Microbiological study of lactic acid fermentation of Caper berries by molecular and culture-dependent methods

Physicochemical and microbial community dynamics of Kocho fermented from different enset varieties in South West Ethiopia

Enset (Ensete ventricosum (Welw.) Cheesman) is an indigenous multipurpose plant in Ethiopia. More than 20 % of people in Ethiopia rely on enset for their subsistence livelihood. Its fermentation produces a starchy food named Kocho, which is yet poorly studied. In this study, physicochemical and microbial community dynamics of Kocho fermented from different enset varieties (Maziya, Genna, and Arkiya) were collected at Dawro Zone (Southern Ethiopia). Samples were collected at various fermentation times (days 1-60) for physicochemical and microbial (culture-dependent and culture-independent) characterization. Results showed that increasing fermentation time has a significantly strong positive (R2 = 0.768, p = 0.004) correlation between titrable acidity, and a significantly strong negative association with pH (R2 = -0.715, p = 0.009), moisture (R2 = -0.982, p < 0.05), ash (R2 = -0.932, p < 0.05), fat (R2 = -0.861, p < 0.05), fiber (R2 = -0.981, p < 0.05) and carbohydrate (R2 = -0.994, p < 0.001) contents. An increasing or decreasing trend of physicochemical parameters observed during enset fermentation is significantly associated with microbial community dynamics. Shifts of microbial community observed during culture-dependent analysis were also confirmed by metagenomic results. During fermentation, Firmicutes (39-68 %) > Proteobacteria (7-53 %) > Cyanobacteria (7-24 %) were dominant phyla in the three enset varieties. Gamma (traditional starter culture) is dominated by Lactobacillus plantrum and Lactobacillus manihotivorans most probably the two species that play a significant role in initiating enset fermentation.

Capparis spinosa L. as a potential source of nutrition and its health benefits in foods: A comprehensive review of its phytochemistry, bioactivities, safety, and application

Capparis spinosa L. (C. spinosa) is an edible plant with health-promoting benefits. C. spinosa possesses various biological activities, including antioxidant, antidiabetic, anticancer, hepatoprotective, neuroprotective, anti-inflammatory, anti-arthritic, antibacterial, and insecticidal effects. The active compounds associated with these effects mainly include flavonoids, phenolic acids, alkaloids, volatile oils, fatty acids, and polysaccharides. Moreover, C. spinosa has considerable nutritional value. Apart from being a food condiment, it belongs to a class of functional ingredients that act as preservatives and antioxidants in food products. C. spinosa has also shown good potential applications in novel food packaging materials. In this article, in addition to systematically reviewing the botanical characteristics, traditional edible uses, phytochemical composition, bioactivities and safety of C. spinosa, we highlight for the first time its potential applications in the foods. The findings will provide critical information for the future development of C. spinosa into a multifunctional food product with essential roles in health benefits.

Towards Recreation of Food Commodities Based on Ancient Texts; The Case of Avyrtake

The aim of the present study was to attempt the recreation of a highly appreciated food commodity of antiquity, called avyrtake, using information derived from ancient texts. The available information included the raw materials, the texture and the taste of the raw materials. On the contrary, the relative proportion of the raw materials as well as the production procedure had to be inferred on the basis of their modern-day use. For that purpose, and based on the above, a mixture of shredded cabbage and leek, salt, pomegranate seeds, raisins, and shredded garlic, as well as ground green cardamon and mustard seeds were pressed into a fermentation jar in order to form a brine and left at 18 °C for fermentation to take place. The latter was driven by lactic acid bacteria, mostly by Lactiplantibacillus plantarum. The final product had a sour character, which matched the organoleptic description available from the ancient texts, and it received high ranks.

Antibiotic susceptibility of Lactobacillus plantarum strains, isolated from katak

Several Lactobacillus species are accepted as microorganisms with Qualified Presumption of Safety (QPS) in the EFSA’s list. One of them, Lactobacillus plantarum is a widely distributed species with a proven probiotic potential and technological relevance. In addition, every strain must complete several requirements, before implementation. Antibiotic susceptibility is one of EFSA’s important criteria regarding the safety of probiotics. The reason is to avoid any possibility of antibiotic resistance genes transfer to opportunistic pathogens in the gut. In the present study 14 Lactobacillus plantarum strains were assessed for susceptibility to 21 antibiotics from different groups. A high number of resistant strains was determined toward 12 antibiotics (penicillins – penicillin, piperacillin; IIIth generation cephalosporins – cefotaxime, ceftriaxone, ceftazidime; glycopeptides – vancomycin; tetracyclines – tetracycline; aminoglycosides – gentamicin; macrolides – clarithromycin; quinolones – nalidixic acid, ciprofloxacin, levofloxacin). Concerning the other tested antibiotics, strain-specific antibiotic-sensitivity patterns were observed. Antibiotic resistance was also discussed as an advantage in the selection of probiotic strains, however only when it is not transferable. Estimated susceptibility patterns of some of tested candidate probiotic strains are also important, considering the use of the latter as agents accompanying antibiotic therapy

Biotreatment efficiency, hydrolytic potential and bacterial community dynamics in an immobilized cell bioreactor treating caper processing wastewater under highly saline conditions

Although caper processing wastewaters (CPW) are characterized by high organic content and salt concentration, no attempt has been made to treat these effluents. In this study, an immobilized cell bioreactor efficiently treated CPW even at hypersaline conditions (100 g/L salinity). Nitrogen was mainly assimilated during biotreatment, as nitrification was inhibited at elevated salinities. The hydrolytic potential was assessed by determining glucanase, xylanase, glucosidase, lipase and protease activities, which were negatively affected above 20 g/L salinity as the consequence of the inhibition of non-halotolerant microbiota. Succession of non-halotolerant taxa by the slightly halotolerant bacteria Defluviimonas, Amaricoccus, Arenibacter, Formosa and Muricauda, and then by the moderately/extremely halotolerant genera Halomonas, Roseovarius and Idiomarina occurred over salinity increase. Diversity indices were reduced during transition from moderately saline to hypersaline conditions. A distinct network was formed at hypersaline conditions, consisting of the halotolerant genera Halomonas, Idiomarina, Saliterribacillus and Gracilibacillus.

Microbial Profile Antibacterial Properties and Chemical Composition of Raw Donkey Milk

The human interest in donkey milk is growing due to its nutritional, functional properties and excellent microbiological quality according to published reports. However, more research needs to be conducted to assess the above variables from various breeds. In the present study, milk samples were collected from 17 Cypriot and six Arcadian healthy Greek donkeys. The microbiological quality, somatic cell counts (SCC), chemical composition analysis, and antimicrobial activity of the samples was assessed. In addition, clustering and identification of the bacterial composition was performed by RAPD-PCR and 16S rDNA sequencing, respectively. The good microbiological quality of the samples as estimated by the total aerobic mesophilic and psychrotrophic counts, which ranged from 2.18 to 2.71 log CFU/mL and from 1.48 to 2.37 log CFU/mL, respectively, was also verified. SCC were below 4.4 log CFU/mL. However, potential pathogenic species of Staphylococcus aureus, Bacillus cereus, and Clostridium spp. were enumerated in the milk of both breeds. The gross chemical composition showed mean values for fat, protein, and lactose from 0.82% to 1.24%, 1.22% to 1.87%, and 6.01% to 6.78%, respectively. All milk samples exhibited an antimicrobial activity against St. haemolyticus and Listeria monocytogenes, although quality control measures should be taken for health and safety prior to human consumption.

LC-DAD-ESI-MS/MS-based assessment of the bioactive compounds in fresh and fermented caper (Capparis spinosa) buds and berries

The main objective of this study was to compare bioactive compounds and other important quality parameters of fresh and fermented caper buds and berries. Fresh samples were fermented using dry-salted and brined techniques. The higher phenolic content was determined in the fresh (1843.71 mg/100 g DW) and fermented buds (1198.54-1539.49 mg/100 g DW) rather than the berries (29.72-40.75 mg/100 g DW). Quercetin-3-O-rutinoside, kaempferol-3-O-rutinoside, and quercetin-O-galloly-O-hexoside were the principal phenolic components in fresh and fermented buds while quercetin-3-O-rutinoside in fresh and fermented berries. The amounts of isorhamnetin, quercetin, and kaempferol increased in fermented buds and berries compared to fresh samples. Similarly, antioxidant capacity of buds was found to be markedly higher than berries. As for sugar compounds, it was found that fructose in buds (1.56-3.23 g/100 g DW) and glucose in berries (1.96-6.38 g/100 g DW) had the highest amount. When total phenolics and antioxidant properties were evaluated, it was observed that they were better preserved in the dry-salted samples than the brined samples.

Polyphenol Compounds and Biological Activity of Caper (Capparis spinosa L.) Flowers Buds

The aim of the study was to analyze potential health-promoting components of caper flower buds (Capparis spinosa L.) at six stages of development in two cultivars. Polyphenol compounds (flavonols, hydroxycinnamic acids, flavan-3-ols) were identified by Liquid Chromatography- quadrupole Time-of-Flight -Mass Spectrofotometer/Mass Spectrofotometer (LC-qTOF-MS/MS) and quantified by Ultra Performance Liquid Chromatography-Photodiode Array-Fluorescence Detector (UPLC-PDA-FL). Moreover, antioxidant properties (ABTS+•, FRAP, and ORAC), anti-diabetic potential (α-amylase and α-glucosidase), and anti-aging activity (acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE)) of the buds were examined. Total phenolic compounds in the investigated caper varied from 10,720 to 3256 mg/100 g dry weight (DW), and depended on a genotype and growing stage of caper flowers. Among six different growing stages, the one named 'nonpareilles' was characterized by significantly higher content of polyphenols than the remaining five stages. The flavonols in caper flowers represented a mixture of different glycosylated quercetin, kaempferol, myricetin, and isorhamnetin derivatives, accounting for 38%-67%, 15%-36%, 4%-7%, and 0.8%-3%, respectively, of total flavonols,. Their contents strongly depended on the growth stage. 'Nonpareilles' and 'surfines' were richer in flavonols than 'fines' and 'gruesas'. Of the six investigated growth stages, 'nonpareilles' accumulated the greatest amounts of bioactive compounds that correlated with antioxidant and anti-diabetic properties, and were more potent BuChE than AChE inhibitors.

Screening of lactic starter from Tunisian fermented vegetables and application for the improvement of caper (Capparis spinosa) fermentation through an experimental factorial design

Purpose

This study aims at designing a lactic starter for caper fermentation isolated from Tunisian fermented vegetables to improve the process and produce consistent and high-quality product.

Methods

In this study, the lactic starter was isolated by exploring the lactic acid bacteria (LAB) of Tunisian artisanal fermented vegetables. Identification was carried out by partial 16S rRNA gene sequencing. Screening was based on salt tolerance and antagonistic activities against Escherichia coli ATCC 10536 and Enterococcus faecalis ATCC 10541. Caper fermentation was optimized through a full factorial experimental design (23), by exploring three factors: starter inoculum size, NaCl concentration, and acetate content. Differences in pH values, Total aerobic mesophilic bacteria and LAB counts between the beginning and end of fermentation are selected as responses and corresponding regression coefficients were calculated.

Results

The lactic microbiota is mainly represented by Lactobacillus plantarum group. Based on salt tolerance and antimicrobial activity, the strain Lactobacillus plantarum F3 was selected as starter for caper fermentation. The effect of NaCl concentration, acetate content, and inoculum size on acidity, total aerobic mesophilic bacteria count, and LAB count after 1 week and 1 month of caper fermentation was studied. Depending on the fermentation time, either 1 week or 1 month, the initial conditions should comprise 0% acetate, 108 CFU/mL inoculum, and 5% NaCl for 1 week against 5% acetate, 107 CFU/mL inoculum, and 10% NaCl for 1 month lasting caper fermentation. A protocol for caper fermentation was set up ensuring hygienic quality and LAB viability.

Conclusion

Lb. plantarum F3 was selected as lactic starter for caper fermentation, and initial fermentation conditions were optimized through a full factorial design. This work has shown loss in LAB viability after 1 week of fermentation. Based on results obtained, an optimized fermentation protocol was set up. This protocol ensures LAB survival and high hygienic quality of the product.

Characterization of Aroma-Active Compounds, Phenolics, and Antioxidant Properties in Fresh and Fermented Capers (Capparis spinosa) by GC-MS-Olfactometry and LC-DAD-ESI-MS/MS

Caper (Capparis spinosa) is an important food ingredient whose fresh parts, particularly the flower buds, are consumed as a starter with olives, cheese, and nuts, or are used as a component in other foods. It is one of the most popular species of aromatic plants grown in the Mediterranean zone. Fermentation makes the caper edible and affects the overall aroma as well as sensory and nutritional characteristics. This study aimed to evaluate the changes in aroma, aroma-active, and phenolic compounds of caper as affected by fermentation. Purge and trap method was used for the extraction of the aroma compounds, while gas chromatography-mass spectrometry olfactometry and Liquid chromatography coupled to diode array detection and electrospray ionization tandem mass spectrometry (LC-DAD-ESI-MS/MS) were employed for the detection of aroma-active compounds and phenolics, respectively. The results showed that the total amount of aroma compounds decreased drastically (62,616 to 21,471 µg/kg) in fermented sample. Twelve and 10 aroma-active compounds were detected in fresh and fermented caper buds, respectively, for the first time by the application of aroma extract dilution analysis. Among these compounds, methyl isothiocyanate (flavor dilution [FD] factor = 512) in fresh caper and acetic acid (FD factor = 128) in the fermented caper had the highest FD factor. With regard to the phenolic compounds, a total of 16 components were identified in fresh and fermented capers. As observed in aroma compounds, the total phenolic concentration decreased as a result of fermentation. Two phenolic compounds being kaempferol-3-O-glucosyl-rhamnosyl-glucoside and isorhamnetin hexoside were newly identified in caper. PRACTICAL APPLICATIONS: Capparis spinosa is one of the most popular sources of different secondary metabolites of interest to consumers. The results of the present study showed that the fermentation process of the capers is highly influential on the neutral composition of the sample. The total concentrations of aroma and phenolic compounds were reduced by 66% and 78%, respectively, in response to fermentation process.

Pharmacological Effects of Capparis spinosa L

Medicinal plants have been known as one of the most important therapeutic agents since ancient times. During the last two decades, much attention has been paid to the health-promoting effects of edible medicinal plants, because of multiple beneficial effects and negligible adverse effects. Capparis spinosa L. is one of the most common medicinal plants, used widely in different parts of the world to treat numerous human diseases. This paper aims to critically review the available scientific literature regarding the health-promoting effects of C. spinosa, its traditional uses, cultivation protocols and phytochemical constituents. Recently, a wide range of evidence has shown that this plant possesses different biological effects, including antioxidant, anticancer and antibacterial effects. Phytochemical analysis shows that C. spinosa has high quantities of bioactive constituents, including polyphenolic compounds, which are responsible for its health-promoting effects, although many of these substances are present in low concentrations and significant changes in their content occur during processing. In addition, there is negligible scientific evidence regarding any adverse effects. Different health promotion activities, as well as tremendous diversity of active constituents, make C. spinosa a good candidate for discovering new drugs. However these findings are still in its infancy and future experimental and clinical studies are needed. Copyright © 2016 John Wiley & Sons, Ltd.

Optimised method for the analysis of phenolic compounds from caper (Capparis spinosa L.) berries and monitoring of their changes during fermentation

In this work, an ad hoc method to identify and quantify polyphenols from caper berries was developed on high-performance liquid chromatography/electrospray ionisation source/mass spectrometry (HPLC-ESI-MS). The method was applied during fermentation carried out with Lactobacillus pentosus OM13 (Trial S) and without starter (Trial C). A total of five polyphenols were identified. All samples contained high concentrations of rutin. Epicatechin was found in untreated fruits, on the contrary quercetin was detected during fermentation. Trial S was characterised by a more rapid acidification and lower levels of spoilage microorganisms than Trial C. L. pentosus dominated among the microbial community of both trials and the highest biodiversity, in terms of strains, was displayed by Trial C. Aureobasidium pullulans was the only yeast species found. The analytical method proposed allowed a high polyphenolic compound recovery from untreated and processed caper berries in short time. The starter culture reduced the bitter taste of the final product.

Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC

Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.

Bacillus species isolated from tungrymbai and bekang, naturally fermented soybean foods of India

Tungrymbai and bekang are naturally fermented soybean foods commonly consumed in Meghalaya and Mizoram states of India. A total of 39 samples of tungrymbai and 43 samples of bekang were collected from different villages and markets of Meghalaya and Mizoram, respectively and were analysed for microbial load. In both tungrymbai and bekang, the average population of Bacillus spp. was 8.2±0.1 log cfu/g. A total of 428 isolates of Bacillus were isolated from tungrymbai (211) and bekang (217) for detailed identification. On the basis of a combination of phenotypic and molecular characterisation using ARDRA, ITS-PCR and RAPD-PCR techniques, species of Bacillus isolated from tungrymbai were identified as Bacillus licheniformis (25.5%), Bacillus pumilus (19.5%) and Bacillus subtilis (55%), and species of Bacillus from bekang were Bacillus brevis (2%), Bacillus circulans (7.5%), Bacillus coagulans (6.5%), B. licheniformis (16.5%), B. pumilus (9.1%), Bacillus sphaericus (4.6%), B. subtilis (51.8%), and Lysinibacillus fusiformis (2%). The most dominant bacterium in both products was B. subtilis.

Effect of ripening stage on the development of the microbial community during spontaneous fermentation of green tomatoes

BACKGROUND

Spontaneous fermentation of plant-derived material is mainly performed on a small scale, with the exception of fermented olives, cucumbers, sauerkraut and kimchi, which have met worldwide commercial significance.

RESULTS

This study of spontaneous fermentation of green tomatoes at different stages of ripening revealed a significant effect on the growth kinetics of lactic acid bacteria and the final pH value. Leuconostoc mesenteroides dominated spontaneous fermentation when the initial pH value ranged from 3.8 to 4.8 whereas at higher pH values (4.9-5.4) it co-dominated with Leu. citreum and Lactobacillus casei. Application of RAPD-PCR and rep-PCR allowed differentiation at sub-species level, suggesting a microbial succession at that level accompanying the respective at species level.

CONCLUSION

Ripening stage affected the development of the micro-ecosystem through the growth of lactic acid bacteria and concomitant pH value reduction; however, the outcome of the fermentation was only marginally different.

Microbial diversity and flavor formation in onion fermentation

The fermentation of onions is not well understood. In this work, we focused on the analysis of microbial diversity and flavor formation in onion fermentation with indigenous flora (without starter cultures). Two different methods were used to establish the relationship between the microbes and the production of flavor. A link was made between the substrates, metabolites, and the microbes identified.

Applicability of Lactobacillus plantarum IMDO 788 as a starter culture to control vegetable fermentations

BACKGROUND

Fermentation of vegetables and fruits is a traditional preservation technique, e.g. in Eastern Europe. Although usually spontaneous fermentation processes are applied, the addition of lactic acid bacteria (LAB) starter cultures could accelerate processing and improve the consistency and quality of the end-products.

RESULTS

The application of Lactobacillus plantarum IMDO 788 as a starter culture strain for cauliflower and mixed vegetable fermentations resulted in accelerated acidification as compared with the spontaneous fermentations. The strain dominated the background microbiota throughout the process, whereas the spontaneous fermentations were characterised by widely variable species diversity. During the spontaneous fermentations, almost all carbohydrates were converted into lactic acid, ethanol, mannitol and acetic acid, indicating the participation of both heterofermentative and homofermentative LAB species. During the starter culture-added fermentations, residual carbohydrates were found and lactic acid and ethanol were the main end-metabolites. Vegetable-associated aromas, ethyl acetate and isoamyl acetate were produced during all fermentations. The high concentration of ethanol and the production of ethyl acetate and isoamyl acetate suggested the involvement of yeasts during all fermentations.

CONCLUSION

Lactobacillus plantarum IMDO 788 was an adequate starter culture strain for vegetable fermentations, prevailing over endogenous LAB communities. Further optimisation of the starter culture formulation is necessary to avoid yeast growth.

Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant

The in silico reconstruction of metabolic networks has become an effective and useful systems biology approach to predict and explain many different cellular phenotypes. When simulation outputs do not match experimental data, the source of the inconsistency can often be traced to incomplete biological information that is consequently not captured in the model. To address this problem, general approaches continue to be needed that can suggest experimentally testable hypotheses to reconcile inconsistencies between simulation and experimental data. Here, we present such an approach that focuses specifically on correcting cases in which experimental data show a particular gene to be essential but model simulations do not. We use metabolic models to predict efficient compensatory pathways, after which cloning and overexpression of these pathways are performed to investigate whether they restore growth and to help determine why these compensatory pathways are not active in mutant cells. We demonstrate this technique for a ppc knockout of Salmonella enterica serovar Typhimurium; the inability of cells to route flux through the glyoxylate shunt when ppc is removed was correctly identified by our approach as the cause of the discrepancy. These results demonstrate the feasibility of our approach to drive biological discovery while simultaneously refining metabolic network reconstructions.

Bacterial community dynamics, lactic acid bacteria species diversity and metabolite kinetics of traditional Romanian vegetable fermentations

BACKGROUND

Artisanal vegetable fermentations are very popular in Eastern European countries. Fresh vegetables undergo a spontaneous fermentation in the presence of salt, which is mainly carried out by lactic acid bacteria (LAB).

RESULTS

Culture-dependent and culture-independent analyses of end-samples of various spontaneous vegetable fermentations carried out in houses of the Chiodju region (central Romania) revealed Lactobacillus plantarum and Lactobacillus brevis as the most frequently isolated LAB species. Leuconostoc mesenteroides and Leuconostoc citreum were also found. Furthermore, the community dynamics of spontaneous cauliflower and mixed-vegetable (green tomatoes, carrots and cauliflower) fermentations revealed three steps: an initial phase characterised by the presence of Enterobacteriaceae and a wide LAB species diversity, encompassing Weissella species; a second phase from day 3 onwards wherein L. citreum and Lb. brevis occurred; and a final phase characterised by the prevalence of Lb. brevis and Lb. plantarum. Metabolite target analysis revealed that glucose and fructose were mostly depleted at the end of fermentation. The main products of carbohydrate metabolism were lactic acid, acetic acid, ethanol and small amounts of mannitol, indicating heterolactate fermentation.

CONCLUSION

Given their prevalence at the end of vegetable fermentations, Lb. brevis and Lb. plantarum appear to be good candidate starter cultures for controlled vegetable fermentation processes.

Combination of culture-independent and culture-dependent molecular methods for the determination of bacterial community of iru, a fermented Parkia biglobosa seeds

In this study, bacterial composition of iru produced by natural, uncontrolled fermentation of Parkia biglobosa seeds was assessed using culture-independent method in combination with culture-based genotypic typing techniques. PCR-denaturing gradient gel electrophoresis (DGGE) revealed similarity in DNA fragments with the two DNA extraction methods used and confirmed bacterial diversity in the 16 iru samples from different production regions. DNA sequencing of the highly variable V3 region of the 16S rRNA genes obtained from PCR-DGGE identified species related to Bacillus subtilis as consistent bacterial species in the fermented samples, while other major bands were identified as close relatives of Staphylococcus vitulinus, Morganella morganii, B. thuringiensis, S. saprophyticus, Tetragenococcus halophilus, Ureibacillus thermosphaericus, Brevibacillus parabrevis, Salinicoccus jeotgali, Brevibacterium sp. and uncultured bacteria clones. Bacillus species were cultured as potential starter cultures and clonal relationship of different isolates determined using amplified ribosomal DNA restriction analysis (ARDRA) combined with 16S-23S rRNA gene internal transcribed spacer (ITS) PCR amplification, restriction analysis (ITS-PCR-RFLP), and randomly amplified polymorphic DNA (RAPD-PCR). This further discriminated B. subtilis and its variants from food-borne pathogens such as B. cereus and suggested the need for development of controlled fermentation processes and good manufacturing practices (GMP) for iru production to achieve product consistency, safety quality, and improved shelf life.

Assessment of bacterial diversity in selected Philippine fermented food products through PCR-DGGE

The bacterial population in several Philippine fermented food preparations was assessed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) of the 16S rRNA gene (16S rDNA). Genomic DNA was isolated directly from alamang (fermented shrimp paste), burong isda (fermented fish and rice), burong hipon (fermented shrimp and rice), burong mustasa (fermented mustard leaves), tuba (sugar cane wine), suka (vinegar) and sinamak (spiced vinegar) using one of two protocols, namely - MoBio DNA Extraction Kit procedure and a cetyltrimethylammonium bromide-based method. Samples recalcitrant to both methods underwent enrichment in three culture broths prior to DNA isolation. Isolated DNA was amplified using nested primer pairs targeting the bacterial 16S rDNA. PCR products were subjected to DGGE to elucidate the bacterial diversity in each fermented food. 16S rDNA sequence analyses revealed that lactic acid bacteria (LAB) and acetic acid bacteria (AAB) were dominant in the food samples. The LAB identified were Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus panis, Lactobacillus pontis and Weissella cibaria. Identified AAB were Acetobacter pomorum, Acetobacter ghanensis, Acetobacter orientalis, and Acetobacter pasteurianus. Among these, L. fermentum, L. plantarum and W. cibaria are established probiotic bacteria, while L. panis and L. pontis are potential probiotic bacteria. This finding would increase the appeal and significance of local fermented foods to consumers. Furthermore, the majority of the identified bacteria in the study have not been reported before in culture-dependent studies of similar food preparations. As such, some of the bacterial 16S rDNA obtained were cloned to have an initial partial bacterial 16S rDNA library for Philippine fermented foods.

Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis)

Three strains of lactic acid bacteria (LAB) were isolated from the faeces of apparently healthy wild Canada geese (Branta canadensis) in 2010 by cultivating faecal LAB on Rogosa SL agar under aerobic conditions. These three isolates were found to share 99.9 % gene sequence similarity of their 16S rRNA, their 16S-23S intergenic transcribed spacer region (ITS), partial 23S rRNA, rpoB, rpoC, rpoA and pheS gene sequences. However, the three strains exhibited lower levels of sequence similarity of these genetic targets to all known LAB, and the phylogenetically closest species to the geese strains were Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus and Lactobacillus saniviri. In comparison to L. casei ATCC 393(T), L. paracasei ATCC 25302(T), L. rhamnosus ATCC 7469(T) and L. saniviri DSM 24301(T), the novel isolates reacted uniquely in tests for cellobiose, galactose, mannitol, citric acid, aesculin and dextrin, and gave negative results in tests for l-proline arylamidase and l-pyrrolydonyl-arylamidase, and in the Voges-Proskauer test. Biochemical tests for cellobiose, aesculin, galactose, gentiobiose, mannitol, melezitose, ribose, salicin, sucrose, trehalose, raffinose, turanose, amygdalin and arbutin could be used for differentiation between L. saniviri and the novel strains. On the basis of phenotypic and genotypic characteristics, and phylogenetic data, the three isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus brantae sp. nov. is proposed. The type strain is SL1108(T) (= ATCC BAA-2142(T) = LMG 26001(T) = DSM 23927(T)) and two additional strains are SL1170 and SL60106.

Polyphasic approach to bacterial dynamics during the ripening of Spanish farmhouse cheese, using culture-dependent and -independent methods

We studied the dynamics of the microbial population during ripening of Cueva de la Magahá cheese using a combination of classical and molecular techniques. Samples taken during ripening of this Spanish goat's milk cheese in which Lactococcus lactis and Streptococcus thermophilus were used as starter cultures were analyzed. All bacterial isolates were clustered by using randomly amplified polymorphic DNA (RAPD) and identified by 16S rRNA gene sequencing, species-specific PCR, and multiplex PCR. Our results indicate that the majority of the 225 strains isolated and enumerated on solid media during the ripening period were nonstarter lactic acid bacteria, and Lactobacillus paracasei was the most abundant species. Other Lactobacillus species, such as Lactobacillus plantarum and Lactobacillus parabuchneri, were also detected at the beginning and end of ripening, respectively. Non-lactic-acid bacteria, mainly Kocuria and Staphylococcus strains, were also detected at the end of the ripening period. Microbial community dynamics determined by temporal temperature gradient gel electrophoresis provided a more precise estimate of the distribution of bacteria and enabled us to detect Lactobacillus curvatus and the starter bacteria S. thermophilus and L. lactis, which were not isolated. Surprisingly, the bacterium most frequently found using culture-dependent analysis, L. paracasei, was scarcely detected by this molecular approach. Finally, we studied the composition of the lactobacilli and their evolution by using length heterogeneity PCR.

Taxonomic structure and stability of the bacterial community in belgian sourdough ecosystems as assessed by culture and population fingerprinting

A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment rather than the type or batch of flour largely determines the development of a stable LAB population in sourdoughs.