Biodiversity of bacterial ecosystems in traditional Egyptian Domiati cheese

Molecular characterization of Vibrio species isolated from dairy and water samples

Vibrio species can cause foodborne infections and lead to serious gastrointestinal illnesses. The purpose of this research was to detect the Vibrio cholerae and Vibrio parahaemolyticus in raw milk, dairy products, and water samples. Also, it investigated the virulence factors, antibiotic resistance and biofilm formation in isolated bacteria. Conventional and molecular approaches were used to identify the isolates in this study. Vibrio species were detected in 5% of the samples. Vibrio cholerae and Vibrio parahaemolyticus were isolated from 1.25 and 1.5%, respectively, of the total samples. Penicillin resistance was detected in all strains of Vibrio cholerae and Vibrio parahaemolyticus, with a MAR index ranging from 0.16 to 0.5. Four isolates were moderate biofilm producer and three of them were MDR. When Vibrio cholerae was screened for virulence genes, ctxAB, hlyA, and tcpA were found in 80, 60, and 80% of isolates, respectively. However, tdh + /trh + associated-virulence genes were found in 33.3% of Vibrio parahaemolyticus isolates.

Microbiological Characterization of Greek Galotyri Cheese PDO Products Relative to Whether They Are Marketed Fresh or Ripened

Galotyri is the most popular traditional Greek PDO soft acid-curd cheese. This study compared the microbial numbers and types and characterized the lactic acid bacteria (LAB) biota of two artisan-type Galotyri PDO cheese varieties, one marketed fresh (Brand-K) and the other ripened (Brand-Z). Two retail batches of each cheese variety were analyzed, and a total of 102 LAB isolates were biochemically identified. LAB (7.2–9.3 log CFU/g) prevailed in all cheeses, followed by yeasts (5.8–6.8 log CFU/g). Typical starter strains of Streptococcus thermophilus and Lactobacillus delbrueckii were the most abundant species in all batches. However, the fresh Brand-K cheeses had 1–3 log units higher thermophilic starter LAB counts than the ripened Brand-Z cheeses, which contained a more diverse viable LAB biota comprising Lacticaseibacillus paracasei, Leuconostocmesenteroides, Lentilactobacillus (L. diolivorans, L. kefiri, L. hilgardii), Pediococcusinopinatus/parvulus, few spontaneous nonstarter thermophilic streptococci and lactobacilli, and Enterococcus faecium and E. faecalis at higher subdominant levels.Conversely, the fresh Brand-K cheeses were enriched in members of the Lactiplantibacillus plantarum group; other LAB species were sporadically isolated, including Lactococcus lactis. All retail cheeses were safe (pH 3.9–4.0). No Salmonella spp. or Listeria monocytogenes were detected in 25-g samples by culture enrichment; however, Listeria innocua and coagulase-positive staphylococci (850 CFU/g) survived in one ripened batch. Gram-negative bacteria were <100 CFU/g in all cheeses. In conclusion, ripening reduced the starter LAB viability but increased the nonstarter LAB species diversity in the present Galotyri PDO market cheeses.

Technological and Safety Characterization of Kocuria rhizophila Isolates From Traditional Ethnic Dry-Cured Ham of Nuodeng, Southwest China

Nuodeng ham is known for its unique processing techniques and flavor. In the present study, proteolytic microorganisms from cured artisanal Nuodeng ham were investigated in order to identify and select potential starter cultures for its faster and safer fermentation. Eight isolates, accounting for 57% of proteolytic microorganisms, were found to be related to Kocuria rhizophila. Relevant properties of K. rhizophila as potential starter culture were evaluated in vitro for the first time. Intra-species diversities were found in phylogenetic and physiological properties of K. rhizophila isolates. Nevertheless, desirable attributes, such as halo-tolerance, nitrate reductase and protease activity, as well as the absence of antimicrobial resistance and amino acid decarboxylase activity, were observed in selected isolates. Moreover, genome analysis of isolates K24 and K45 confirmed their lack of typical genes for virulence, antimicrobial resistance and amino acid decarboxylase. K. rhizophila may thus represent a novel starter candidate of coagulase-negative cocci group and contribute to color and flavor development of fermented meats.

Bacteria and yeasts associated to Colonial cheese production chain and assessment of their hydrolytic potential

Abstract Different types of microorganisms are important in cheese-making because of the contributions their metabolism offers during the process. Few microorganisms present in Colonial cheese are known, in addition to the ones that are introduced to kick-start the processes or the ones that are associated with infections or poisonings. This study aimed to identify, by MALDI-TOF and/or DNA sequencing, the bacteria and yeasts isolated from samples collected in the main stages of Colonial cheese production, i.e., a type of cheese produced in the southern region of Brazil. The lytic capacity of these microorganisms at 5 °C and 30 °C was also evaluated. The 58 bacterial strains were distributed in 10 species among the genera Bacillus, Citrobacter, Klebsiella, Lactococcus, Paenibacillus, Staphylococcus and Raoutella. From the 13 yeasts strains analyzed, three species were identified as following: Candida pararugosa; Meyerozyma guilliermondii; and Rhodotorula mucilaginosa. In three yeasts isolates it was possible to identify only the genus Candida sp. and Trichosporon sp. The species L. lactis (48%) and M. guilliermondii (46%) were, respectively, the predominant bacteria and yeasts species isolated. The highest microbial lytic activity observed was at 30 °C. Lipase activity on isolates was proportionally more observed with yeasts and proteolytic activity with bacteria. Lower caseinase and lipase activity was observed at 5 °C, demonstrating the importance of refrigeration in controlling microbial activity. This research highlighted the cultivation of some microorganisms that are part of the Colonial cheese microbiota as well as that several of them can hydrolyze various compounds present in milk and that could be associated with its maturation or, in uncontrolled circumstances, could be the cause of product deterioration.

Isolation of enterotoxigenic Staphylococcus aureus harboring seb gene and enteropathogenic Escherichia coli (serogroups O18, O114, and O125) from soft and hard artisanal cheeses in Egypt

Background:

Soft and hard artisanal cheeses are regularly consumed in Egypt. These products are usually processed from raw milk which may harbor many pathogenic and spoilage microorganisms.

Aim:

To evaluate the safety of some artisanal cheeses in Egypt, such as Ras, Domiati, and Mish, through chemical and microbiological examination.

Methods:

One hundred and fifty random samples of traditional Ras, Domiati, and Mish cheeses (50 each) were microbiologically and chemically analyzed. Counts of total bacteria, presumptive coliform, staphylococci, yeast, and mold were estimated. Furthermore, isolation of Escherichia coli and Staphylococcus aureus was performed, followed by PCR confirmation; isolates of E. coli were examined for the presence of virulence genes; on the other hand, the detection of the five classical enterotoxin genes of S. aureus was performed using multiplex PCR. Regarding chemical analysis, moisture, salt, and acidity content were measured. Correlations between chemical and microbial findings were investigated.

Results:

Mean counts of total bacteria, presumptive coliform, staphylococci, yeast, and mold were (2 × 10⁸, 3 × 10⁶ and 1 × 10⁷ ), (3 × 10⁵, 5 × 10 and 5 × 10²), (1 × 10⁶, 4 × 10⁵and 1 × 10⁵), (3 × 10⁵, 1 × 10⁵ and 5 × 10⁵), and (7 × 10³, 4 × 10³ and 3 × 10⁴) for Ras, Domiati and Mish cheeses, respectively. Serological identification of suspected E. coli revealed that E. coli O125 was isolated from Ras and Domiati samples, E. coli O18 was recovered from Ras samples, while E. coli O114 was isolated from Mish samples. PCR results revealed that all detected isolates of E. coli were positive for both iss (increased serum survival) and fimH (type 1 fimbriae) genes. Concerning isolated S. aureus, all examined products were harboring S. aureus enterotoxigenic strains, with seb and sed genes being the most common. The mean values of moisture, salt, and acidity were (30.03, 56.44, and 58.70), (3.30, 6.63, and 7.56) and (0.65, 0.68, and 0.50) for Ras, Domiati, and Mish cheeses, respectively.

Conclusion:

Enterotoxigenic S. aureus harboring seb gene and enteropathogenic E. coli (serogroups O18, O114, and O125) were frequently isolated from soft and hard artisanal cheeses in Egypt. Therefore, strict hygienic measures should be applied during their manufacture, handing, and distribution.

Determination of the microbial flora in traditional İzmir Tulum cheeses by Denaturing Gradient Gel Electrophoresis

In this study, it was aimed to determine microbial flora members in three traditional Tulum cheeses (C1, C2 and C3) produced in different villages and settlement areas in İzmir, Turkey. For this purpose, culture depended and 16S rRNA based culture independent methods were used. According to the results of culture depended method, Lactococcus spp., Enterococcus spp., Staphylococcus spp., Lactobacillus spp., Pediococcus spp. and yeast-mold were detected in all samples at different levels. In order to determine and identify both of the culturable and non-culturable microorganisms, denaturing gradient gel electrophoresis (DGGE) method was used. DGGE results have shown that there were eight different dominant microorganisms (Streptococcus thermophilus, Lactococcus lactis subs. lactis, Streptococcus infantarius subs. infantarius, Lactobacillus gallinarum, Streptococcus equinus, Enterococcus faecalis, Enterococcus faecium, Lactococcus garvieae) in three regionally cheese samples. Further more, total bacterial loads were monitored with real-time PCR (qPCR) method. According to the results, 3.5 × 10⁸, 3.8 × 10⁸, 8.4 × 10⁸ copy number of DNA was detected in C1, C2 and C3 cheese samples, respectively. This study is the first description for the dynamics of microbial composition of Izmir Tulum cheese after the production and brining processes.

Identification of Microbial Profile of Koji Using Single Molecule, Real-Time Sequencing Technology

Koji is a kind of Japanese traditional fermented starter that has been used for centuries. Many fermented foods are made from koji, such as sake, miso, and soy sauce. This study used the single molecule real-time sequencing technology (SMRT) to investigate the bacterial and fungal microbiota of 3 Japanese koji samples. After SMRT analysis, a total of 39121 high-quality sequences were generated, including 14354 bacterial and 24767 fungal sequence reads. The high-quality gene sequences were assigned to 5 bacterial and 2 fungal plyla, dominated by Proteobacteria and Ascomycota, respectively. At the genus level, Ochrobactrum and Wickerhamomyces were the most abundant bacterial and fungal genera, respectively. The predominant bacterial and fungal species were Ochrobactrum lupini and Wickerhamomyces anomalus, respectively. Our study profiled the microbiota composition of 3 Japanese koji samples to the species level precision. The results may be useful for further development of traditional fermented products, especially optimization of koji preparation. Meanwhile, this study has demonstrated that SMRT is a robust tool for analyzing the microbial composition in food samples.

Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods

Artisanal Minas cheese is produced in Minas Gerais state, Brazil and its varieties are named according to their geographical origin (Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes). The cheese is produced with raw cow's milk and the whey from the previous cheese production ("pingo"). The high economic and cultural importance of artisanal cheese in Brazil justifies the efforts to ensure its safety, quality and provenance. This study aimed to characterize the microbial diversity composition, and geographical distribution of artisanal Minas cheese, focusing on the characterization of its autochthonous lactic acid bacteria (LAB) microbiota. Artisanal Minas cheese varieties from Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes were analyzed by culture-dependent (culturing and LAB sequencing) and -independent (repetitive extragenic palindromic-PCR (rep-PCR) and length heterogeneity-PCR, LH-PCR) methods to characterize the microbiota. The microbial counts were variable between cheese samples, and some samples presented high number of coagulase positive bacteria and coliforms that may be associated with hygienic issues. In all samples was observed a prevalence of LAB. 16S rRNA sequencing and rep-PCR of the LAB strains identified four genus (Lactobacillus, Lactococcus, Enterococcus and Weissella), ten species and more than one strain per species. Lactobacillus was the most prevalent genera in all the cheeses. LH-PCR revealed a further six genera and ten species that were not identified by culturing, highlighting the importance of combining both culture-dependent and -independent methods to fully characterize microbiota diversity. Principal component analysis of the LH-PCR data and cluster analysis of rep-PCR data revealed that the artisanal Minas cheese microbiota was influenced not only by their geographical origin but also by the cheese farm. The lack of standardization in the milking and cheese manufacturing procedures between artisanal cheese farms could explain the microbial diversity.

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.

Activities of amylase, proteinase, and lipase enzymes from Lactococcus chungangensis and its application in dairy products

Several enzymes are involved in the process of converting milk to lactic acid and coagulated milk to curd and, therefore, are important in dairy fermented products. Amylase, proteinase, and lipase are enzymes that play an important role in degrading milk into monomeric molecules such as oligosaccharides, amino acids, and fatty acids, which are the main molecules responsible for flavors in cheese. In the current study, we determined the amylase, proteinase, and lipase activities of Lactococcus chungangensis CAU 28(T), a bacterial strain of nondairy origin, and compared them with those of the reference strain, Lactococcus lactis ssp. lactis KCTC 3769(T), which is commonly used in the dairy industry. Lactococcus chungangensis CAU 28(T) and L. lactis ssp. lactis KCTC 3769(T) were both found to have amylase, proteinase, and lipase activities in broth culture, cream cheese, and yogurt. Notably, the proteinase and lipase activities of L. chungangensis CAU 28(T) were higher than those of L. lactis ssp. lactis KCTC 3769(T), with proteinase activity of 10.50 U/mL in tryptic soy broth and 8.64 U/mL in cream cheese, and lipase activity of 100 U/mL of tryptic soy broth, and 100 U/mL of cream cheese. In contrast, the amylase activity was low, with 5.28 U/mL in tryptic soy broth and 8.86 U/mL in cream cheese. These enzyme activities in L. chungangensis CAU 28(T) suggest that this strain has potential to be used for manufacturing dairy fermented products, even though the strain is of nondairy origin.

Complete genome sequence and description of Lactococcus garvieae M14 isolated from Algerian fermented milk

We describe using a polyphasic approach that combines proteomic by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) analysis, genomic data and phenotypic characterization the features of Lactococcus garvieae strain M14 newly isolated from the fermented milk (known as raib) of an Algerian cow. The 2 188 835 bp containing genome sequence displays a metabolic capacity to form acid fermentation that is very useful for industrial applications and encodes for two bacteriocins responsible for its eventual bioprotective properties.

Assessment of the bacterial and fungal diversity in home-made yoghurts of Xinjiang, China by pyrosequencing

BACKGROUND

The aim of this study was to gain a deeper knowledge of the bacterial and fungal community diversity in local home-made yoghurts from Zhaosu and Tekesi counties, Xinjiang, China, where a relatively high proportion of the ethnic minority population resides.

RESULTS

The bacterial and fungal community diversity in 22 home-made yoghurt samples was analyzed by pyrosequencing. This approach revealed the presence of six bacterial and two fungal phyla, comprising 69 bacterial and 20 fungal genera respectively, among all samples. Firmicutes and Ascomycota were the dominant phyla and Lactobacillus and Saccharomyces the predominant genera of bacteria and fungi respectively. Based on redundancy analysis, the bacterial diversity in samples from the two counties differed mainly because of eight responsive operational taxonomic units of Lactobacillus. However, no obvious difference existed in the fungal population of samples from the two counties.

CONCLUSION

The results indicated that the microbial community of home-made yoghurts varied with their geographical origin and manufacturing process. The study showed that pyrosequencing could provide a better understanding of microbiological diversity as well as useful information for future studies on the selection of starter cultures for yoghurts.

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.

Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis

Herve cheese is a Belgian soft cheese with a washed rind, and is made from raw or pasteurized milk. The specific microbiota of this cheese has never previously been fully explored and the use of raw or pasteurized milk in addition to starters is assumed to affect the microbiota of the rind and the heart. The aim of the study was to analyze the bacterial microbiota of Herve cheese using classical microbiology and a metagenomic approach based on 16S ribosomal DNA pyrosequencing. Using classical microbiology, the total counts of bacteria were comparable for the 11 samples of tested raw and pasteurized milk cheeses, reaching almost 8 log cfu/g. Using the metagenomic approach, 207 different phylotypes were identified. The rind of both the raw and pasteurized milk cheeses was found to be highly diversified. However, 96.3 and 97.9% of the total microbiota of the raw milk and pasteurized cheese rind, respectively, were composed of species present in both types of cheese, such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens were present at low levels (0.5 and 1.6%, respectively) on the rind of both the raw and the pasteurized milk cheeses, even though this bacterium had been inoculated during the manufacturing process. Interestingly, Psychroflexus casei, also described as giving a red smear to Raclette-type cheese, was identified in small proportions in the composition of the rind of both the raw and pasteurized milk cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the common species of bacteria reached more than 99%. The main species identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum. Interestingly, 93 phylotypes were present only in the raw milk cheeses and 29 only in the pasteurized milk cheeses, showing the high diversity of the microbiota. Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer was present in the pasteurized milk cheeses. However, this specific microbiota represented a low proportion of the cheese microbiota. This study demonstrated that Herve cheese microbiota is rich and that pasteurized milk cheeses are microbiologically very close to raw milk cheeses, probably due to the similar manufacturing process. The characterization of the microbiota of this particular protected designation of origin cheese was useful in enabling us to gain a better knowledge of the bacteria responsible for the character of this cheese.

Bacterial ecology of PDO Coppa and Pancetta Piacentina at the end of ripening and after MAP storage of sliced product

The objective of this study was to evaluate the microbiota of two typical Italian PDO delicatessens Coppa and Pancetta Piacentina, produced in Piacenza area (Italy). Classical and molecular approaches were employed, in order to acquire knowledge on their bacterial ecology and its evolution after slicing and MAP storing; thus, the biodiversity of characteristic bacterial community, already present or introduced during such procedures, was studied in both full ripened and sliced samples from two producers (A and B) of the PDO district, packaged under MAP and stored at 2 and 8 °C for 30 days. The microbiota of the two kinds of Italian delicatessen demonstrated peculiar differences, particularly regarding the staphylococci and lactic acid bacteria (LAB) ratio. Moreover, some species within these two groups appeared to be linked to the kind of product: Leuconostoc, Lactobacillus versmoldensis and Staphylococcus saprophyticus were found only in Pancetta while Lactobacillus pentosus, Staphylococcus equorum, Staphylococcus xylosus, Staphylococcus sciuri and Macrococcus caseolyticus occurred only in Coppa. Also, both delicatessens from producer A were richer in LAB compared to those of producer B and the opposite applied for staphylococci. Interestingly, Tetragenococcus halophilus was detectable in all the samples and its presence in the sausage environment has been reported only for Capocollo. Storage did not substantially modify the microbiota composition, the only changes being the relative abundance of same sequences; S. xylosus was prevalent before slicing process and S. equorum at the end of MAP storage at both 2 °C and 8 °C. Concerning microbial contamination during the slicing process, our results suggest that the adopted procedures assure high hygienic quality standard of these typical products, with exception of a contamination by Psychrobacter psychrophilus in Coppa B. The possible origin of species rarely or never reported in the sausage environment and detected in this study is discussed.

Dynamics of bacterial communities during the ripening process of different Croatian cheese types derived from raw ewe's milk cheeses

Microbial communities play an important role in cheese ripening and determine the flavor and taste of different cheese types to a large extent. However, under adverse conditions human pathogens may colonize cheese samples during ripening and may thus cause severe outbreaks of diarrhoea and other diseases. Therefore in the present study we investigated the bacterial community structure of three raw ewe's milk cheese types, which are produced without the application of starter cultures during ripening from two production sites based on fingerprinting in combination with next generation sequencing of 16S rRNA gene amplicons. Overall a surprisingly high diversity was found in the analyzed samples and overall up to 213 OTU97 could be assigned. 20 of the major OTUs were present in all samples and include mostly lactic acid bacteria (LAB), mainly Lactococcus, and Enterococcus species. Abundance and diversity of these genera differed to a large extent between the 3 investigated cheese types and in response to the ripening process. Also a large number of non LAB genera could be identified based on phylogenetic alignments including mainly Enterobacteriaceae and Staphylococcacae. Some species belonging to these two families could be clearly assigned to species which are known as potential human pathogens like Staphylococcus saprophyticus or Salmonella spp. However, during cheese ripening their abundance was reduced. The bacterial genera, namely Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Brevibacterium, Corynebacterium, Clostridium, Staphylococcus, Thermoanerobacterium, E. coli, Hafnia, Pseudomonas, Janthinobacterium, Petrotoga, Kosmotoga, Megasphaera, Macrococcus, Mannheimia, Aerococcus, Vagococcus, Weissella and Pediococcus were identified at a relative low level and only in selected samples. Overall the microbial composition of the used milk and the management of the production units determined the bacterial community composition for all cheese types to a large extend, also at the late time points of cheese ripening.

Facility-specific "house" microbiome drives microbial landscapes of artisan cheesemaking plants

Cheese fermentations involve the growth of complex microbial consortia, which often originate in the processing environment and drive the development of regional product qualities. However, the microbial milieus of cheesemaking facilities are largely unexplored and the true nature of the fermentation-facility relationship remains nebulous. Thus, a high-throughput sequencing approach was employed to investigate the microbial ecosystems of two artisanal cheesemaking plants, with the goal of elucidating how the processing environment influences microbial community assemblages. Results demonstrate that fermentation-associated microbes dominated most surfaces, primarily Debaryomyces and Lactococcus, indicating that establishment of these organisms on processing surfaces may play an important role in microbial transfer, beneficially directing the course of sequential fermentations. Environmental organisms detected in processing environments dominated the surface microbiota of washed-rind cheeses maturing in both facilities, demonstrating the importance of the processing environment for populating cheese microbial communities, even in inoculated cheeses. Spatial diversification within both facilities reflects the functional adaptations of microbial communities inhabiting different surfaces and the existence of facility-specific "house" microbiota, which may play a role in shaping site-specific product characteristics.

New developments in the study of the microbiota of raw-milk, long-ripened cheeses by molecular methods: the case of Grana Padano and Parmigiano Reggiano

Microorganisms are an essential component of cheeses and play important roles during both cheese manufacture and ripening. Both starter and secondary flora modify the physical and chemical properties of cheese, contributing and reacting to changes that occur during the manufacture and ripening of cheese. As the composition of microbial population changes under the influence of continuous shifts in environmental conditions and microorganisms interactions during manufacturing and ripening, the characteristics of a given cheese depend also on microflora dynamics. The microbiota present in cheese is complex and its growth and activity represent the most important, but the least controllable steps. In the past, research in this area was dependent on classical microbiological techniques. However, culture-dependent methods are time-consuming and approaches that include a culturing step can lead to inaccuracies due to species present in low numbers or simply uncultivable. Therefore, they cannot be used as a unique tool to monitor community dynamics. For these reasons approaches to cheese microbiology had to change dramatically. To address this, in recent years the focus on the use of culture-independent methods based on the direct analysis of DNA (or RNA) has rapidly increased. Application of such techniques to the study of cheese microbiology represents a rapid, sound, reliable, and effective way for the detection and identification of the microorganisms present in dairy products, leading to major advances in understanding this complex microbial ecosystem and its impact on cheese ripening and quality. In this article, an overview on the recent advances in the use of molecular methods for thorough analysis of microbial communities in cheeses is given. Furthermore, applications of culture-independent approaches to study the microbiology of two important raw-milk, long-ripened cheeses such as Grana Padano and Parmigiano Reggiano, are presented.

Comparative Genomic Analysis of Lactococcus garvieae Strains Isolated from Different Sources Reveals Candidate Virulence Genes

Lactococcus garvieae is a major pathogen for fish. Two complete (ATCC 49156 and Lg2) and three draft (UNIUD074, 8831, and 21881) genome sequences of L. garvieae have recently been released. We here present the results of a comparative genomic analysis of these fish and human isolates of L. garvieae. The pangenome comprised 1,542 core and 1,378 dispensable genes. The sequenced L. garvieae strains shared most of the possible virulence genes, but the capsule gene cluster was found only in fish-pathogenic strain Lg2. The absence of the capsule gene cluster in other nonpathogenic strains isolated from mastitis and vegetable was also confirmed by PCR. The fish and human isolates of L. garvieae contained the specific two and four adhesin genes, respectively, indicating that these adhesion proteins may be involved in the host specificity differences of L. garvieae. The discoveries revealed by the pangenomic analysis may provide significant insights into the biology of L. garvieae.

Persistent bloodstream infection with Kocuria rhizophila related to a damaged central catheter

A case of persistent bloodstream infection with Kocuria rhizophila related to a damaged central venous catheter in a 3-year-old girl with Hirschsprung's disease is reported. The strain was identified as K. rhizophila by 16S rRNA gene sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry. Arbitrarily primed PCR analysis showed a clonal strain. The repeated septic episodes were resolved with the catheter repair.

Biodiversity in Oscypek, a traditional Polish cheese, determined by culture-dependent and -independent approaches

Oscypek is a traditional Polish scalded-smoked cheese, with a protected-designation-of-origin (PDO) status, manufactured from raw sheep's milk without starter cultures in the Tatra Mountains region of Poland. This study was undertaken in order to gain insight into the microbiota that develops and evolves during the manufacture and ripening stages of Oscypek. To this end, we made use of both culturing and the culture-independent methods of PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing of 16S rRNA gene amplicons. The culture-dependent technique and PCR-DGGE fingerprinting detected the predominant microorganisms in traditional Oscypek, whereas the next-generation sequencing technique (454 pyrosequencing) revealed greater bacterial diversity. Besides members of the most abundant bacterial genera in dairy products, e.g., Lactococcus, Lactobacillus, Leuconostoc, Streptococcus, and Enterococcus, identified by all three methods, other, subdominant bacteria belonging to the families Bifidobacteriaceae and Moraxellaceae (mostly Enhydrobacter), as well as various minor bacteria, were identified by pyrosequencing. The presence of bifidobacterial sequences in a cheese system is reported for the first time. In addition to bacteria, a great diversity of yeast species was demonstrated in Oscypek by the PCR-DGGE method. Culturing methods enabled the determination of a number of viable microorganisms from different microbial groups and their isolation for potential future applications in specific cheese starter cultures.