Polyphasic approach to bacterial dynamics during the ripening of Spanish farmhouse cheese, using culture-dependent and -independent methods

The Human Milk Microbiota Produces Potential Therapeutic Biomolecules and Shapes the Intestinal Microbiota of Infants

Human milk not only provides a perfect balance of nutrients to meet all the needs of the infant in the first months of life but also contains a variety of bacteria that play a key role in tailoring the neonatal faecal microbiome. Microbiome analysis of human milk and infant faeces from mother-breastfed infant pairs was performed by sequencing the V1-V3 region of the 16S rRNA gene using the Illumina MiSeq platform. According to the results, there is a connection in the composition of the microbiome in each mother-breastfed infant pair, supporting the hypothesis that the infant's gut is colonised with bacteria from human milk. MiSeq sequencing also revealed high biodiversity of the human milk microbiome and the infant faecal microbiome, whose composition changes during lactation and infant development, respectively. A total of 28 genetically distinct strains were selected by hierarchical cluster analysis of RAPD-PCR (Random Amplified Polymorphic DNA-Polymerase Chain Reaction) electrophoresis profiles of 100 strains isolated from human milk and identified by 16S RNA sequencing. Since certain cellular molecules may support their use as probiotics, the next focus was to detect (S)-layer proteins, bacteriocins and exopolysaccharides (EPSs) that have potential as therapeutic biomolecules. SDS-PAGE (Sodium Dodecyl-Sulfate Polyacrylamide Gel Electrophoresis) coupled with LC-MS (liquid chromatography-mass spectrometry) analysis revealed that four Levilactobacillus brevis strains expressed S-layer proteins, which were identified for the first time in strains isolated from human milk. The potential biosynthesis of plantaricin was detected in six Lactiplantibacillus plantarum strains by PCR analysis and in vitro antibacterial studies. ¹H NMR (Proton Nuclear Magnetic Resonance) analysis confirmed EPS production in only one strain, Limosilactobacillus fermentum MC1. The overall microbiome analysis suggests that human milk contributes to the establishment of the intestinal microbiota of infants. In addition, it is a promising source of novel Lactobacillus strains expressing specific functional biomolecules.

Current Trends of Enterococci in Dairy Products: A Comprehensive Review of Their Multiple Roles

As a genus that has evolved for resistance against adverse environmental factors and that readily exchanges genetic elements, enterococci are well adapted to the cheese environment and may reach high numbers in artisanal cheeses. Their metabolites impact cheese flavor, texture, and rheological properties, thus contributing to the development of its typical sensorial properties. Due to their antimicrobial activity, enterococci modulate the cheese microbiota, stimulate autolysis of other lactic acid bacteria (LAB), control pathogens and deterioration microorganisms, and may offer beneficial effects to the health of their hosts. They could in principle be employed as adjunct/protective/probiotic cultures; however, due to their propensity to acquire genetic determinants of virulence and antibiotic resistance, together with the opportunistic character of some of its members, this genus does not possess Qualified Presumption of Safety (QPS) status. It is, however, noteworthy that some putative virulence factors described in foodborne enterococci may simply reflect adaptation to the food environment and to the human host as commensal. Further research is needed to help distinguish friend from foe among enterococci, eventually enabling exploitation of the beneficial aspects of specific cheese-associated strains. This review aims at discussing both beneficial and deleterious roles played by enterococci in artisanal cheeses, while highlighting the need for further research on such a remarkably hardy genus.

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.

Microbiological Changes during Ripening of Chihuahua Cheese Manufactured with Raw Milk and Its Seasonal Variations

Chihuahua cheese is a traditional cheese produced in Northwest Mexico that is consumed shortly after production. Cheeses prepared during autumn, winter and summer were collected from five dairies, and analyzed to determine seasonal influence on proximate analysis, texture profile and the microbiological dynamic during a ripening period of 270 days. Coliforms, coagulase-positive staphylococci, molds, yeast, as well as presumptive mesophilic lactobacilli, thermophilic lactobacilli, lactococci, thermophilic cocci and enterococci, were enumerated by plate count on selective agar. Manufacturing dairy had an effect on Chihuahua cheese composition and texture profile. Seasonality influence on the microbial dynamic was observed, since the highest initial counts of coliforms (5.14 log CFU/g), coagulase-positive staphylococci (4.13 log CFU/g) and mesophilic lactobacilli (7.86 log CFU/g) were detected on summer samples. Also, ripening time affected the survival of coliforms and presumptive lactococci after 270 days (1.24 and 5.89 log CFU/g respectively) while from day 90th, coagulase-positive staphylococci were absent. Microbial changes and seasonal influence provide information on the microbiota that can influence the sensorial characteristics of Chihuahua cheese.

Evaluation of autochthonous lactic acid bacteria as starter and non-starter cultures for the production of Traditional Mountain cheese

Lactococcus lactis subsp. lactis 68, Streptococcus thermophilus 93 and Lactobacillus rhamnosus BT68, previously isolated from Traditional Mountain (TM) cheese, were tested for the production of four experimental mountain cheeses, with the aim to assess their effectiveness in leading the TM-cheese-making process. Lactococcus lactis subsp. lactis 68 and Streptococcus thermophilus 93 were used as starter cultures, whereas Lactobacillus rhamnosus BT68 was used as non-starter culture. Three control (CTRL) cheeses were manufactured without adding any starter, according to the traditional cheese-making process; nine, cheeses were produced inoculating the vat milk with the starters (ST), starter and low concentration of non-starter culture (STLC), starter and high concentration of non-starter culture (STHC). Samples of vat milk, cheese after 24 h and 7 months ripening were processed for microbiological counts. Mesophilic cocci were dominant in all 24 h-cheese samples, while a dominance of both cocci and lactobacilli was observed after 7 months ripening. The total genomic DNA was extracted, and a fragment of V1-V3 region was amplified and pyrosequenced. Lactococci and streptococci were the most abundant species, and Lc. lactis ssp. lactis 68 affected the proliferation of milk-resident Lc. lactis ssp. cremoris, during the early fermentation. Lb. rhamnosus BT68 showed to be responsible in reducing the abundance of other Lactobacillus species. Moreover, it likely competed against Sc. thermophilus 93 for the same energetic sources, when added in concentration higher than 5 × 10³ CFU/mL milk. The sensorial and fatty acid (FA) composition analysis were performed on cheese samples at the end of ripening, demonstrating that the inoculated cheeses had better sensorial characteristics (aspect, smell, taste, texture) than CTRL cheeses, and that Lb. rhamnosus BT68 at high concentration is related to the increase of short chain fatty acids and conjugated linoleic acid in cheese after 7 months ripening.

LAB Bacteriocins Controlling the Food Isolated (Drug-Resistant) Staphylococci

Staphylococci are a group of microorganisms that can be often found in processed food and they might pose a risk for human health. In this study we have determined the content of staphylococci in 7 different fresh goat-milk cheeses. These bacteria were present in all of them, ranging from 103 to 106 CFU/g based on growth on selective media. Thus, a set of 97 colonies was randomly picked for phenotypic and genotypic identification. They could be clustered by RAPD-PCR in 10 genotypes, which were assigned by 16S rDNA sequencing to four Staphylococcus species: Staphylococcus aureus, Staphylococcus chromogenes, S. simulans, and S. xylosus. Representative strains of these species (n = 25) were tested for antibiotic sensitivity, and 11 of them were resistant to at least one of the antibiotics tested, including erythromycin, amoxicillin-clavulanic acid and oxacillin. We also tested two bacteriocins produced by lactic acid bacteria (LAB), namely the circular bacteriocin AS-48 and the lantibiotic nisin. These peptides have different mechanism of action at the membrane level. Nevertheless, both were able to inhibit staphylococci growth at low concentrations ranging between 0.16-0.73 μM for AS-48 and 0.02-0.23 μM for nisin, including the strains that displayed antibiotic resistance. The combined effect of these bacteriocins were tested and the fractional inhibitory concentration index (FICI) was calculated. Remarkably, upon combination, they were active at the low micromolar range with a significant reduction of the minimal inhibitory concentration. Our data confirms synergistic effect, either total or partial, between AS-48 and nisin for the control of staphylococci and including antibiotic resistant strains. Collectively, these results indicate that the combined use of AS-48 and nisin could help controlling (pathogenic) staphylococci in food processing and preventing antibiotic-resistant strains reaching the consumer in the final products.

Advancement in LH-PCR methodology for multiple microbial species detections in fermented foods

The length-heterogeneity PCR is a low throughput molecular biology methods explored to monitor bacteria populations in different environments. It could be more used in food microbiology analysis, not only for fingerprinting analysis, but it has been hampered until now by a limiting factor which relates to the high percentage of secondary peaks. With the aim to overcome this problem, different experiments were performed focusing on changing PCR parameters in order to obtain more specific amplicon patterns and also to reduce the complexity of community patterns. With this purpose, different annealing temperatures were tested on complex fermented food matrices taken from both animal and vegetable origin and also on the bacteria isolated from the same food source. In particular, the optimal annealing temperature identified for the fermented food samples is 59 °C and the optimal for bacterial strains varied between 63 °C and 65 °C. The approach allowed the modification of the LH-PCR protocol increasing the amplification efficiency and therefore the bacteria species discrimination. These temperatures also allowed the implementation of the previous LH-PCR published database. The modification in the level of accuracy of the LH-PCR technique could also allow an improvement in the relative species quantification by the peak area evaluation.

Characterization of Bacteria in Nigerian Yogurt as Promising Alternative to Antibiotics in Gastrointestinal Infections

Gastrointestinal infections are endemic in Nigeria and several factors contribute to their continual survival, including bacterial resistance to commonly used antibiotics. Nigerian yogurts do not include probiotics, and limited information is available about the antimicrobial properties of the fermenters in the yogurt against gastrointestinal pathogens. Therefore, the antimicrobial potentials of bacteria in Nigeria-produced yogurts against intestinal pathogens were investigated in this study. Viable counts of lactic acid bacteria (LAB) in 15 brands of yogurt were enumerated and the bacteria identified by partial sequencing of 16S rRNA gene. Susceptibility of the gastrointestinal pathogens (Salmonella, Shigella and E. coli ) to antibiotics by disc diffusion method, to viable LAB by the agar overlay method, and to the cell-free culture supernatant (CFCS) of the LAB were investigated. Co-culture analysis of LAB and pathogens were also done. Viable counts of 1.5 × 10¹¹ cfu/ml were observed in some yogurt samples. Two genera were identified: Lactobacillus (70.7%) and Acetobacter (29.3%). The Lactobacillus species reduced multidrug-resistant gastrointestinal pathogens by 4 to 5 log while the zones of inhibition ranged between 11 and 23. The Lactobacillus and Acetobacter strains examined displayed good activities against the multidrug-resistant tested pathogens. This is the first report of antimicrobial activities of acetic acid bacteria isolated from yogurt in Nigeria.

Microbiological characterization using combined culture dependent and independent approaches of Casizolu pasta filata cheese

AIMS

Casizolu is a traditional Sardinian (Italy) pasta filata cheese made with cow raw milk belonging to Sardo-Modicana and/or Bruno-Sarda breeds added with natural whey starter. This work aims to describe the traditional technology of this product and to evaluate the microbial groups/species involved in the first month of ripening.

METHODS AND RESULTS

Raw milk, curd after stretching and Casizolu cheese samples from two different farmsteads were subjected to enumeration of microbial groups, isolation and genotypic characterization of isolates and PCR temporal temperature gel electrophoresis (TTGE) analysis. The counts of lactobacilli and lactococci groups in raw milk were about 5-6 log UFC ml(-1) of milk. These counts tended to increase in curd and cheeses, reaching values higher than 8 log UFC g(-1) of cheese. Culture dependent and independent approaches employed in this work highlighted the fundamental role of Lactococcus lactis subsp. lactis, Streptococcus thermophilus and Lactobacillus paracasei in the manufacture and ripening of Casizolu cheese. Other species frequently isolated were Enterococcus durans, Enterococcus faecium, Enterococcus italicus while Enterococcus lactis, Streptococcus parauberis, Lactobacillus plantarum, Lactobacillus pentosus, Lactobacillus brevis, Lactobacillus fermentum and Lactococcus raffinolactis were isolated occasionally.

CONCLUSIONS

Lactococcus lactis subsp. lactis, Strep. thermophilus and Lact. paracasei were the principal bacterial species involved in the Casizolu cheese manufacturing and ripening. For the first time, Ent. italicus and Ent. lactis were isolated in the pasta filata cheese.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows the first data on microbial groups and species involved in the manufacture of Casizolu cheese and highlights the role of Lact. paracasei and Enterococcus spp. from the earliest stages of ripening cheese; furthermore, provides evidence that raw milk cheese is a source of new strains and therefore a reservoir of microbial biodiversity.

Identification of non-Listeria spp. bacterial isolates yielding a β-D-glucosidase-positive phenotype on Agar Listeria according to Ottaviani and Agosti (ALOA)

Agar Listeria according to Ottaviani and Agosti (ALOA) is the mandatory medium used for the detection and enumeration of Listeria monocytogenes in foods according to the official International Organization for Standardization (ISO) methods. On ALOA, Listeria spp. appear as bluish-green colonies due to the production of β-D-glucosidase, an enzyme that cleaves 5-bromo-4-chloro-3-indolyl-β-D-glucopyranoside, a chromogenic substrate included in the formulation of the medium. The present work reports on bacterial isolates (n=64) from ready-to-eat soft cheeses, which are able to grow on ALOA, forming bluish-green colonies and therefore phenotypically resemble Listeria spp. All isolates were also capable of growing on the selective media PALCAM and RAPID L'mono. The isolates were characterised with biochemical tests including those specified in the ISO standards for the confirmation of Listeria spp. and identified via partial sequencing of their 16S rRNA gene. According to sequencing results the isolates represented 12 different bacterial species or species-groups belonging to seven different genera: Bacillus spp. (B. circulans, B. clausii, B. licheniformis and B. oleronius), Cellulosimicrobium spp. (C. funkei), Enterococcus spp. (E. faecalis, E. faecium/durans), Kocuria spp. (K. kristinae), Marinilactibacillus spp. (M. psychrotolerans), Rothia spp. (R. terrae) and Staphylococcus spp. (S. sciuri and S. saprophyticus subsp. saprophyticus/xylosus). Cellulosimicrobium spp. have never been previously isolated from foods. These results significantly extend the list of bacteria previously known as capable of growing on ALOA as bluish-green colonies and suggest that there may be room for further improvement in the medium's inhibitory properties towards non-Listeria spp., Gram-positive bacteria present in foods.

Traditional cheeses: rich and diverse microbiota with associated benefits

The risks and benefits of traditional cheeses, mainly raw milk cheeses, are rarely set out objectively, whence the recurrent confused debate over their pros and cons. This review starts by emphasizing the particularities of the microbiota in traditional cheeses. It then describes the sensory, hygiene, and possible health benefits associated with traditional cheeses. The microbial diversity underlying the benefits of raw milk cheese depends on both the milk microbiota and on traditional practices, including inoculation practices. Traditional know-how from farming to cheese processing helps to maintain both the richness of the microbiota in individual cheeses and the diversity between cheeses throughout processing. All in all more than 400 species of lactic acid bacteria, Gram and catalase-positive bacteria, Gram-negative bacteria, yeasts and moulds have been detected in raw milk. This biodiversity decreases in cheese cores, where a small number of lactic acid bacteria species are numerically dominant, but persists on the cheese surfaces, which harbour numerous species of bacteria, yeasts and moulds. Diversity between cheeses is due particularly to wide variations in the dynamics of the same species in different cheeses. Flavour is more intense and rich in raw milk cheeses than in processed ones. This is mainly because an abundant native microbiota can express in raw milk cheeses, which is not the case in cheeses made from pasteurized or microfiltered milk. Compared to commercial strains, indigenous lactic acid bacteria isolated from milk/cheese, and surface bacteria and yeasts isolated from traditional brines, were associated with more complex volatile profiles and higher scores for some sensorial attributes. The ability of traditional cheeses to combat pathogens is related more to native antipathogenic strains or microbial consortia than to natural non-microbial inhibitor(s) from milk. Quite different native microbiota can protect against Listeria monocytogenes in cheeses (in both core and surface) and on the wooden surfaces of traditional equipment. The inhibition seems to be associated with their qualitative and quantitative composition rather than with their degree of diversity. The inhibitory mechanisms are not well elucidated. Both cross-sectional and cohort studies have evidenced a strong association of raw-milk consumption with protection against allergic/atopic diseases; further studies are needed to determine whether such association extends to traditional raw-milk cheese consumption. In the future, the use of meta-omics methods should help to decipher how traditional cheese ecosystems form and function, opening the way to new methods of risk-benefit management from farm to ripened cheese.

Natural populations of lactic acid bacteria in douchi from Yunnan Province, China

This research was aimed at isolating and identifying the predominant lactic acid bacteria (LAB) in the traditional Chinese salt-fermented soybean food, douchi, from Yunnan, China. The predominant LAB present were isolated and identified by conventional culture-dependent methods combined with molecular biological methods. Two hundred and sixty isolates were obtained from thirty kinds of traditional fermented douchi from six cities and counties in Yunnan, and those strains were divided into twelve groups by their morphological and biochemical characteristics. Based on 16S ribosomal DNA (rDNA) sequencing and analysis, 56 representative strains were identified as belonging to 6 genera and 14 species: Lactobacillus (4 spp.), Weissella (3 spp.), Pediococcus (2 spp.), Staphylococcus (2 spp.), Enterococcus (1 sp.), and Bacillus (2 spp.). The results show that douchi contains a large natural population of LAB of diverse composition from which some strains could be selected as starters for functional fermented foods. This is the first study on the original douchi from Yunnan, and the results suggest that it may be a useful source for the isolation of LAB. This study has also laid a foundation for further research on developing functional douchi products.

Assessment of bacterial diversity in selected Philippine fermented food products through PCR-DGGE

The bacterial population in several Philippine fermented food preparations was assessed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) of the 16S rRNA gene (16S rDNA). Genomic DNA was isolated directly from alamang (fermented shrimp paste), burong isda (fermented fish and rice), burong hipon (fermented shrimp and rice), burong mustasa (fermented mustard leaves), tuba (sugar cane wine), suka (vinegar) and sinamak (spiced vinegar) using one of two protocols, namely - MoBio DNA Extraction Kit procedure and a cetyltrimethylammonium bromide-based method. Samples recalcitrant to both methods underwent enrichment in three culture broths prior to DNA isolation. Isolated DNA was amplified using nested primer pairs targeting the bacterial 16S rDNA. PCR products were subjected to DGGE to elucidate the bacterial diversity in each fermented food. 16S rDNA sequence analyses revealed that lactic acid bacteria (LAB) and acetic acid bacteria (AAB) were dominant in the food samples. The LAB identified were Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus panis, Lactobacillus pontis and Weissella cibaria. Identified AAB were Acetobacter pomorum, Acetobacter ghanensis, Acetobacter orientalis, and Acetobacter pasteurianus. Among these, L. fermentum, L. plantarum and W. cibaria are established probiotic bacteria, while L. panis and L. pontis are potential probiotic bacteria. This finding would increase the appeal and significance of local fermented foods to consumers. Furthermore, the majority of the identified bacteria in the study have not been reported before in culture-dependent studies of similar food preparations. As such, some of the bacterial 16S rDNA obtained were cloned to have an initial partial bacterial 16S rDNA library for Philippine fermented foods.