Detection and Enumeration of Lactic Acid Bacteria, Acetic Acid Bacteria and Yeast in Kefir Grain and Milk Using Quantitative Real-Time PCR

Improving red-color performance, immune response and resistance to Vibrio parahaemolyticus on white shrimp Penaeus vannamei by an engineered astaxanthin yeast

Astaxanthin (AST), a super antioxidant with coloring and medical properties, renders it a beneficial feed additive for shrimp. This study conducted a white shrimp feeding trial of 3S, 3'S isoform AST, which was derived from metabolic-engineered Kluyveromyces marxianus fermented broth (TB) and its extract (TE) compared to sources from two chemically synthetic ASTs (Carophyll Pink [CP] and Lucantin Pink [LP]), which contain 3S, 3'S, 3R, 3'S (3S, 3'R) and 3R, 3'R isoforms ratio of 1:2:1. The effects on red coloration, immune parameters and resistance to Vibrio infection were evaluated. Four AST sources were incorporated into the diets at concentrations of 0 (control), 100 mg kg^-1 (TB100, TE100, CP100, and LP100), and 200 mg kg^-1 (TB200, TE200, CP200, and LP200). Results revealed that in week 4, shrimps that received AST-supplemented feeds, especially TB100, TB200, and TE200, significantly increased redness (a*) values. Immune responses including phagocytosis activity, superoxide-anion production, phenoloxidase activity, and immune-related genes were examined on days 0, 1, 2, 4, 7, 14, 21, and 28. Generally, shrimps that received AST-supplemented feeds exhibited higher immune responses on days 7 and 14 than the control feed. Gene expression levels of superoxide dismutase and glutathione peroxidase were significantly upregulated on days 7 and 14 in shrimps that received AST-supplemented feeds, while genes of penaeidins, antilipopolysaccharide factor, and lysozyme were upregulated on days 4, 7, and 14, especially received TB200 and TE200. Furthermore, shrimps that received TB100, TE100, CP100, and LP100 7 days were then challenged with Vibrio parahaemolyticus and the result demonstrated higher survival rates especially TB100 at 168 h than the control feed. In conclusion, incorporating AST into the diets enhanced shrimp red coloration, immune parameters, and resistance against V. parahaemolyticus infection. The K. marxianus-derived AST exhibited higher performance than did chemical AST to be a potential feed additive in shrimp aquaculture.

Simultaneous detection of viable Salmonella spp., Escherichia coli, and Staphylococcus aureus in bird's nest, donkey-hide gelatin, and wolfberry using PMA with multiplex real-time quantitative PCR

Salmonella spp., Escherichia coli, and Staphylococcus aureus are common microbial contaminants within the homology of medicine and food that can cause serious food poisoning. This study describes a highly efficient, sensitive, specific, and simple multiplex real-time quantitative PCR (mRT-qPCR) method for the simultaneous detection of viable Salmonella spp., E. coli, and S. aureus. Primers and probes were designed for the amplification of the target genes invA, uidA, and nuc. Dead bacterial genetic material was excluded by propidium monoazide (PMA) treatment, facilitating the detection of only viable bacteria. This method was capable of detecting Salmonella spp., E. coli, and S. aureus at 102, 102, and 101 CFU/ml, respectively, in pure culture. PMA combined with mRT-qPCR can reliably distinguish between dead and viable bacteria with recovery rates from 95.7% to 105.6%. This PMA-mRT-qPCR technique is a highly sensitive and specific method for the simultaneous detection of three pathogens within the homology of medicine and food.

Screening and Molecular Identification of Lactic Acid Bacteria Producing β-Glucan in Boza and Cider

The goal of this study was screening and molecular identification of Lactic Acid Bacteria (LAB) producing β-glucan from different species isolated from boza and cider compared to a standard strain for Lactobacillus rhamnosus NRRL 1937 (LGG). From 48 unknown isolates, four LAB strains were selected. Based on the NCBI database, their nomenclature was A3, B6, and C9 for Limosilactobacillus fermentum SH1, SH2, and SH3 along with D6 for Leuconostoc mesenteroides SH4. Also, their similarity values were 100%, 99.8%, 100%, and 100%, respectively. The potential of Exopolysaccharide (EPS) (as β-glucan) production for selected LAB strains by gtf gene, conventional PCR and gene expression using both LGG as a control and LAB 16S rRNA gene as a house-keeping gene was investigated. In addition, EPS (mg/100 mL), cell mass (mg/100 mL), pH, total carbohydrate%, total protein% and β-glucan% by the HPLC for all selected LAB isolates were studied. All results of genetic and chemical tests proved the superiority of B6 treatment for L. fermentum SH2. The results showed the superiority of B6 treatment in gtf gene expression (14.7230 ± 0.070-fold) followed by C9 and A3 treatments, which were 10.1730 ± 0.231-fold and 8.6139 ± 0.320-fold, respectively. while D6 treatment recorded the lowest value of gene expression (0.8566 ± 0.040-fold) compared to the control LGG (one-fold). The results also demonstrated that B6 treatment was superior to the other treatments in terms of EPS formation, with a value of 481 ± 1.00 mg/100 mL, followed by the C9 treatment at 440 ± 2.00 mg/100 mL, compared to the LGG (control) reaching 199.7 ± 3.51 mg/100 mL. Also, the highest % of quantitative and qualitative β-glucan in EPS was observed in B6 followed by C9, D6 and A3 which were 5.56 ± 0.01%, 4.46 ± 0.01%, 0.25 ± 0.008% and 0.12 ± 0.008%, respectively compared to control (0.31 ± 0.01%). Finally, the presented results indicate the importance of screening the local LAB isolates to obtain a superior strain for β-glucan production which will be introduced in a subsequent study under optimum conditions.

Survivability of Kluyveromyces marxianus Isolated From Korean Kefir in a Simulated Gastrointestinal Environment

Kluyveromyces marxianus accounts for > 90% of the yeast population of kefir, and recently, its probiotic potential has been actively explored with a focus on its health benefits and safety. Herein, the survivability of five kefir-isolated K. marxianus strains (Km A1–A5) in a simulated gastrointestinal (GI) environment was evaluated and compared with those of commercial probiotic yeast, Saccharomyces boulardii MYA-796. To further explore the potential to survive in the host GI tract, biochemical activities, hydrophobicity assay, biofilm formation, auto-aggregation analysis, and phenol tolerance of the strains were assessed. K. marxianus A4 exhibited the best survivability among all tested strains, including the clinically proven probiotic yeast strain S. boulardii MYA-796 (p = 0.014) in the artificial GI tract ranging from pH 2.0 to 7.5. In addition, the five K. marxianus strains and S. boulardii MYA-796 displayed different assimilation of lactose, xylitol, D-sorbitol, and DL-lactate, indicating that K. marxianus metabolized a wide range of substances and, thus, might be more feasible to nourish themselves in the host GI tract for survival. K. marxianus strains showed a greater hydrophobicity of cell surface, abilities to biofilm formation and auto-aggregation, and phenol tolerance than S. boulardii MYA-796, suggesting greater potential for survival in the host GI tract.

Kefir modulates gut microbiota and reduces DMH-associated colorectal cancer via regulation of intestinal inflammation in adulthood offsprings programmed by neonatal overfeeding

Obesity is associated with chronic inflammation, intestinal dysbiosis, and colorectal cancer risk. The anti-cancer effects of kefir are highlighted. Here, lactating Wistar rats were divided into: Normal litter (NL); Kefir normal litter (KNL); Small litter (SL); Kefir small litter (KSL). The NL and SL groups received 1 mL of water/day; KNL and KSL received kefir milk daily (10⁸ CFU/mL) during lactation. After weaning, the pups continued to receive the same treatments until 60 days. At 67 days old, colorectal carcinogenesis was induced through intraperitoneal injection of 1,2-dimethylhydrazine. At 240 days, visceral adipose tissue was higher in SL compared to NL, KNL, and KSL. Kefir intake was found to suppress the number of tumors in both KNL and KSL groups (-100% and -71.43%; p < 0.01, respectively). IL-1β, IL-6, TNF-α, and NO levels in the colon were higher in the NL and SL compared to the KNL and KSL. The gut microbiota in cecal samples of SL was enriched with Alloprevotella, Acinetobacter, and Bacteroides. In contrast, the cecal contents of KSL and KNL were higher Romboutsia. Thus, neonatal overfeeding leads to greater adiposity, inflammation and number of colon tumors in adulthood. Early-life nutrition based on kefir reverted these alterations.

Diversity and dynamics of sourdough lactic acid bacteriota created by a slow food fermentation system

Sourdough is a naturally fermented dough that is used worldwide to produce a variety of baked foods. Various lactic acid bacteria (LAB), which can determine the quality of sourdough baked foods by producing metabolites, have been found in the sourdough ecosystem. However, spontaneous fermentation of sourdough leads to unpredictable growth of various micro-organisms, which result in unstable product quality. From an ecological perspective, many researchers have recently studied sourdough LAB diversity, particularly the elucidation of LAB community interactions and the dynamic mechanisms during the fermentation process, in response to requests for the control and design of a desired sourdough microbial community. This article reviews recent advances in the study of sourdough LAB diversity and its dynamics in association with unique characteristics of the fermentation system; it also discusses future perspectives for better understanding of the complex sourdough microbial ecosystem, which can be attained efficiently by both in vitro and in situ experimental approaches.

An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?

The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.

Quantification of Major Bacteria and Yeast Species in Kefir Consortia by Multiplex TaqMan qPCR

Kefir grains are complex microbial systems of several groups of microorganisms. The identification and quantification of the microbial composition of milk kefirs was described in several studies, which provided an insight into the microbial consortia in this complex ecosystem. Nevertheless, the current methods for identification and quantification are not appropriate for deeper studies on kefir consortia, e.g., population dynamics and microbial interactions in kefir grains. This requires another sensitive and reliable quantitative method. Therefore, this study aims to develop multiplexed qPCR assays to specifically detect and quantify, as an example, several microorganisms of the milk kefir microbial community. Primer-probe sets, which target species-specific genes in six bacteria and five yeasts, were designed, and their sensitivity and specificity to the target species was analyzed in simplex as well as four multiplex qPCR assays. The self-designed multiplex assays were applied for the detection of target bacteria and yeast species in milk kefirs, in both, grain and beverage fractions. Detection of all target microorganisms in simplex and multiplex qPCR was achieved by good linearity, efficiency, repeatability and reproducibility in all assays. When the designed assays were applied on six kefirs, all target microorganisms were detected in different samples, but not all in one kefir sample. The two ubiquitous lactobacilli Lactobacillus kefiranofaciens and Lb. kefiri were present in all six kefirs studied, but were associated with different other yeasts and bacteria. Especially on the yeast community a significant diversity was observed. In general, multiplex TaqMan qPCR as developed here was proven to have high potential for specific identification of target microorganisms in kefir samples and for the first time, eleven target bacteria and yeasts of kefir microbiota were rapidly detected and quantified. This study, thus, provides a fast and reliable protocol for future studies on kefir and other similar microbial ecosystems.

Influence of the production technology on kefir characteristics: Evaluation of microbiological aspects and profiling of phosphopeptides by LC-ESI-QTOF-MS/MS

The influence of production technology, namely, temperature, pH and 2-step fermentation (back-slopping approach), on the microbiological characteristics and on the phosphopeptide profile of kefir obtained with kefir grains was investigated. The growth of yeasts, lactic acid bacteria (LAB) and acetic acetic bacteria (AAB) in both grains and kefir was affected by the incubation temperature and by the use of back-slopping. In particular, at 25 °C the microbiota of kefir grains was mainly composed by LAB and yeasts, while at 18 °C yeasts represented the dominant group in kefir. Back-slopping at 25 °C determined a significant increase of AAB. A comprehensive characterization of potentially bioactive peptides, including caseino-phosphopeptides (CPPs), was performed, for the first time, in kefir obtained with kefir grains, using preliminary enrichment on hydroxyapatite followed by dephosphorylation and analysis by Liquid Chromatography-ElectroSpray Ionization-Quadrupole-Time of Flight-tandem mass spectrometry (LC-ESI-QTOF-MS/MS). As a result, seventy-three phosphopeptides, mostly arising from caseins (79% β-casein, 8% α_s1-casein and 9% α_s2-casein) and all including from three to five serine residues in their sequences, were identified. Seventy-one of them showed the typical motif "SerP-SerP-SerP-Glu-Glu", which is crucial for the ability of caseins to bind to minerals. Several peptides were observed, for the first time, from the 1-40 region of β-casein. As for the effect of production technology, phosphopeptide profiles of kefirs obtained at 25 °C and 18 °C were very similar, whereas kefir produced under acidic conditions showed a predominance of smaller peptides, suggesting a higher level of proteolysis. Conversely, kefir obtained through back-slopping at 25 °C contained longer peptides, thus indicating a lower proteolytic activity and a poor reproducibility in the kefir phosphopeptide profile occurring when grains are reused.

A Culture-Independent Method for Enumeration of Viable Load of Lactobacillus acidophilus NCFM by using Real-Time PCR

The study was performed to develop a non-culture method to quantify viable loads of Lactobacillus acidophilus NCFM using RNA-based molecular technique. The ‘growth curve’ and ‘cycle threshold curve’ were developed respectively by plate counting and using cycle threshold (CT) values. ‘Standard curve’ was constructed using cells per milliliter and relative CT values. A maximum viable count (1.5 ± 0.15) × 1010 cells/mL with a minimum CT value 20.18 ± 0.56 was achieved following 18 h of growth. The two parameters were inversely proportional to each other over the exponential growth. The ‘standard curve’ corresponded to equation y = 2E + 28e−2.034x (y = cells/mL, x = CT value; R2 = 0.993), and no sample showed significant difference between ‘plate count’ and relative ‘PCR count’ following the validation process. Industrial adaptation of this method in dairy processing could potentially contribute to a faster enumeration of viable L. acidophilus NCFM compared to plate counting.

Culture supernatant produced by Lactobacillus kefiri from kefir inhibits the growth of Cronobacter sakazakii

Cronobacter sakazakii is a life-threatening foodborne pathogen found in powdered infant formula and dairy products. Kefir is a dairy probiotic product and its antimicrobial activity against C. sakazakii was reported in our previous study. To identify key microorganisms that mediate growth suppression, we tested the antimicrobial activity of culture supernatants derived from lactic acid bacteria found in kefir. Lactobacillus kefiri DH5, L. kefiranofaciens DH101, and Bifidobacterium longum 720 (a commercial probiotic strain that served as a positive control) all significantly inhibited the growth of C. sakazakii ATCC 29544, delaying the initiation of exponential growth from 3 to 9 h in the nutrient broth. Among them, L. kefiri DH5 exerted the strongest antimicrobial effects against C. sakazakii, showing bactericidal effect at the addition of 300 µl of supernatant in 1 ml of nutrient broth. Interestingly, the supernatant of L. kefiri DH5 has higher pH and lower titrable acidity than that of L. kefiranofaciens DH101, suggesting metabolites produced by heterofermentation of L. kefiri acted more effectively to antagonise the growth of C. sakazakii. In addition, the supernatant of L. kefiri DH5 induced the leakage of cytoplasmic materials including nucleic acid and proteins, suggesting L. kefiri DH5 disrupted the cellular membrane integrity of C. sakazakii. Considering that pH neutralisation reduced the L. kefiri-dependent growth suppression, it is inferred that this activity is mainly due to organic acids produced during the fermentation process.

Fermented Foods as a Dietary Source of Live Organisms

The popularity of fermented foods and beverages is due to their enhanced shelf-life, safety, functionality, sensory, and nutritional properties. The latter includes the presence of bioactive molecules, vitamins, and other constituents with increased availability due to the process of fermentation. Many fermented foods also contain live microorganisms that may improve gastrointestinal health and provide other health benefits, including lowering the risk of type two diabetes and cardiovascular diseases. The number of organisms in fermented foods can vary significantly, depending on how products were manufactured and processed, as well as conditions and duration of storage. In this review, we surveyed published studies in which lactic acid and other relevant bacteria were enumerated from the most commonly consumed fermented foods, including cultured dairy products, cheese, fermented sausage, fermented vegetables, soy-fermented foods, and fermented cereal products. Most of the reported data were based on retail food samples, rather than experimentally produced products made on a laboratory scale. Results indicated that many of these fermented foods contained 105-7 lactic acid bacteria per mL or gram, although there was considerable variation based on geographical region and sampling time. In general, cultured dairy products consistently contained higher levels, up to 109/mL or g. Although few specific recommendations and claim legislations for what constitutes a relevant dose exist, the findings from this survey revealed that many fermented foods are a good source of live lactic acid bacteria, including species that reportedly provide human health benefits.

Growth Inhibition of Cronobacter sakazakii in Experimentally Contaminated Powdered Infant Formula by Kefir Supernatant

Kefir is a type of fermented milk containing lactic and acetic acid bacteria and yeast. In this study, we evaluated the antimicrobial activity of kefir supernatant against Cronobacter sakazakii in powdered infant formula (PIF). In a spot-on-lawn test, the growth of 20 C. sakazakii strains, including 10 clinical and 10 food isolates, was completely inhibited in the presence of kefir supernatant. Significant differences in the diameters of inhibition zones were observed upon treatment with kefir compared with the results for Lactobacillus kefiri and Candida kefyr culture supernatants or solutions of lactic and acetic acid and ethyl alcohol in the agar well diffusion test (P < 0.05). The addition of 100 μl of kefir supernatant to 1 ml of nutrient broth completely inhibited the growth of C. sakazakii, as evaluated by spectrophotometry. The antimicrobial activity of kefir supernatant in experimentally contaminated PIF was also tested; we found no viable C. sakazakii cells remaining in PIF rehydrated with 30% kefir supernatant solution for 1 h, demonstrating that the antimicrobial activity of kefir supernatant against C. sakazakii could be applied in real food samples.