Molecular Monitoring of Bacterial Community Structure in Long-Aged Nukadoko: Pickling Bed of Fermented Rice Bran Dominated by Slow-Growing Lactobacilli

Direct contact of fermented rice bran beds promotes food-to-hand transmission of lactic acid bacteria

The skin microbiome, which varies widely between individuals, plays a crucial role in human health. It also interacts with the environment in various ways, including during the preparation of fermented food. Nukadoko is a pickle and traditional fermented food in Japan that utilizes lactic acid bacteria to ferment vegetables. When preparing or maintaining Nukadoko, it is mixed with bare hands. Despite the known interaction between Nukadoko and human skin, no studies have explored its impact on Nukadoko quality or skin microbiome changes. This study examines these effects during Nukadoko maintenance. Three participants were asked to stir commercially available late-stage Nukadoko for 14 days and not stir it for the remaining 14 days to examine microbial settlement and shedding. Microbiome analysis was performed on human skin and Nukadoko. We found that microorganisms from rice bran beds can temporarily settle on human skin but are shed quickly. Stirring rice bran beds by hand may have short-term effects on the skin microbiome. This study provides insights into the communication between human and food microbiomes in traditional Japanese fermented foods.

Microbiological and Chemical Characteristics of Wet Coffee Fermentation Inoculated With Hansinaspora uvarum and Pichia kudriavzevii and Their Impact on Coffee Sensory Quality

Hansinaspora uvarum and Pichia kudriavzevii were used as starter cultures to conduct inoculated wet fermentations of coffee beans, and their growth, metabolic activities and impact on the flavor, aroma and overall sensory quality of coffee were compared with spontaneous fermentation (control). H. uvarum and P. kudriavzevii dominated the fermentations, growing to maximum populations of about 10.0 log CFU/ml compared with 8.0 log CFU/ml in the spontaneous fermentation. The dominance of the inoculated yeasts led to faster and more complete utilization of sugars in the mucilage, with resultant production of 2–3 fold higher concentrations of metabolites such as glycerol, alcohols, aldehydes, esters, and organic acids in the fermented green beans. Cup tests showed coffee produced from the inoculated fermentations, especially with P. kudriavzevii, received higher scores for flavor, aroma and acidity than the control. The findings of this study confirmed the crucial role of yeasts in the wet fermentation of coffee beans and their contribution to high quality coffee, and demonstrated the potential H. uvarum and P. kudriavzevii as starter cultures in the process.

Evaluation of Rate of Adhesion of Lactobacillus namurensis Strain GYP-74 to Porous Fine Ceramics

This study aimed to evaluate the ratio of adherence of lactic acid bacteria (LAB) to porous fine ceramics in order to develop a novel LAB-rich pickle container for the production of functional fermented vegetables. Some LAB were isolated from the salted rice bran used for pickling (Nukadoko in Japanese). These isolates were classified in Lactobacillus namurensis by phylogenetic analysis. Some pottery-shard (PS) samples were prepared by varying the mixing rate of polyacetal (POM) resin to clay (0–30% (v/v)) and the burning temperature (1000 °C or 1100 °C). A test of the adherence of strain GYP-74 to the PSs was performed. The results showed that the adherence rate was significantly higher in the PSs burned at 1100 °C as compared with those burned at 1000 °C. A pore distribution analysis showed that pore sizes of less than a few µm and pore sizes in the range of a few µm to a few hundred µm were mainly distributed in the PSs without and with POM, respectively. X-ray diffraction analysis showed that both PSs with and without POM contained quartz and hematite. The PSs burned at 1000 °C and 1100 °C specifically contained microcline and mullite, respectively. This study revealed the basal information regarding what makes PSs adequate for LAB adhesion.

The relationships between microbiota and the amino acids and organic acids in commercial vegetable pickle fermented in rice-bran beds

The microbial community during fermented vegetable production has a large impact on the quality of the final products. Lactic acid bacteria have been well-studied in such processes, but knowledge about the roles of non-lactic acid bacteria is limited. This study aimed to provide useful knowledge about the relationships between the microbiota, including non-lactic acid bacteria, and metabolites in commercial pickle production by investigating Japanese pickles fermented in rice-bran. The samples were provided by six manufacturers, divided into two groups depending on the production conditions. The microbiological content of these samples was investigated by high-throughput sequencing, and metabolites were assessed by liquid chromatography-mass spectrometry and enzymatic assay. The data suggest that Halomonas, halophilic Gram-negative bacteria, can increase glutamic acid content during the pickling process under selective conditions for bacterial growth. In contrast, in less selective conditions, the microbiota consumed glutamic acid. Our results indicate that the glutamic acid content in fermented pickle is influenced by the microbiota, rather than by externally added glutamic acid. Our data suggest that both lactic acid bacteria and non-lactic acid bacteria are positive key factors in the mechanism of commercial vegetable fermentation and affect the quality of pickles.

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.

qPCR quantification of Carnobacterium maltaromaticum, Brochothrix thermosphacta, and Serratia liquefaciens growth kinetics in mixed culture

Quantifying growth kinetics of specific spoilage microorganisms in mixed culture is required to describe the evolution of food microbiomes. A qPCR method was developed to selectively amplify individual meat spoilage bacteria, Carnobacterium maltaromaticum, Brochothrix thermosphacta and Serratia liquefaciens, within a broth medium designed to simulate the composition of beef. An optimized method of DNA extraction was produced for standard curve construction. Method specificity was determined by individual single peaks in melt curves. Reaction efficiency for standard curves of C. maltaromaticum, B. thermosphacta and S. liquefaciens was high (R² = 0.98-0.99), and linear quantification was achieved over a 5 log CFU/ml range. Coefficient of variation was calculated considering both threshold cycle (C_t) and bacterial concentration; the value did not exceed 14% for inter- or intra-runs for either method. Comparison of growth kinetic parameters derived from plate count and qPCR showed no significant variation (P > .05) for growth rate (GR) and maximum population density (MPD); lag phase duration (LPD) was not included in this comparison due to high innate variability. Log quantification of each isolate was validated in a mixed-culture experiment for all three species with qPCR and plate count differing less than 0.3 log CFU/ml (average 0.10 log CFU/ml, R² = 0.98).

Ingestion of paddy rice increases intestinal mucin secretion and goblet cell number and prevents dextran sodium sulfate-induced intestinal barrier defect in chickens

Paddy rice is a potential feed grain for chickens, whose strong gizzards can crush the hull. Here, we investigated whether paddy rice rich in hull-derived water-insoluble dietary fiber stimulates intestinal mucin secretion and production, as well as the possible involvement of paddy rice in intestinal barrier function. Layer male chicks at 7 d of age were divided into four groups according to the diet: corn, polished rice, brown rice, or paddy rice (650 g/kg diet), which they ate for 14 consecutive days. At 21 d of age, the birds were refed their experimental diets, and small intestinal mucin fractions were collected to determine intestinal mucin content. Small intestinal mucin secretion was induced most strongly in the paddy rice group (Experiment 1). The rank order of diet-induced mucin secretion was paddy rice > corn = brown rice > polished rice. Ileal MUC2 gene expression and ileal number of goblet cells were highest in the paddy rice group (Experiment 1). A study of bromodeoxy-U uptake into ileal epithelial cells indicated the increase in goblet cells in the paddy rice group was related to accelerate epithelial cell migration (Experiment 2). A single supplementation of isolated rice hulls without kernels increased MUC2 gene expression and goblet cell numbers (Experiment 3), suggesting the importance of the hull's bulk-forming capacity on mucin production. Finally, chicks fed corn or paddy rice were orally administered dextran sodium sulfate (DSS) to disrupt intestinal barrier function. In the DSS-treated birds, the intestinal permeability of fluorescein isothiocyanate dextran in the everted gut sacs was much lower in the paddy rice group than in the corn group (Experiment 4), showing that paddy rice protects against mucosal disruption. In conclusion, ingestion of paddy rice increases intestinal mucin secretion and production through enhanced MUC2 gene expression and epithelial turnover and prevents DSS-induced intestinal barrier defects in chickens.

Human microbiome versus food-borne pathogens: friend or foe

As food safety advances, there is a great need to maintain, distribute, and provide high-quality food to a much broader consumer base. There is also an ever-growing "arms race" between pathogens and humans as food manufacturers. The human microbiome is a collective organ of microbes that have found community niches while associating with their host and other microorganisms. Humans play an important role in modifying the environment of these organisms through their life choices, especially through individual diet. The composition of an individual's diet influences the digestive system-an ecosystem with the greatest number and largest diversity of organisms currently known. Organisms living on and within food have the potential to be either friends or foes to the consumer. Maintenance of this system can have multiple benefits, but lack of maintenance can lead to a host of chronic and preventable diseases. Overall, this dynamic system is influenced by intense competition from food-borne pathogens, lifestyle, overall diet, and presiding host-associated microbiota.

Effects of Japanese pepper and red pepper on the microbial community during nukadoko fermentation

Nukadoko is a fermented rice bran bed traditionally used for pickling vegetables in Japan. To date, the production of both homemade and commercial nukadoko has depended on natural fermentation without using starter cultures. Spices, Japanese pepper, and red pepper, are added to nukadoko empirically, but the functions of spices in nukadoko have not been fully elucidated. To investigate the effects of Japanese pepper and red pepper on nukadoko fermentation, we compared the chemical and microbiological changes during 2 months of fermentation of a laboratory model nukadoko with or without spices. The successive pH values and colony counts in the first 10 days showed that the spices promoted lactic acid bacteria (LAB) growth and fermentation in the nukadoko niche. The successive bacterial communities during natural fermentation of nukadoko were carefully monitored by pyrotag 16S rRNA analysis, and the effect of spices on the development and maintenance of the nukadoko microbiota was investigated. It was shown that addition of Japanese peppers and red peppers shortened the pre-lactic acid fermentation phase, during which Staphylococcus saprophyticus grew dominantly, and promoted the development of a microbiota that LAB dominated. Notably, the growth of the dominant LAB, Pediococcus pentosaceus, was improved by adding either Japanese pepper or red pepper. The differences in the LAB species, which were associated with the differences in chemical composition of the nukadoko, were dependent on the type of pepper used. We conclude that the spices used can affect the bacterial community and modulate its metabolic profile in nukadoko.

Lactobacillus furfuricola sp. nov., isolated from Nukadoko, rice bran paste for Japanese pickles

Two strains of lactic acid bacteria, Nu27T and Nu29, were isolated from Nukadoko, rice bran paste for Japanese pickles. The isolates were Gram-stain-positive, rod-shaped, catalase-negative, non-motile and facultatively anaerobic lactic acid bacteria. The isolates showed identical 16S rRNA gene sequences. The closest relatives to strain Nu27T based on 16S rRNA gene sequence similarities were Lactobacillus versmoldensis KU-3T (98.9 % 16S rRNA gene sequence similarity), Lactobacillus nodensis iz4bT (96.3 %) and Lactobacillus tucceti CECT 5290T (97.2 %). DNA–DNA relatedness values revealed genotype separation of the two isolates from the above three species. Based on the physiological, biochemical and genotypic characteristics provided, the isolates represent a novel species of the genus Lactobacillus , for which name is Lactobacillus furfuricola proposed. The type strain is Nu 27T ( = JCM 18764T = NRIC 0900T = DSM 27174T).

Draft Genome Sequence of Lactobacillus namurensis Chizuka 01, Isolated from Nukadoko, a Pickling Bed of Fermented Rice Bran

Lactobacillus namurensis Chizuka 01 was isolated from nukadoko, which is a fermented rice bran bed traditionally used in Japan for pickling vegetables. Here, we report the first draft of an annotated genome sequence of this organism. This paper is the first published report of the genomic sequence of L. namurensis.

Identification and characterization of novel multiple bacteriocins produced by Lactobacillus sakei D98

AIM

To characterize novel multiple bacteriocins produced by Lactobacillus sakei D98.

METHODS AND RESULTS

Lactobacillus sakei D98 isolated from Shubo (rice malt) produced at least three bacteriocins. Using three purification steps, three novel antimicrobial peptides termed sakacin D98a, sakacin D98b and sakacin D98c were purified from the culture supernatant. Amino acid and DNA sequencing analysis revealed that the sakacins D98a, D98b and D98c are novel class IIa-like or class IId bacteriocins. In particular, sakacin D98b has a variant pediocin-box sequence, YANGVXC (with Ala instead of Gly), and a different location for the disulfide bridge (Cys(11) and Cys(18)) from that found in other class IIa bacteriocins.

CONCLUSIONS

Three novel bacteriocins were identified from Lactobacillus sakei D98. Their antimicrobial spectra and intensities indicate that these sakacins would have different modes of action. In addition, sakacin D98b showed low inhibitory activity against Listeria, probably due to the differences in amino acids and position of the disulfide bridge compared with the other class IIa bacteriocins.

SIGNIFICANCE AND IMPACT OF STUDY

Sakacins D98a and D98c are novel bacteriocins belonging to class IId bacteriocins. On the other hand, sakacin D98b, a class IIa-like bacteriocin, has a unique internal structure and activity spectrum.

Production potency of folate, vitamin B(12), and thiamine by lactic acid bacteria isolated from Japanese pickles

We investigated the extracellular production of folate, vitamin B(12), and thiamine in cultures of lactic acid bacteria (LAB) isolated from nukazuke, a traditional Japanese pickle, and the relationships between the vitamin production and such properties of LAB as tolerance to salts, ethanol, etc. Among the 180 isolates of LAB, two strains of Lactobacillus (Lb.) sakei and a strain of Lb. plantarum extracellularly produced high levels of folate (about 100 µg/L). A strain of Lb. coryniformis and one of Lb. plantarum produced about 2 µg/L of vitamin B(12), although the level was not high. No isolates produced a high level of thiamine. The type cultures of LBA (53 strains) did not show any higher production of these vitamins. Some isolates showed tolerance to high concentrations of salts and alcohol, and low initial pH. No significant relationships between folate or vitamin B(12) productions and these properties of LAB were apparent.

Microbial dynamics and biodiversity in table olive fermentation: culture-dependent and -independent approaches

The microbial ecology of the table olive fermentation process is a complex set of dynamics in which the roles of the lactic acid bacteria (LAB) and yeast populations are closely related, and this synergism is of fundamental importance to obtain high quality products. Several studies on the ecology of table olives, both in spontaneous fermentations and in inoculated ones, have focused on the identification and characterization of yeasts, as they play a key role in the definition of the final organoleptic profiles through the production of volatile compounds. Moreover, these are able to promote the growth of LAB, which is responsible for the stabilization of the final product through the acidification activity and the inhibition of the growth of pathogenic bacteria. The current empirical production process of table olives could be improved through the development of mixed starter cultures. These can only be developed after a deep study of the population dynamics of yeasts and LAB by means of molecular methods. Until now, most studies have exploited culture-dependent approaches to define the natural microbiota of brine and olives. These approaches have identified two main species of LAB, namely Lactobacillus plantarum and L. pentosus, while, as far as yeasts are concerned, the most frequently isolated genera are Candida, Pichia, and Saccharomyces. However, there are a few studies in literature in which a culture-independent approach has been employed. This review summarizes the state of the art of the microbial ecology of table olive fermentations and it focuses on the different approaches and molecular methods that have been applied.

Comparison of PCR-DGGE and PCR-SSCP analysis for bacterial flora of Japanese traditional fermented fish products, aji-narezushi and iwashi-nukazuke

BACKGROUND

The bacterial flora of two Japanese traditional fermented fish products, aji-narezushi (salted and long-fermented horse mackerel (Trachurus japonicas) with rice) and iwashi-nukazuke (salted and long-fermented sardine (Sardinops melanostica) with rice bran), was analysed using non-culture-based polymerase chain reaction (PCR) denaturing gradient gel electrophoresis (DGGE) and culture-based PCR single-strand conformation polymorphism (SSCP) methods.

RESULTS

Viable plate counts in aji-narezushi and iwashi-nukazuke were about 6.3-6.6 and 5.7-6.9 log colony-forming units g(-1) respectively. In the PCR-DGGE analysis, Lactobacillus acidipiscis was detected as the predominant bacterium in two of three aji-narezushi samples, while Lactobacillus versmoldensis was predominant in the third sample. By the PCR-SSCP method, Lb. acidipiscis and Lactobacillus plantarum were isolated as the predominant bacteria, while Lb. versmoldensis was not detected. The predominant bacterium in two of three iwashi-nukazuke samples was Tetragenococcus muriaticus, while Tetragenococcus halophilus was predominant in the third sample.

CONCLUSION

The results suggest that the detection of some predominant lactic acid bacteria species in fermented fish by cultivation methods is difficult.

Identification and characterization of novel multiple bacteriocins produced by Leuconostoc pseudomesenteroides QU 15

AIM

To characterize novel multiple bacteriocins produced by Leuconostoc pseudomesenteroides QU 15.

METHODS AND RESULTS

Leuconostoc pseudomesenteroides QU 15 isolated from Nukadoko (rice bran bed) produced novel bacteriocins. By using three purification steps, four antimicrobial peptides termed leucocin A (ΔC7), leucocin A-QU 15, leucocin Q and leucocin N were purified from the culture supernatant. The amino acid sequences of leucocin A (ΔC7) and leucocin A-QU 15 were identical to that of leucocin A-UAL 187 belonging to class IIa bacteriocins, but leucocin A (ΔC7) was deficient in seven C-terminal residues. Leucocin Q and leucocin N are novel class IId bacteriocins. Moreover, the DNA sequences encoding three bacteriocins, leucocin A-QU 15, leucocin Q and leucocin N were obtained.

CONCLUSIONS

These bacteriocins including two novel bacteriocins were identified from Leuc. pseudomesenteroides QU 15. They showed similar antimicrobial spectra, but their intensities differed. The C-terminal region of leucocin A-QU 15 was important for its antimicrobial activity. Leucocins Q and N were encoded by adjacent open reading frames (ORFs) in the same operon, but leucocin A-QU 15 was not.

SIGNIFICANCE AND IMPACT OF STUDY

These leucocins were produced concomitantly by the same strain. Although the two novel bacteriocins were encoded by adjacent ORFs, a characteristic of class IIb bacteriocins, they did not show synergistic activity.