Characterization of Microbial Shifts during the Production and Ripening of Raw Ewe Milk-Derived Idiazabal Cheese by High-Throughput Sequencing

Abstract

In this study, we used high-throughput sequencing technologies (sequencing of V3–V4 hypervariable regions of 16S rRNA gene) to investigate for the first time the microbiota of Latxa ewe raw milk and the bacterial shifts that occur during the production and ripening of Idiazabal cheese. Results revealed several bacterial genera not reported previously in raw ewe milk and cheese, such as Buttiauxella and Obesumbacterium. Both the cheese making and ripening processes had a significant impact on bacterial communities. Overall, the growth of lactic acid bacteria (LAB) (Lactococcus, Lactobacillus, Leuconostoc, Enterococcus, Streptococcus and Carnobacterium) was promoted, whereas that of non-desirable and environmental bacteria was inhibited (such as Pseudomonas and Clostridium). However, considerable differences were observed among producers. It is noteworthy that the starter LAB (Lactococcus) predominated up to 30 or 60 days of ripening and then, the growth of non-starter LAB (Lactobacillus, Leuconostoc, Enterococcus and Streptococcus) was promoted. Moreover, in some cases, bacteria related to the production of volatile compounds (such as Hafnia, Brevibacterium and Psychrobacter) also showed notable abundance during the first few weeks of ripening. Overall, the results of this study enhance our understanding of microbial shifts that occur during the production and ripening of a raw ewe milk-derived cheese (Idiazabal), and could indicate that the practices adopted by producers have a great impact on the microbiota and final quality of this cheese.

Relationship between the Dynamics of Gross Composition, Free Fatty Acids and Biogenic Amines, and Microbial Shifts during the Ripening of Raw Ewe Milk-Derived Idiazabal Cheese

“…However, the growth of environmental or non-desirable bacteria was negatively affected, mainly, that of Psychrobacter and to a lesser extent, that of Erwinia , Pseudomonas and Pantoea . In general, this would confirm that the evolution of the gross composition determines the bacterial dynamics during ripening, as previously proposed [ 12 ]. Specifically, the NaCl concentrations used are considered an important factor that controls the microbiological quality of cheese [ 18 ] and the results obtained could indicate that it is the most limiting factor for the proliferation of environmental and non-desirable bacteria in Idiazabal cheese.…”

“…Among these genera, the abundance of Buttiauxella decreased during ripening, while that of Staphylococcus increased and the rest showed an increase at intermediate points (at 7, 14 or 30 days of ripening). More details can be found in Santamarina-García et al [ 12 ].…”

“…However, it is noteworthy that the evolution of Ca, Mg and P content during ripening has not been studied until now, only Aldalur et al [ 70 ] have reported an increase after pressing up to two months of ripening. Through HTS analysis, it has been observed that the starter Lactococcus remains dominant until the first month of ripening, but from that moment on other bacteria proliferate, mainly NSLAB [ 12 ]. Therefore, the lactic acid production by Lactococcus could lead to a decrease in the pH until 30 days of ripening, but the subsequent catabolism of lactate and amino acids by other microorganisms, such as NSLAB, would favour the aforementioned increase [ 18 ].…”

“…To characterize the bacterial communities and the shifts that occur during the ripening of the collected Idiazabal cheese samples, an HTS analysis was performed, as previously described [ 12 ]. Briefly, 10 g of cheese was added to 90 mL of 2% ( w / v ) sterile sodium citrate (pH 8.0), and homogenized in a sample homogenizer (Masticator Basic 400; IUL Instruments, Königswinter, Germany) six times (cycles of 20 s ON and 10 s OFF each).…”

“…In fact, some bacterial genera not reported so far in raw ewe milk and cheese have been identified. It should be noted that notable differences were observed among producers, which was attributed to the different practices carried out among producers in relation to herd management, such as feeding; or cheese making, for example, the type of rennet used or the technological settings [ 12 ].…”