Technological characterization of Geotrichum candidum strains isolated from a traditional Spanish goats’ milk cheese

Pretreatment of agave bagasse with ruminal fluid to improve methane recovery

Agave bagasse, a lignocellulosic waste that results from the milling and juice extraction of Agave tequilana var azul pineapples, is a suitable substrate for the production of methane through anaerobic digestion. However, it is necessary to apply a pretreatment to convert the bagasse into energy. In this context, this paper proposes using ruminal microorganisms to hydrolyze agave bagasse. This study evaluated the effect of the initial agave bagasse to ruminal fluid (S0/X0) ratio (0.33, 0.5, 1, and 2) on the hydrolysis efficiency. Subsequently, the supernatant was used for methane production. The hydrolysis efficiency increased as the S0/X0 ratio decreased. A hydrolysis efficiency of 60 % was achieved using an S0/X0 ratio of 0.33. The S0/X0 ratio of 0.33 optimally improved the specific methane production and energy recovery (155 ± 2 mL CH4/g TS and 6.1 ± 0.1 kJ/g TS) compared to raw biomass. The most abundant hydrolytic bacteria were Prevotella, Ruminococcus and Fibrobacter, and Engyodontium was the most abundant proteolytic fungus.

Extracellular enzymes producing yeasts study: cost-effective production of α-amylase by a newly isolated thermophilic yeast Geotrichum candidum PO27

Enzymes are biocatalysts mainly used for their industrial potential in various applications. The present study aims to understand the enzyme production for biotechnological interest from a local yeast strain. From 100 isolates obtained from various biotopes, 78 strains were selected for their enzymatic heritage. Screening of α-amylase, lipase/esterase, and cellulase activities by rapid plate detection methods was carried out and the PO27 yeast was selected for its high capacity to produce α-amylase. In addition, this yeast strain exhibited good lipolytic and esterolytic activities, as well as low cellulase activity. A sequence analysis of the D1/D2 region of the 26S ribosomal RNA (26S rRNA) and a study of morphological characteristics identified the PO27 strain as Geotrichum candidum. The production of α-amylase has been studied in solid medium fermentation using various natural substrates without any supplementation such as olive pomace, potato peels, leftover bread, and mastic cake. G. candidum PO27 showed an improved production of α-amylase with olive pomace, thus reaching approximately 180.71 U/g. To evaluate the ability of this isolate to produce α-amylase in submerged fermentation, multiple concentrations of olive pomace substrate were tested. The best activity of submerged fermentation was statistically compared to the solid-state fermentation result in order to select the appropriate fermentation type. A high significant difference was found to rank the 6% olive pomace medium as the best substrate concentration with 34.395 U/mL of α-amylase activity. This work showed that the new isolate Geotrichum candidum PO27 has a better potential to produce α-amylase at a low cost in solid-state fermentation compared to submerged fermentation. Optimization conditions for PO27 α-amylase production through solid-state fermentation were achieved ‎ using a one factor at a time (OFAT) approach. The findings revealed that a high temperature (60 °C), an acidic pH, malt extract, and soluble starch were the highly significant medium components for enhancing α-‎amylase production. The use of olive pomace waste by Geotrichum candidum PO27 is expected to be effective in producing an industrially useful α-amylase.

Characterization of kefir yeasts with antifungal capacity against Aspergillus species

Kefir is a fermented probiotic drink obtained by placing kefir granules in a suitable substrate. The kefir granules are a consortium of bacteria and yeasts embedded in a exopolysaccharide matrix. The aim of this research was the isolation and identification of yeasts from kefir of different origin, the evaluation of their antifungal capacity against Aspergillus spp., and the characterization of virulence related traits. Using RFLP of ITS1/ITS4 region, D1/D2 region sequencing, and RAPD techniques, 20 kefir isolates were identified as Geotrichum candidum, Pichia kudriavzevii, Pichia membranifaciens, Saccharomyces cerevisiae, and Candida ethanolica. Their antifungal capacity was evaluated by their conidia germination reduction, which allowed the selection of eight isolates with high to moderate conidia germination reduction against Aspergillus flavus and Aspergillus parasiticus. Furthermore, these selected isolates showed growth inhibition on contact in the dual culture assay for both Aspergillus species and 3 of them-belonging to S. cerevisiae and P. kudriavzevii species-generated volatile organic compounds which significantly affected the growth of both fungi. For the evaluation of virulence-related traits, growth at high temperatures, enzymatic activities, and the adhesion to Caco-2 cells were analyzed. The isolates did not present more than one positive virulence-related trait simultaneously. In particular, it is important to highlight that the adhesion capacity to the model of intestinal barrier was extremely low for all of them. According to the results obtained, further studies would be of interest for the possible use of these promising yeasts as biocontrol agents against fungi in food.

Serbian Traditional Goat Cheese: Physico-Chemical, Sensory, Hygienic and Safety Characteristics

This research project aimed to investigate the physico-chemical, sensory, hygienic and safety characteristics of raw goat milk, whey, brine and traditional goat cheese during the ripening period of 28 days. Physico-chemical parameters included the determination of dry matter, fat, ash, protein, pH, water activity and NaCl content. The presence of Enterobacteriaceae and fungi was estimated on milk and cheese samples, and a sensory panel evaluated the products' features and acceptability during ripening. The results show that the cheese under study belongs to the acid full-fat cheese group. A consumer panel attributed high scores to the goat cheese, until the 21st day of ripening. After this period, the overall features altered significantly, including augmented bitterness, odor intensification and the development of molds on the surface. The presence of fungi, associated with Enterobacteriaceae, suggests that the hygiene of the production processes needs to be improved. Regarding microbial safety, the detection of putative pathogens and antibiotic resistances recommend an active surveillance of traditional foods to avoid foodborne infections and/or the dissemination of resistant microorganisms along the food chain.

Broad-Spectrum Activity of Volatile Organic Compounds from Three Yeast-like Fungi of the Galactomyces Genus Against Diverse Plant Pathogens

The application of antagonistic fungi for plant protection has attracted considerable interest because they may potentially replace the use of chemical pesticides. Antipathogenic activities confirmed in volatile organic compounds (VOCs) from microorganisms have potential to serve as biocontrol agents against pre- and post-harvest diseases. In the present study, we investigated Galactomyces fungi isolated from rotten leaves and the rhizosphere of cherry tomato (Lycopersicon esculentum var. cerasiforme). VOCs produced by Galactomyces fungi negatively affected the growth of phytopathogenic fungi and the survival of nematodes. Mycelial growths of all nine examined phytopathogenic fungi were inhibited on agar plate, although the inhibition was more intense in Athelia rolfsii JYC2163 and Cladosporium cladosporioides JYC2144 and relatively moderate in Fusarium sp. JYC2145. VOCs also efficiently suppressed the spore germination and mycelial growth of A. rolfsii JYC2163 on tomatoes. The soil nematode Caenorhabditis elegans exhibited higher mortality in 24 h in the presence of VOCs. These results suggest the broad-spectrum activity of Galactomyces fungi against various plant pathogens and the potential to use VOCs from Galactomyces as biocontrol agents.

Growth dynamics of lactic acid bacteria and dairy microscopic fungus Geotrichum candidum during their co-cultivation in milk

Production of high-quality and microbiologically safe fermented dairy products requires controlled growth and microbial interactions between lactic acid bacteria and microscopic fungi. For this purpose, detailed knowledge of their growth characteristics is needed. Therefore, the objective of this study was to analyse the growth dynamics of lactic acid bacteria of commercial DVS® FRESCO® 1000NG culture and dairy isolate of microscopic fungus Geotrichum candidum during their co-cultivation in milk. The growth dynamics of microorganisms was studied in dependence on their initial counts at 12, 15, 18, 21 and 30 °C. Growth parameters were calculated by two primary predictive models, model of Baranyi and Roberts and Huang's model. Both models showed good ability to describe the growth dynamics of studied microorganisms, as it was confirmed by low values of RMSE index. Both microbial cultures, Fresco culture and Geotrichum candidum, showed good growth ability in milk since they reached the average maximum density of 9.50 ± 0.13 log CFU/mL and 5.85 ± 0.69 log CFU/mL (n = 45), in order. Maximum density of studied microorganisms was not affected by their initial counts or incubation temperature. On the other hand, effect of mutual ratio of microbial initial counts and increasing temperature had a significant impact on growth dynamics.

Microbiological characterization of Gioddu, an Italian fermented milk

Gioddu, also known as "Miciuratu", "Mezzoraddu" or "Latte ischidu" (literally meaning acidulous milk), is the sole variety of traditional Italian fermented milk. The aim of the present study was to elucidate the microbiota and the mycobiota occurring in artisan Gioddu sampled from three Sardinian producers by combining the results of viable counting on selective culture media and high-throughput sequencing. Physico-chemical parameters were also measured. The overall low pH values (3.80-4.22) recorded in the analyzed Gioddu samples attested the strong acidifying activity carried out by lactic acid bacteria during fermentation. Viable counts revealed the presence of presumptive lactococci, presumptive lactobacilli and non-Saccharomyces yeasts. A complex (kefir-like) microbiota of bacteria and yeasts was unveiled through sequencing. In more detail, Lactobacillus delbrueckii was found to dominate in Gioddu together with Streptococcus thermophilus, thus suggesting the establishment of a yogurt-like protocooperation. Unexpectedly, in all the three analyzed batches from two out of the three producers Lactobacillus kefiri was also detected, thus representing an absolute novelty, which suggests the presence of bioactive compounds (e.g. exopolysaccharides) similar to those characterizing milk kefir beverage. Mycobiota population, studied for the very first time in Gioddu, revealed a more complex composition, with Kluyveromyces marxianus, Galactomyces candidum and Geotrichum galactomyces constituting the core species. Further research is needed to disclose the eventual occurence in Gioddu of probiotic cultures and bioactive compounds (e.g. exopolysaccharides, angiotensin-converting enzyme inhibitory peptides and antimicrobial compounds) with potential health-benefits for the consumers.

Evaluation of bacterial and fungal communities during the fermentation of Baixi sufu, a traditional spicy fermented bean curd

BACKGROUND

Baixi sufu (BS) is a traditional Chinese spicy fermented bean curd manufactured with a natural starter. In this study, the bacterial and fungal communities during BS fermentation were determined by culture and by the culture-independent method of high-throughput sequencing (HTS). Correlation analyses were performed to select the microorganisms potentially contributing to this fermentation.

RESULTS

During the fermentation of BS, 162 bacterial and 97 fungal strains were isolated and identified, and a total of 268 314 bacterial and 287 844 fungal high-quality sequences were analyzed. In general, lactic acid bacteria (LAB), especially Enterococcus and Lactococcus, were dominant in the early stage of fermentation, and spore-forming bacteria, especially Bacillus spp., became the predominant bacteria by the end of fermentation. Geotrichum, Mortierella, and unclassified Ascomycota, were the major fungal populations, which could not be detected in the final product. Correlation analyses indicated that Enterococcus, Bacillus, Geotrichum, and unclassified Ascomycota correlated significantly and positively with amino nitrogen. However, due to the sporulation characteristics of Bacillus, they may have little effect on BS ripening. The presence of Bifidobacterium spp. in sufu is reported for the first time, but the excessive counts of the Bacillus cereus group (>10⁵  CFU g^-1 ) indicate a potential hazard to consumers.

CONCLUSION

The profiles obtained from this study will contribute to the development of autochthonous starter cultures to control BS fermentation, and may lead to the development of novel strategies to shorten the fermentation time of sufu products. © 2019 Society of Chemical Industry.

Penicillium commune affects textural properties and water distribution of hard and extra-hard cheeses

We analyzed the effects of growth of Penicillium commune, one of the most frequent fungal species associated with cheese, on the water diffusion and texture of hard and extra-hard cheeses. A total of 36 hard cheese blocks and 36 extra-hard cheese blocks were manufactured, salted at different levels (0.5, 1.25 and 2% w/w), and assigned to different treatments (control and inoculated). Cheese texture was analyzed using a penetration needle probe at 2 and 5 weeks after ripening. Firmness, defined as the maximum force detected in the penetration probe, was higher in both hard and extra-hard inoculated cheese blocks compared with the control. In addition, the presence of fungal growth on cheese rind increased the total work of penetration (a measure of resistance to probe penetration), but only in extra-hard cheeses, suggesting that the moisture of cheese might be affecting the growth capacities and performance of P. commune. The change in textural properties of cheeses was linked to desiccation of the upper 0.5-cm rind layer mediated by P. commune.

Potential antibiotic-producing fungal strains isolated from pharmaceutical waste sludge

Background

Antibiotic resistance and dearth of novel compounds from natural sources warrants the need to search other environments for potential antibiotic-producing microbial species. The study investigated isolation and identification of antibiotic-producing fungi from pharmaceutical waste sludge.

Results

Seven hundred and ninety-seven isolates obtained from sludge of seven pharmaceutical industries in Sango Ota, Ogun State using several growth media, with mould isolates highest (696). Isolated species were from genera Aspergillus (28.55%), Penicillium (18.35%), Trichoderma (13.44%), Rhizopus (10.21%) and Geotrichum (4.01%), and Stachybotrys (0.13%). The CFS of strains named Geotrichum candidum OMON-1, Talaromyces pinophilus OKHAIN-12, and Penicillium citrinum PETER-OOA1 had high reproducible bioactivity against Staphylococcus aureus (32 ± 0.12 mm) and Klebsiella pneumoniae (29 ± 0.12 mm) while P. citrinum MASTER-RAA2 had activity against K. pneumoniae only. Active metabolites were successfully extracted using Diaion HP-20 and methanol:iso-propanol:acetone (6:3:1 v/v). Antibacterial-active fractions of fungal extract successfully eluted with 40–60% NaCl on ion-exchange chromatography using a cation column.

Conclusions

The study successfully screened antibiotic-producing fungal species from pharmaceutical waste storage facilities. Study also showed that similar species from same toxic environment could potentially produce different metabolites.

Cheese yeasts

Numerous traditionally aged cheeses are surface ripened and develop a biofilm, known as the cheese rind, on their surfaces. The rind of such cheeses comprises a complex community of bacterial and fungal species that are jointly responsible for the typical characteristics of the various cheese varieties. Surface ripening starts directly after brining with the rapid colonization of the cheese surface by yeasts. The initially dominant yeasts are acid and salt-tolerant and are capable of metabolizing the lactate produced by the starter lactic acid bacteria and of producing NH₃ from amino acids. Both processes cause the pH of the cheese surface to rise dramatically. This so-called deacidification process enables the establishment of a salt-tolerant, Gram-positive bacterial community that is less acid-tolerant. Over the past decade, knowledge of yeast diversity in cheeses has increased considerably. The yeast species with the highest prevalence on surface-ripened cheeses are Debaryomyces hansenii and Geotrichum candidum, but up to 30 species can be found. In the cheese core, only lactose-fermenting yeasts, such as Kluyveromyces marxianus, are expected to grow. Yeasts are recognized as having an indispensable impact on the development of cheese flavour and texture because of their deacidifying, proteolytic, and/or lipolytic activity. Yeasts are used not only in the production of surface-ripened cheeses but also as adjunct cultures in the vat milk in order to modify ripening behaviour and flavour of the cheese. However, yeasts may also be responsible for spoilage of cheese, causing early blowing, off-flavour, brown discolouration, and other visible alterations of cheese.

Roles of aging in the production of light-flavored Daqu

Daqu, a complex starting material used for Baijiu production, contains microorganisms, enzymes, and volatile compounds. An important part of Daqu production is aging, but the physicochemical and microbial changes during aging remain largely unknown. This study characterized aging according to physicochemical parameters, volatile compounds, and microbial communities. Aging was found to aid in the stabilization of the physicochemical parameters. Solid-phase microextraction-gas chromatography-mass spectrometry was used to detect 72 types of volatile compounds, which were predominantly alcohols, esters, aldehydes, alkenes, and alkanes. During aging, these compounds changed considerably, but their structures eventually stabilized. A high-throughput sequencing approach was used to analyze the changing composition of the microbial communities. In general, aging helped to enrich and stabilize the microbial population for making Baijiu. A total of 35 bacteria were detected as prokaryotic; among these, 15 had a diversity abundance ratio of more than 1%. The dominant bacteria were from the genus Pantoea, but these decreased with aging, while bacteria from Lactobacillus and Weissella increased. After aging for 2 months, Pantoea, Lactobacillus and Weissella accounted for 0.4%, 54.0%, and 18.9%, respectively. A total of 12 eukaryotic yeast and fungi were detected, the most abundant of which were Incertae_Sedis_incertae_sedis, Saccharomycopsis, Trichocomaceae_unclassified, Pichia, Tremellales_unclassified, and Galactomyces. During aging, the levels of Trichocomaceae_unclassified, Saccharomycopsis, and Galactomyces initially decreased but then increased. Pichia stayed unchanged as aging progressed. In conclusion, aging led to rebalanced interactions among Daqu microbes and was important in improving Daqu quality and ensuring its stability.

Characterisation of microbial communities in Chinese liquor fermentation starters Daqu using nested PCR-DGGE

In this study, characterises of the microbial community structures of three typical Chinese liquor Daqu, as well as different kinds of light flavour Daqu were investigated using nested PCR-denaturing gradient gel electrophoresis (DGGE). The results showed that microbial diversity was considerably different, and the microfloral compositions were highly variable among various Daqu. Lactic acid bacteria, which accounted for 30.95 % of all identified bacteria, were dominant in all Daqu samples, whereas Bacillus species were also predominant in the Luzhou (14.8 %) and Langjiu Daqu (18.2 %). Citrobacter and Burkholderia were first identified in light flavour Daqu. Aspergillus was the dominant moulds, and the non-Saccharomyces yeast species, Saccharomycopsis fibuligera, Wallemia sebi, Wallemia muriae, and Pichia subpelliculosa, were the dominant yeasts. Rasamsonia, Galactomyces, Geotrichum and Wallemia were first identified using nested PCR-DGGE. Cluster analysis indicated that the microbial community structures of different Daqu samples exhibited some differences. These may be ascribed to the different peak production temperatures, raw material constituents and microhabitats around the liquor enterprises. The current study provides insights into the microbial community structures of three typical Daqu samples, and may facilitate the development of starter cultures for manufacturing Chinese liquor.

The complex microbiota of raw milk

Here, we review what is known about the microorganisms present in raw milk, including milk from cows, sheep, goats and humans. Milk, due to its high nutritional content, can support a rich microbiota. These microorganisms enter milk from a variety of sources and, once in milk, can play a number of roles, such as facilitating dairy fermentations (e.g. Lactococcus, Lactobacillus, Streptococcus, Propionibacterium and fungal populations), causing spoilage (e.g. Pseudomonas, Clostridium, Bacillus and other spore-forming or thermoduric microorganisms), promoting health (e.g. lactobacilli and bifidobacteria) or causing disease (e.g. Listeria, Salmonella, Escherichia coli, Campylobacter and mycotoxin-producing fungi). There is also concern that the presence of antibiotic residues in milk leads to the development of resistance, particularly among pathogenic bacteria. Here, we comprehensively review these topics, while comparing the approaches, both culture-dependent and culture-independent, which can be taken to investigate the microbial composition of milk.

Genetic diversity of dairy Geotrichum candidum strains revealed by multilocus sequence typing

The introduction of multilocus sequence typing (MLST) for strain characterization provided the first sequence-based approach for genotyping many fungi, leading to reproducible, reliable, and exchangeable data. A MLST scheme based on the analysis of six housekeeping genes was developed for genotyping Geotrichum candidum. The scheme was first developed using 18 isolates for which the complete sequences of the alanyl-tRNA synthetase (ALA1), pyruvate kinase (CDC19), acetyl-coA acetyltransferase (ERG10), glutaminyl-tRNA synthase (GLN4), phosphoglucoisomerase (PGI1), and phosphoglucomutase (PGM2) housekeeping genes were determined. Multiple sequence alignments of these genes were used to define a set of loci showing, as closely as possible, the same phylogenetic resolution level as complete gene sequences. This scheme was subsequently validated with 22 additional isolates from dairy and non-dairy sources. Overall, 58 polymorphic sites were indexed among 3,009 nucleotides analyzed. Depending on the loci, four to eight alleles were detected, generating 17 different sequence types, of which ten were represented by a single strain. MLST analysis suggested a predominantly clonal population for the 40 G. candidum isolates. Phylogenetic analysis of the concatenated sequences revealed a distantly related group of four isolates. Interestingly, this group diverged with respect to internal transcribed spacers 1 (ITS1), 5.8S, and ITS2 analysis. The reproducibility of the MLST approach was compared to random amplification of microsatellites by PCR (RAM-PCR), a gel profiling method previously proposed for G. candidum strain typing. Our results found MLST differentiation to be more efficient than RAM-PCR, and MLST also offered a non-ambiguous, unique language, permitting data exchange and evolutionary inference.