Microbial Dynamics during labneh Ambaris Production in Earthenware Jars

Abstract

The responses of various microbial populations to modifications in the physicochemical properties of a food matrix, as well as interactions between these populations already present, are the main factors that shape microbial dynamics in that matrix. This work focused on the study of microbial dynamics during labneh Ambaris production, a traditional Lebanese concentrated fermented goat milk made in jars during 3 months. This was assessed in two earthenware jars at a production facility. DNA metabarcoding of the ITS2 region as well as the V3-V4 region of the 16S rRNA gene was used to characterize the fungal and bacterial communities, respectively. Viable bacterial isolates were also identified by Sanger sequencing of the V1-V4 region of the 16S rRNA gene. Our results showed that the dominant microorganisms identified within labneh Ambaris (Lactobacillus kefiranofaciens, Lentilactobacillus kefiri, Lactococcus lactis, Geotrichum candidum, Pichia kudriavzevii and Starmerella sp.) settle early in the product and remain until the end of maturation with varying abundances throughout fermentation. Microbial counts increased during early fermentation stage, and remained stable during mid-fermentation, then declined during maturation. While microbial compositions were globally comparable between the two jars during mid-fermentation and maturation stages, differences between the two jars were mainly detected during early fermentation stage (D0 until D10). No significant sensorial differences were observed between the final products made in the two jars. Neither coliforms nor Enterobacteriaceae were detected in their viable state, starting D7 in both jars, suggesting the antimicrobial properties of the product.

Keywords: DNA metabarcoding; goat’s milk; microbial dynamics; milk fermentation.

Figure 1

Analytical approach for the analyses of 2 labneh Ambaris productions during fermentation in earthenware jars A and B.

Figure 2

Evolution of the pH values (A) and salt contents (B) of labneh Ambaris samples collected throughout production from two earthenware jars A and B. The values showed here represent the average of the triplicates (n = 3) for pH and salt contents. Standard deviations were <1% for pH and <2% for salt contents and therefore were not shown on the figures.

Figure 3

Microbial counts obtained on five nutritive and selective media for (A) Total mesophilic aerobic flora, (B) presumptive lactobacilli, (C) yeasts and molds, (D) Enterobacteriaceae family and coliforms, during production of labneh Ambaris from D0 until D103. The counts are expressed as the average (n = 2) log cfu/g of fermented milk samples and log cfu/mL of raw milk samples. All the values recorded are available in Table S1.

Figure 4

Bacterial (A,B) and fungal (C,D) metrics of alpha diversity indices for labneh Ambaris samples collected at different production stages from two earthenware jars: A and B.

Figure 5

Hierarchical Ascendant Classification (HAC) based on Bray–Curtis dissimilarity indices for bacterial (A) and fungal (B) communities of labneh Ambaris samples collected from 2 earthenware jars A and B throughout production. Samples are color-coded according to the fermentation stages: pink for early fermentation (D2 to D10), green for mid-fermentation (D29 to D47) and blue for maturation (D93 to D103).

Figure 6

Bacterial communities’ dynamics in labneh Ambaris samples collected during production from 2 earthenware jars, jar A (A) and jar B (B), in addition to the raw milks added during production by sequencing of the V3–V4 region of the 16S rRNA gene.

Figure 7

Fungal communities’ dynamics in labneh Ambaris samples collected during production from 2 earthenware jars, A (A) and B (B), in addition to the raw milks added during production by sequencing of the ITS2 region.