertilizer production, were also articulated.

Arthroderma tuberculatum and Arthroderma multifidum Isolated from Soils in Rook (Corvus frugilegus) Colonies as Producers of Keratinolytic Enzymes and Mineral Forms of N and S

Keratinolytic fungi representing the genus Arthroderma that were isolated from the soils of a rook (Corvus frugilegus) colony were used as biological agents for the disposal of waste feathers. The aim of this study was to assess the abilities of Arthroderma tuberculatum and Arthroderma multifidum fungi with a varied inflow of keratin matter to biodegrade waste feathers. The evaluation was based on the determination of feather mass loss, the activity of keratinolytic enzymes, and the content of mineral N and S forms. It was found that the activity of protease released by the fungi contributed to an increase in the level of soluble proteins and peptides and the concentration of ammonium ions, as well as alkalization of the culture medium. Keratinase activity was significantly correlated with sulfate release, especially in A. tuberculatum cultures. The strains of A. tuberculatum fungi isolated from the soil with the highest supply of organic matter, i.e., strains III, IV, and V, had the lowest enzymatic activity, compared to the A. multifidum strains, but they released mineral nitrogen and sulfur forms that are highly important for fertilization, as well as nutritionally important peptides and amino acids. A. tuberculatum strains can be used for the management of waste feathers that can be applied in agricultural practice.

The tale of a versatile enzyme: Molecular insights into keratinase for its industrial dissemination

Keratinases are unique among proteolytic enzymes for their ability to degrade recalcitrant insoluble proteins, and they are of critical importance in keratin waste management. Over the past few decades, researchers have focused on discovering keratinase producers, as well as producing and characterizing keratinases. The application potential of keratinases has been investigated in the feed, fertilizer, leathering, detergent, cosmetic, and medical industries. However, the commercial availability of keratinases is still limited due to poor productivity and properties, such as thermostability, storage stability and resistance to organic reagents. Advances in molecular biotechnology have provided powerful tools for enhancing the production and functional properties of keratinase. This critical review systematically summarizes the application potential of keratinase, and in particular certain newly discovered catalytic capabilities. Furthermore, we provide comprehensive insight into mechanistic and molecular aspects of keratinases including analysis of gene sequences and protein structures. In addition, development and current advances in protein engineering of keratinases are summarized and discussed, revealing that the engineering of protein domains such as signal peptides and pro-peptides has become an important strategy to increase production of keratinases. Finally, prospects for further development are also proposed, indicating that advanced protein engineering technologies will lead to improved and additional commercial keratinases for various industrial applications.

Microbial Bioremediation of Feather Waste for Keratinase Production: An Outstanding Solution for Leather Dehairing in Tanneries

In leather industries and tanneries, large amount of wastes has been disposed; which polluting water, soil, and atmosphere and causing serious human health problems. In particular, chemical dehairing process of leather industries produces fair amount of toxic wastes. It is, thus, urgently needed to use alternative processes free from pollution. As more than 90% of keratin is contained in feather, it is desirable to develop bioremediation process using keratinolytic microorganisms. In the present investigation, therefore, we first identified Bacillus cereus and Pseudomonas sp. to be able to produce keratinase. Then, the optimization was performed to maximize the keratinase activity with respect to cultivation temperature, pH, and incubation time. Moreover, the effects of metal ions and various substrates on keratinase activity were also investigated. The result indicates that keratinase activity became maximum at 50°C for both strains, whereas the optimal pH was 10.0 for B. cereus and 7.0 for Pseudomonas sp. The highest keratinase activity of 74.66 ± 1.52 U/mL was attained by B. cereus, whereas 57.66 ± 2.52 U/mL was attained by Pseudomonas sp. Enzymatic dehairing efficiency of leathers was also compared with chemical dehairing (Na₂S and CaO), where complete dehairing was achieved by treating them with crude keratinase. Partial enzyme purification was performed by acetone precipitation. Batch cultivation of B. cereus using 1 L fermentor indicates a potential candidate for large-scale keratinase production. Thus, keratinase enzyme by degrading poultry wastes (feather) can be an alternative approach to chemical dehairing in leather industries, thus preventing environmental pollution through bioremediation.

Comprehensive insights into microbial keratinases and their implication in various biotechnological and industrial sectors: A review

Enormous masses of keratinous wastes are annually accumulated in the environment as byproducts of poultry processing and agricultural wastes. Keratin is a recalcitrant fibrous protein, which represents the major constituent of various keratin-rich wastes, which released into the environment in the form of feathers, hair, wool, bristle, and hooves. Chemical treatment methods of these wastes resulted in developing many hazardous gases and toxins to the public health, in addition to the destruction of several amino acids. Accordingly, microbial keratinases have been drawing much interest as an eco-friendly approach to convert keratinous wastes into valuable products. Numerous keratinolytic microorganisms have been identified, which revealed the competence to hydrolyze keratins into peptides and amino acids. Several types of keratinolytic proteases have been produced that possess diverse biochemical characteristics, conferring them the versatility for implementing in multifarious applications such as detergents, leather and textile industries, animal feeding, and production of bio-fertilizers, in addition to medical and pharmaceutical treatments. This review article emphasizes the significance of keratinases and keratinase based-products via comprehensive insights into the keratin structure, diversity of keratinolytic microorganisms, and mechanisms of keratin hydrolysis. Furthermore, we discuss the biochemical properties of the produced keratinases and their feasible applications in diverse disciplines.

HacA Governs Virulence Traits and Adaptive Stress Responses in Trichophyton rubrum

The ability of fungi to sense environmental stressors and appropriately respond is linked to secretory system functions. The dermatophyte infection process depends on an orchestrated signaling regulation that triggers the transcription of genes responsible for adherence and penetration of the pathogen into host-tissue. A high secretion system is activated to support the host-pathogen interaction and assures maintenance of the dermatophyte infection. The gateway of secretion machinery is the endoplasmic reticulum (ER), which is the primary site for protein folding and transport. Current studies have shown that ER stress that affects adaptive responses is primarily regulated by UPR and supports fungal pathogenicity; this has been assessed for yeasts and Aspergillus fumigatus, in regard to how these fungi cope with host environmental stressors. Fungal UPR consists of a transmembrane kinase sensor (Ire1/IreA) and a downstream target Hac1/HacA. The active form of Hac is achieved via non-spliceosomal intron removal promoted by endonuclease activity of Ire1/IreA. Here, we assessed features of HacA and its involvement in virulence and susceptibility in Trichophyton rubrum. Our results showed that exposure to antifungals and ER-stressing agents initiated the activation of HacA from T. rubrum. Interestingly, the activation occurs when a 20 nt fragment is removed from part of the exon-2 and part of intron-2, which in turn promotes the arisen of the DNA binding site motif and a dimer interface domain. Further, we found changes in the cell wall and cellular membrane composition in the ΔhacA mutant as well as an increase in susceptibility toward azole and cell wall disturbing agents. Moreover, the ΔhacA mutant presented significant defects in important virulence traits like thermotolerance and growth on keratin substrates. For instance, the development of the ΔhacA mutant was impaired in co-culture with keratinocytes or human nail fragments. Changes in the pro-inflammatory cytokine release were verified for the ΔhacA mutant during the co-culture assay, which might be related to differences in pathogen-associated molecular patterns (PAMPs) in the cell wall. Together, these results suggested that HacA is an integral part of T. rubrum physiology and virulence, implying that it is an important molecular target for antidermatophytic therapy.

Challenges and Opportunities in Identifying and Characterising Keratinases for Value-Added Peptide Production

Keratins are important structural proteins produced by mammals, birds and reptiles. Keratins usually act as a protective barrier or a mechanical support. Millions of tonnes of keratin wastes and low value co-products are generated every year in the poultry, meat processing, leather and wool industries. Keratinases are proteases able to breakdown keratin providing a unique opportunity of hydrolysing keratin materials like mammalian hair, wool and feathers under mild conditions. These mild conditions ameliorate the problem of unwanted amino acid modification that usually occurs with thermochemical alternatives. Keratinase hydrolysis addresses the waste problem by producing valuable peptide mixes. Identifying keratinases is an inherent problem associated with the search for new enzymes due to the challenge of predicting protease substrate specificity. Here, we present a comprehensive review of twenty sequenced peptidases with keratinolytic activity from the serine protease and metalloprotease families. The review compares their biochemical activities and highlights the difficulties associated with the interpretation of these data. Potential applications of keratinases and keratin hydrolysates generated with these enzymes are also discussed. The review concludes with a critical discussion of the need for standardized assays and increased number of sequenced keratinases, which would allow a meaningful comparison of the biochemical traits, phylogeny and keratinase sequences. This deeper understanding would facilitate the search of the vast peptidase family sequence space for novel keratinases with industrial potential.

Recombinant expression and biochemical characterization of a novel keratinase BsKER71 from feather degrading bacterium Bacillus subtilis S1-4

Bacillus subtilis S1-4, isolated from chicken feather could efficiently degrade feathers by secreting several extracellular proteases. In order to get insight into the individual protease involved in keratin hydrolysis, a keratinase designed as BsKER71 was cloned and expressed in Bacillus subtilis WB600. In silico analysis revealed that BsKER71 protein contained a mature protein of 36.1 kDa. Further, purified BsKER71 could hydrolyze a variety of natural proteins, such as fibrous protein, collagen protein, casein, keratin and bovine serum albumin. In addition, this keratinase exhibited high enzyme activity in a wide range of pH and optimal pH of 10.0 and 9.0 in the hydrolysis of casein and keratin, respectively. Similarly, the optimal temperature was 55 °C and 50 °C for the hydrolysis of above two substrates, respectively. The hydrolytic activity was significantly inhibited by phenylmethanesulfonyl fluoride (PMSF), indicating the presence of serine residue in the active site. Moreover, ethylenediaminetetraacetic acid (EDTA) and phenanthroline moderately inhibited the hydrolytic activity. The catalytic activity was stimulated by Mg²⁺ and Ca²⁺, but greatly inhibited by Cu²⁺. Furthermore, several chemicals exhibited different effects on the hydrolysis of casein and keratin by BsKER71. These results provided a better understanding of BsKER71 from feather degrading bacterium B. subtilis S1-4.

Alternative Splicing in Heat Shock Protein Transcripts as a Mechanism of Cell Adaptation in Trichophyton rubrum

Heat shock proteins (HSPs) are involved in critical processes like host tissue invasion, resistance, and pathogenicity in dermatophytes. RNA-Seq analysis of Trichophyton rubrum exposed to undecanoic acid (UDA) revealed intron retention events in HSP transcripts. Because HSPs are modulated in response to various stimuli and as alternative splicing (AS) can result in a broad diversity in the proteome of eukaryotic cells, our objective was to confirm the aforementioned retention events, investigating their consequences and extent. Furthermore, we aimed to determine: (1) the expression profile of HSP genes in an infection-like scenario and (2) the importance of Hsp90 for the keratinolytic potential of T. rubrum. RT and qPCR analyses comparing the exposure to UDA and terbinafine (TRB) confirmed the presence of two mRNA isoforms of the hsp7-like gene, with distinct expression patterns in response to UDA and TRB. The HSP expression profile revealed two upregulated, three downregulated, and four unmodulated transcripts; Hsp90 inhibition by 17-AAG resulted in a significant decrease in keratinolytic potential at 37 °C. Altogether, these results broaden the current knowledge on the importance of HSP-mediated pathways for cell adaptation and other aspects of dermatophyte biology, indicating that HSP network proteins can be potential targets for antifungal therapy.

Cloning and expression of a thermostable keratinase gene from Thermoactinomyces sp. YT06 in Escherichia coli and characterization of purified recombinant enzymes

The feather-degrading strain Thermoactinomyces sp. YT06 secretes an extracellular keratinolytic protease (KERTYT); however, the gene encoding this protease remains unknown. The kerT1 gene (1170 bp) encoding keratinase was cloned and expressed in Escherichia coli BL21(DE3). Purified recombinant keratinase (rKERTYT) was achieved at a yield of 39.16% and 65.27-fold purification with a specific activity of 1325 U/mg. It was shown that rKERTYT has many similarities to the native enzyme (KERTYT) by characterization of rKERTYT. The molecular weight of rKERTYT secreted by recombinant E. coli was approximately 28 kDa. The optimal temperature and the pH values of rKERTYT were 65 °C and 8.5, respectively, and the protein remained stable from 50 to 60 °C and pH 6-11. The keratinase was strongly inhibited by phenyl methane sulfonyl fluoride (PMSF), suggesting that it belongs to the serine protease family. It was significantly activated by Mn²⁺ and β-mercaptoethanol (β-Me). rKERTYT showed stability and retained over 80% activity with the existence of organic solvents such as acetone, methylbenzene and dimethyl sulfoxide. These findings indicated that rKERTYT will be a promising candidate for the enzymatic processing of keratinous wastes.

Feather degrading, phytostimulating, and biocontrol potential of native actinobacteria from North Eastern Indian Himalayan Region

Twelve actinobacterial strains were isolated from tomato rhizospheric soil from Manipur, a state in North East Indian Himalayan Region and screened for keratinolytic and plant growth promoting traits. Nine promising isolates were identified as Streptomyces species using partial 16S rRNA gene sequencing. Among the seven isolates showing chicken feather degradation activity, three keratinolytic strains RCM-SSR-2, -6, and -12 were found to be the most efficient feather degrading strains achieving 90% feather weight loss within 48 h of incubation. They also showed maximum keratinase and soluble peptide production. Strain RCM-SSR-2, -5, -6, -8, and -11 showed positive results for all plant growth promoting traits tested. Maximum indole-3-acetic acid production was exhibited by RCM-SSR-6. Strain RCM-SSR-1, -2, -5, -6, -9, and -11 showed antagonistic activity against three important plant pathogens. Feather hydrolysate of RCM-SSR-6 was also evaluated for in vitro seed germination test using garden pea seeds. Higher concentration of feather protein hydrolysate (3 mg ml^-1 ) inhibited shoot and root length of the germinating embryo. However, lower concentration (0.01 mg ml^-1 ) of feather protein hydrolysate promoted seed germination. Among the 12 strains, four isolates namely RCM-SSR-1, -2, -5, and -6 were found to be promising as multi-traits plant growth promoting rhizobacteria for development of organic fertilizer, phytostimulator, and biocontrol agents.

Effect of keratinase on ileal amino acid digestibility in five feedstuffs fed to growing pigs

Objective

This study was conducted to evaluate the effect of keratinase (KE) on the apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of amino acids (AA) in rice bran, cottonseed meal (CSM), rapeseed meal (RSM), corn distillers dried grains with solubles (DDGS), and peanut meal (PNM).

Methods

Twelve crossbred barrows (Duroc×Landrace×Yorkshire, 50.5±1.4 kg body weight [BW]) fitted with T-cannulas at the terminal ileum were allotted to a 12×6 Youden Square design with 12 diets and 6 periods. The treatment diets included rice bran, CSM, RSM, corn DDGS, PNM, or corn-soybean meal (cSBM) supplemented with 0.05% KE or not. Diets were given to pigs at a level of 3% BW in two equal meals. The endogenous AA losses were the mean results of three previously experiments determined by a same nitrogen-free diet fed to pigs. Pigs had free access to water during the experiment.

Results

The KE supplementation improved (p<0.05) the AID and SID of Met, Thr, Val, Asp, Cys, and Tyr in rice bran. Inclusion of KE increased (p<0.05) the AID and SID of Met and Val in CSM. The KE supplementation decreased (p<0.05) the AID and SID of His in RSM and all measured AA except for Arg, Met, Trp, Val, Gly, and Pro in corn DDGS. There was an increase (p<0.05) in AID and SID of Leu, Ile, Met, Ala, Cys, Ser, and Tyr in PNM supplemented with KE compared with that without KE. Inclusion of KE increased (p<0.05) the AID and SID of crude protein, Leu, Ile, Phe, Thr, Asp, and Ser in cSBM.

Conclusion

This study indicated that KE had different effects on ileal AA digestibility of feedstuffs for growing pigs, which can give some usage directions of KE in swine feed containing those detected feedstuffs.

Molecular and biochemical characterization of a thermostable keratinase from Bacillus altitudinis RBDV1

A thermostable keratinase designated as KBALT was purified from Bacillus altitudinis RBDV1 from a poultry farm in Gujarat, India. The molecular weight of the native KBALT (nKBALT) purified using ammonium sulfate and ion exchange and gel permeation chromatography with a 40% yield and 80-fold purification was estimated to be ~ 43 kDa. The gene for KBALT was successfully cloned, sequenced and expressed in Escherichia coli. Recombinant KBALT (rKBALT) when purified using a single step Ni-NTA His affinity chromatography achieved a yield of 38.20% and a 76.4-fold purification. Comparison of the deduced amino acid sequence of rKBALT with known proteases of Bacillus species and inhibitory effect of PMSF suggest that rKBALT was a subtilisin-like serine protease. Both native and rKBALT exhibited higher activity at 85 °C and pH 8.0 in the presence of Mg²⁺, Mn²⁺, Zn²⁺, Ba²⁺ and Fe³⁺ metal ions. Interestingly, 70% of their activity was retained at temperatures ranging from 35 to > 95 °C. The keratinolytic activity of both nKBALT and rKBALT was enhanced in the presence of reducing agents. They exhibited broad substrate specificity towards various protein substrates. KBALT was determined for its kinetic properties by calculating its K_m (0.61 mg/ml) and V_max (1673 U/mg/min) values. These results suggest KBALT as a robust and promising contender for enzymatic processing of keratinous wastes in waste processing plants.

Microbial Keratinases: Enzymes with Promising Biotechnological Applications

Keratin is a complex and structurally stable protein found in human and animal hard tissues, such as feathers, wool, hair, hoof and nails. Some of these, like feathers and wool, represent one of the main sources of protein-rich waste with significant potential to be transformed into value-added products such as feed, fertilizers or bioenergy. A major limitation impeding valorization of keratinous substrates is their recalcitrant structure and resistance to hydrolysis by common proteases. However, specialized keratinolytic enzymes produced by some microorganisms can efficiently degrade these substrates. Keratinases have already found a purpose in pharmaceutical, textile and leather industries. However, their wider implementation in other processes, such as cost-effective (pre)treatment of poultry waste, still requires optimization of production and performance of the available enzymes. Here we present a comprehensive review covering molecular properties and characteristics of keratinases, their classification, traditional and novel approaches in discovery of novel enzymes, production, characterization, improvement and biotechnological applications.

Production, partial optimization and characterization of keratinase enzyme by Arthrobacter sp. NFH5 isolated from soil samples

The study was conducted to select the best promising keratinolytic bacterial strain. A good keratinase positive bacterium isolated from the soil samples of Hazaribagh tannery industrial zone, Dhaka was identified as Arthrobacter genus depending on the conventional techniques and confirmed as Arthrobacter sp. by sequencing 16S rRNA gene. The medium components and culture conditions were optimized to enhance keratinase production through shake flask culture. Keratin and feather powder (10 g/l or 1%) were good substrates for the highest keratinase production along with yeast extract (0.2 g/l or 0.02%) as an organic nitrogen source and potassium nitrate (1 g or 0.1%) as an inorganic nitrogen source. Maximum yield of keratinase was found after 24 h of incubation at 37 °C with an initial pH of 7.0 and inoculums volume 5% under 150 rpm when keratin, yeast extract and potassium nitrate were used as nutrient sources. Keratinase production was more than 5.0-fold increased when all optimized parameters were applied simultaneously. The optimum reaction temperature and pH were determined to be 40 °C and 8.0 respectively for crude keratinase activity. Therefore, Arthrobacter sp. NFH5 might be used for large scale production of keratinase for industrial purposes in less time.

Structural characterization, catalytic, kinetic and thermodynamic properties of Keratinase from Bacillus pumilus FH9

Bacillus pumilus FH9 keratinase was purified to homogeneity with a 59.9% yield through a series of three steps. The purified enzyme was a monomeric protein with a molecular mass around 50kDa and containing 7.3% carbohydrates. The pure B. pumilus FH9 keratinase was optimally active at pH 9.0 and 60°C. The calculated activation energy for keratin hydrolysis was 24.52kJmol^-1 and its temperature quotient (Q₁₀) was 1.19. The calculated values of thermodynamic parameters for keratin hydrolysis were as follows: ΔH*=21.75kJmol^-1, ΔG*=65.86kJmol^-1 ΔS*=-132.46Jmol^-1K^-1, (ΔG*_E-S)=4.74kJmol^-1 and ΔG*_E-T=-11.254kJmol^-1. The pure keratinase exhibited K_m, V_max, k_cat and k_cat/K_m of 5.55mg/ml keratin, 5882Umgprotein^-1 323.54s^-1 and 58.28 (s^-1/mgml^-1). The calculated half-life time at 50, 60, 70 and 80°C was 90.69, 59.1, 16.62 and 9.48min, respectively. Similarly, the thermodynamic parameters for irreversible thermal inactivation at temperature ranging from 50 to 80°C were determined. The pure enzyme was stimulated by Ca²⁺ and Mg²⁺. However, Zn²⁺, EDTA, Co²⁺ and Hg²⁺ significantly inhibited the enzyme activity. The purified enzyme was able to hydrolyze different substrates showing its higher proteolytic activity on casein, bovine serum albumin, and collagen, followed by feather, horn and wool.

Skin permeability enhancement by Bacillus subtilis alkaline protease: Application to transdermal drug delivery

Enzymes may offer great potentials in topical pharmaceutical applications provided that treatment conditions are controlled for efficacy and safety. In this study, the effect of alkaline protease produced by recombinant Bacillus subtilis cells on the ex-vivo permeability of rabbit ear skin was investigated under different conditions of enzyme activity (5-60 units) and exposure time (15-60min). Data for transepidermal water loss (TEWL) and permeation of a hydrophilic dye, rhodamine B (Rb), indicated biphasic activity-dependent and exposure time-dependent skin permeability. Maximum effects were obtained at 20 proteolytic units and 30min exposure. Findings proved consistent with histopathological changes indicating progressive stratum corneum (SC) loss and disruption of the dermo-epidermal junction at 20 units and up to 30min exposure time followed by dermal hyalinization at longer exposure. This was associated with progressive loss of skin hair. Applying the identified pretreatment conditions to transdermal delivery of vardenafil in a gel base across dorsal rat skin indicated a significant increase in plasma levels at 30 and 60min with minimal histopathological changes 5days post enzyme treatment. Accordingly, the recombinant B. subtilis alkaline protease offers promise as a pharmaceutical enzyme for transdermal drug delivery bioenhancement and dermatological applications.

Fungi that Infect Humans

Fungi must meet four criteria to infect humans: growth at human body temperatures, circumvention or penetration of surface barriers, lysis and absorption of tissue, and resistance to immune defenses, including elevated body temperatures. Morphogenesis between small round, detachable cells and long, connected cells is the mechanism by which fungi solve problems of locomotion around or through host barriers. Secretion of lytic enzymes, and uptake systems for the released nutrients, are necessary if a fungus is to nutritionally utilize human tissue. Last, the potent human immune system evolved in the interaction with potential fungal pathogens, so few fungi meet all four conditions for a healthy human host. Paradoxically, the advances of modern medicine have made millions of people newly susceptible to fungal infections by disrupting immune defenses. This article explores how different members of four fungal phyla use different strategies to fulfill the four criteria to infect humans: the Entomophthorales, the Mucorales, the Ascomycota, and the Basidiomycota. Unique traits confer human pathogenic potential on various important members of these phyla: pathogenic Onygenales comprising thermal dimorphs such as Histoplasma and Coccidioides; the Cryptococcus spp. that infect immunocompromised as well as healthy humans; and important pathogens of immunocompromised patients-Candida, Pneumocystis, and Aspergillus spp. Also discussed are agents of neglected tropical diseases important in global health such as mycetoma and paracoccidiomycosis and common pathogens rarely implicated in serious illness such as dermatophytes. Commensalism is considered, as well as parasitism, in shaping genomes and physiological systems of hosts and fungi during evolution.

Impact of enzymatic digestion on bacterial community composition in CF airway samples

Background

Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF.

Methods

DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD.

Results

Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella (p < 0.01), Streptococcus (p < 0.01), and Rothia (p < 0.01). Staphylococcus (p < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD: Veillonella (p < 0.01), Granulicatella (p < 0.01), Prevotella (p < 0.01), and Gemella (p = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition.

Discussion

We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP samples. The enhanced identification of Staphylococcus aureus is a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.