Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication

When Saccharomyces cerevisiae grows on mixtures of glucose and galactose, galactose utilization is repressed by glucose, and induction of the GAL gene network only occurs when glucose is exhausted. Contrary to reference GAL alleles, alternative alleles support faster growth on galactose, thus enabling distinct galactose utilization strategies maintained by balancing selection. Here, we report on new wild populations of Saccharomyces cerevisiae harboring alternative GAL versions and, for the first time, of Saccharomyces paradoxus alternative alleles. We also show that the non-functional GAL version found earlier in Saccharomyces kudriavzevii is phylogenetically related to the alternative versions, which constitutes a case of trans-specific maintenance of highly divergent alleles. Strains harboring the different GAL network variants show different levels of alleviation of glucose repression and growth proficiency on galactose. We propose that domestication involved specialization toward thriving in milk from a generalist ancestor partially adapted to galactose consumption in the plant niche.

The impact of botanical fermented foods on metabolic syndrome and type 2 diabetes: a systematic review of randomised controlled trials

Our systematic review assessed the impact of botanical fermented food (BFF) consumption on glucose, lipid, anthropometric, inflammatory and gut microbiota parameters, in adults with metabolic syndrome (MetS), MetS components or type 2 diabetes mellitus (T2DM). Embase, MEDLINE, Cochrane CENTRAL and Google Scholar were searched with no language limits, from inception to 31 August 2022, for eligible randomised controlled trials (RCTs). Two independent reviewers screened 6873 abstracts and extracted relevant data. Risk of bias (ROB) was assessed using the Cochrane Collaboration's ROB2 tool. The final review included twenty-six RCTs, with thirty-one reports published between 2001 and 2022. Significant (p < 0·05) within-group and between-group changes in cardiometabolic outcome means were reported in twenty-three and nineteen studies, respectively. Gut microbiota composition was assessed in four studies, with two finding significant between-group differences. No significant difference between groups of any measured outcomes was observed in five studies. There were fourteen studies at low ROB; ten were of some concern; and two were at high ROB. In 73% of included studies, BFF consumption by participants with obesity, MetS or T2DM led to significant between-group improvements in discrete cardiometabolic outcomes, including fasting blood glucose, lipid profile, blood pressure, waist circumference, body fat percentage and C-reactive protein. BFF consumption increased the abundance of beneficial gut bacteria, such as Bifidobacterium and LAB, whilst reducing potential pathogens such as Bacteroides. To determine the clinical significance of BFFs as therapeutic dietary adjuncts, their safety, tolerability and affordability must be balanced with the limited power and magnitude of these preliminary findings.

Diversity and succession of contaminating yeasts in white-brined cheese during cold storage

Contamination of white-brined cheeses (WBCs) with yeasts is of major concern in the dairy industry. This study aimed to identify yeast contaminants and characterize their succession in white-brined cheese during a shelf-life of 52 weeks. White-brined cheeses added herbs (WBC1) or sundried tomatoes (WBC2) were produced at a Danish dairy and incubated at 5 °C and 10 °C. An increase in yeast counts was observed for both products within the first 12-14 weeks of incubation and stabilized afterwards varying in a range of 4.19-7.08 log CFU/g. Interestingly, higher incubation temperature, especially in WBC2, led to lower yeast counts, concurrently with higher diversity of yeast species. Observed decrease in yeast counts was, most likely, due to negative interactions between yeast species leading to growth inhibition. In total, 469 yeast isolates from WBC1 and WBC2 were genotypically classified using the (GTG)₅-rep-PCR technique. Out of them, 132 representative isolates were further identified by sequencing the D1/D2 domain of the 26 S rRNA gene. Predominant yeast species in WBCs were Candida zeylanoides and Debaryomyces hansenii, while Candida parapsilosis, Kazachstania bulderi, Kluyveromyces lactis, Pichia fermentans, Pichia kudriavzevii, Rhodotorula mucilaginosa, Torulaspora delbrueckii, and Wickerhamomyces anomalus were found in lower frequency. Heterogeneity of yeast species in WBC2 was generally larger compared to WBC1. This study indicated that, along with contamination levels, taxonomic heterogeneity of yeasts is an important factor influencing yeast cell counts, as well as product quality during storage.

Age-related effects on the modulation of gut microbiota by pectins and their derivatives: an in vitro study

Introduction

The present study investigates whether supplementation with pectin-type polysaccharides has potential to improve aging-associated dysbiosis of the gut microbiota. The influence of different types of pectins on the gut microbiota composition and short-chain fatty acids (SCFAs) profiles of elderly was compared to younger adults.

Methods

Pectins studied included a pectin polysaccharide (PEC), a partially hydrolyzed pectin (PPH), and a pectin oligosaccharide (POS). Additionally, inulin was used as a reference prebiotic substrate. Individual fecal samples were collected from healthy elderly volunteers (70-75 years) and younger adults (30-35 years). In vitro fermentations were performed using the CoMiniGut model with controlled temperature and pH. Samples were withdrawn at baseline and after 24 h fermentation for measurement of SCFAs production and microbiota composition by 16S rRNA gene sequencing.

Results and Discussion

The results showed that fermentations with PEC and PPH resulted in a specific stimulation of Faecalibacterium prausnitzii regardless of the age groups. Collinsella aerofaciens became a dominating species in the young adult group with fermentations of all three pectins, which was not observed in the elderly group. No significant differences in SCFAs production were found among the pectins, indicating a high level of functional redundancy. Pectins boosted various bacterial groups differently from the reference prebiotic substrate (inulin). We also found inulin had reduced butyrogenic and bifidogenic effects in the elderly group compared to the younger adult group. In conclusion, the in vitro modulating effects of pectins on elderly gut microbiota showed potential of using pectins to improve age-related dysbiosis.

Complete and Draft Genome Sequences of 52 Bacillus and Priestia Strains Isolated from West African Fermentations and 26 Reference Strains from a Public Culture Collection

The whole genomes of 78 Bacillus and Priestia strains isolated from West African fermented foods (n = 52) or acquired from a public culture collection (n = 26) were sequenced using long-read sequencing and assembled into draft (n = 32) and complete (n = 46) genomes, allowing comparative genomics and taxonomic assignment of these strains with putative uses in fermented foods.

The Potential of Pectins to Modulate the Human Gut Microbiota Evaluated by In Vitro Fermentation: A Systematic Review

Pectin is a dietary fiber, and its health effects have been described extensively. Although there are limited clinical studies, there is a growing body of evidence from in vitro studies investigating the effect of pectin on human gut microbiota. This comprehensive review summarizes the findings of gut microbiota modulation in vitro as assessed by 16S rRNA gene-based technologies and elucidates the potential structure-activity relationships. Generally, pectic substrates are slowly but completely fermented, with a greater production of acetate compared with other fibers. Their fermentation, either directly or by cross-feeding interactions, results in the increased abundances of gut bacterial communities such as the family of Ruminococcaceae, the Bacteroides and Lachnospira genera, and species such as Lachnospira eligens and Faecalibacterium prausnitzii, where the specific stimulation of Lachnospira and L. eligens is unique to pectic substrates. Furthermore, the degree of methyl esterification, the homogalacturonan-to-rhamnogalacturonan ratio, and the molecular weight are the most influential structural factors on the gut microbiota. The latter particularly influences the growth of Bifidobacterium spp. The prebiotic potential of pectin targeting specific gut bacteria beneficial for human health and well-being still needs to be confirmed in humans, including the relationship between its structural features and activity.

Debaryomyces hansenii Strains Isolated From Danish Cheese Brines Act as Biocontrol Agents to Inhibit Germination and Growth of Contaminating Molds

The antagonistic activities of native Debaryomyces hansenii strains isolated from Danish cheese brines were evaluated against contaminating molds in the dairy industry. Determination of chromosome polymorphism by use of pulsed-field gel electrophoresis (PFGE) revealed a huge genetic heterogeneity among the D. hansenii strains, which was reflected in intra-species variation at the phenotypic level. 11 D. hansenii strains were tested for their ability to inhibit germination and growth of contaminating molds, frequently occurring at Danish dairies, i.e., Cladosporium inversicolor, Cladosporium sinuosum, Fusarium avenaceum, Mucor racemosus, and Penicillium roqueforti. Especially the germination of C. inversicolor and P. roqueforti was significantly inhibited by cell-free supernatants of all D. hansenii strains. The underlying factors behind the inhibitory effects of the D. hansenii cell-free supernatants were investigated. Based on dynamic headspace sampling followed by gas chromatography-mass spectrometry (DHS-GC-MS), 71 volatile compounds (VOCs) produced by the D. hansenii strains were identified, including 6 acids, 22 alcohols, 15 aldehydes, 3 benzene derivatives, 8 esters, 3 heterocyclic compounds, 12 ketones, and 2 phenols. Among the 71 identified VOCs, inhibition of germination of C. inversicolor correlated strongly with three VOCs, i.e., 3-methylbutanoic acid, 2-pentanone as well as acetic acid. For P. roqueforti, two VOCs correlated with inhibition of germination, i.e., acetone and 2-phenylethanol, of which the latter also correlated strongly with inhibition of mycelium growth. Low half-maximal inhibitory concentrations (IC50) were especially observed for 3-methylbutanoic acid, i.e., 6.32-9.53 × 10-5 and 2.00-2.67 × 10-4 mol/L for C. inversicolor and P. roqueforti, respectively. For 2-phenylethanol, a well-known quorum sensing molecule, the IC50 was 1.99-7.49 × 10-3 and 1.73-3.45 × 10-3 mol/L for C. inversicolor and P. roqueforti, respectively. For acetic acid, the IC50 was 1.35-2.47 × 10-3 and 1.19-2.80 × 10-3 mol/L for C. inversicolor and P. roqueforti, respectively. Finally, relative weak inhibition was observed for 2-pentanone and acetone. The current study shows that native strains of D. hansenii isolated from Danish brines have antagonistic effects against specific contaminating molds and points to the development of D. hansenii strains as bioprotective cultures, targeting cheese brines and cheese surfaces.

Sustainable Production of African Traditional Beers With Focus on Dolo, a West African Sorghum-Based Alcoholic Beverage

Spontaneously fermented sorghum beers remain by far the most popular traditional cereal-based alcoholic beverages in Africa. Known under various common names (traditional beers, sorghum beers, opaque, native or indigenous beers) they are also recognized under various local names depending on the region or ethnic group. Dolo and pito are two similar traditional beers popular in West African countries including Burkina Faso, Mali, Ghana, Benin, Togo, Nigeria and Ivory Coast. These low-alcoholic beers are nutritious and contribute to the nutritional balance of local populations, as well as to their socio-cultural and economic well-being. The production of African traditional beers remains one of the major economic activities, creating employment and generating substantial income that contributes to livelihoods as well as the countries' economic systems. Their processing (malting and brewing) is still artisanal, based on traditional family know-how. The brewing process involves either an acidification and an alcoholic fermentation phases, or a mixed fermentation combining LAB and yeasts. Saccharomyces cerevisiae has been identified as the dominant yeast species involved in the alcoholic fermentation, with a biodiversity at strain level. LAB involved in the processing belong to the genera of Limosilactobacillus, Lactobacillus, Pediococcus, Leuconostoc, Lactococcus, Streptococcus, and Enterococcus. Molds (Aspergillus, Penicillium, Rhizopus, Geotrichum), and acetic bacteria are often associated with the malting and brewing processes. Challenges for sustainable production of African sorghum beer include inconsistent supply of raw materials, variability in product quality and safety, high energy consumption and its impact on the environment, poor packaging and short shelf-life. For sustainable and environmentally-friendly production of African sorghum beers, there is the need to assess the processing methods and address sustainability challenges. Strategies should promote wider distribution and adoption of improved sorghum varieties among farmers, prevent losses through the adoption of good storage practices of raw material, promote the adoption of improved cook stoves by the brewers, develop and adopt starter cultures for controlled fermentation, regulate the production through the establishment of quality standards and better valorize by-products and wastes to increase the competitiveness of the value chain. Appropriate packaging and stabilization processes should be developed to extend the shelf-life and diversify the channels for sustainable distribution of African cereal-based alcoholic beverages.

In vitro properties of potential probiotic lactic acid bacteria originating from Ghanaian indigenous fermented milk products

Fermented milk products are a major source of health-promoting microorganisms known as probiotics. To characterize the probiotic properties of lactic acid bacteria isolated from Ghanaian traditionally fermented milk, thirty (30) isolates comprising Enterococcus faecium (1), Lactobacillus fermentum (14), Lb. plantarum (2) and Pediococcus acidilactici (13) identified by 16S rRNA gene sequencing, were tested for survival at low pH (2.5) and bile salts (0.3% (w/v)), hydrophobicity, co-aggregation, auto-aggregation and antimicrobial activities against selected pathogens. Safety of potential probiotic bacteria was assessed by hemolytic activity on blood agar and susceptibility to nine different antibiotics. Majority (90%) of the strains showed survival rates above 80% at pH (2.5) and in bile salts (0.3% (w/v)). Hydrophobicity ranged from 5 to 61% while cell auto-aggregation ranged from 41 to 80% after 24 h. Co-aggregation with E. coli (3.7-43.9%) and S. Typhimurium (1.3-49.5%) were similar for the LAB strains at 24 h. Cell- free supernatants of all LAB strains inhibited E. coli while S. Typhimurium was not sensitive to cell-free supernatants of five Pd. acidilactici strains: OS24h20, OS18h3, OY9h19, OS9h8 and 24NL38. None of the LAB strains showed β-hemolysis but 38% of strains showed α-hemolysis. Susceptibilities to antibiotics were strain-specific; only four strains, two Lb. fermentum and two Pd. acidilactici were susceptible to all nine antibiotics tested. Based on high survival rates in bile salts, low pH and generally good hydrophobicity, auto-aggregation, co-aggregation and inhibitory activities, 15 out of 30 strains tested were considered qualified candidates for development of probiotic cultures for fermented milk products in sub-Saharan Africa.

Multifunctional properties and safety evaluation of lactic acid bacteria and yeasts associated with fermented cereal doughs

Spontaneous cereal fermentations involve diverse lactic acid bacteria (LAB) and yeasts which may include multifunctional and safe or unsafe strains. This study assessed acidification ability, safety, antifungal activity and free amino acids release ability of LAB and yeasts previously isolated from spontaneously fermented cereal doughs in Benin. Fourteen LAB and thirteen yeast strains were studied in liquid media and/or in a model cereal dough prepared in laboratory conditions. Antifungal activity was assessed against Candida glabrata in liquid medium. Amino acids were determined by pre-column derivatization and separation with reversed-phase HPLC. Antimicrobial susceptibility was analysed by minimum inhibitory concentration determination. The acidification ability was higher for LAB compared to yeast strains. All LAB strains retarded the growth of C. glabrata Cg1 with the highest inhibition recorded for Weissella confusa Wc1 and Wc2. The highest free amino acid content was found in the doughs fermented with Pichia kudriavzevii Pk2 and Pk3. All the LAB strains were susceptible to ampicillin, chloramphenicol, erythromycin, but displayed phenotypic resistance to kanamycin, streptomycin and tetracycline. Positive PCR amplicon of resistance genes were detected in the following cases: 2 LAB strains were positive for kanamycin (aph(3)III), 5 strains were positive for streptomycin (aadA and/or strA and/or strB) and 3 strains were positive for tetracycline (tet (L) and/or tet (M)). For yeasts, most of the P. kudriavzevii strains were resistant to amphotericin B, fluconazole and itraconazole opposite to K. marxianus and Saccharomyces cerevisiae strains which were susceptible. The results obtained are valuable for selecting safe and multifunctional strains for cereal fermentation in West Africa.

Occurrence of Yeasts in White-Brined Cheeses: Methodologies for Identification, Spoilage Potential and Good Manufacturing Practices

Yeasts are generally recognized as contaminants in the production of white-brined cheeses, such as Feta and Feta-type cheeses. The most predominant yeasts species are Debaryomyces hansenii, Geotrichum candidum, Kluyveromyces marxianus, Kluyveromyces lactis, Rhodotorula mucilaginosa, and Trichosporon spp. Although their spoilage potential varies at both species and strain levels, yeasts will, in case of excessive growth, present a microbiological hazard, effecting cheese quality. To evaluate the hazard and trace routes of contamination, the exact taxonomic classification of yeasts is required. Today, identification of dairy yeasts is mainly based on DNA sequencing, various genotyping techniques, and, to some extent, advanced phenotypic identification technologies. Even though these technologies are state of the art at the scientific level, they are only hardly implemented at the industrial level. Quality defects, caused by yeasts in white-brined cheese, are mainly linked to enzymatic activities and metabolism of fermentable carbohydrates, leading to production of metabolites (CO2, fatty acids, volatile compounds, amino acids, sulfur compounds, etc.) and resulting in off-flavors, texture softening, discoloration, and swelling of cheese packages. The proliferation of spoilage yeast depends on maturation and storage conditions at each specific dairy, product characteristics, nutrients availability, and interactions with the co-existing microorganisms. To prevent and control yeast contamination, different strategies based on the principles of HACCP and Good Manufacturing Practice (GMP) have been introduced in white-brined cheese production. These strategies include milk pasteurization, refrigeration, hygienic sanitation, air filtration, as well as aseptic and modified atmosphere packaging. Though a lot of research has been dedicated to yeasts in dairy products, the role of yeast contaminants, specifically in white-brined cheeses, is still insufficiently understood. This review aims to summarize the current knowledge on the identification of contaminant yeasts in white-brined cheeses, their occurrence and spoilage potential related to different varieties of white-brined cheeses, their interactions with other microorganisms, as well as guidelines used by dairies to prevent cheese contamination.

Technologically relevant Bacillus species and microbial safety of West African traditional alkaline fermented seed condiments

Fermented food condiments serve as a major source of nutrients to many homes in West Africa, especially among the rural poor who use these condiments as a cheap source of protein substitute for milk and other animal protein sources. Traditional fermented West African condiments are produced by spontaneous fermentation of legumes and protein-rich seeds of both cultivated and wild plant species. These fermented condiments are culturally accepted and widely produced in the West African sub-region, and rely on indigenous microbiota responsible for taste, texture, aroma development and the overall unique product characteristics. Detailed understanding of fermentation microbiota and their unique technological and functional properties are fundamental in developing products with enhanced quality and safety, as well as development of specific locally adapted starter cultures. Technologically relevant Bacillus spp., mainly Bacillus subtilis, are the predominant fermentative bacteria responsible for the natural fermentation of condiments across West Africa. Other species of Bacillus including B. amyloliquefaciens, B. licheniformis, B. pumilus, B. megaterium, B. sphaericus, B. cereus, B. badius and B. fusiformis are also frequently involved in the fermentation process. These bacterial species are responsible for flavor development, bio-conversion of complex food molecules, and production of antimicrobial compounds that impact shelf-life and safety, and in some instances, may confer host-beneficial health effects beyond basic nutrition. First, this review provides currently available information on the technologically relevant Bacillus species isolated from fermented food condiments in nine (9) West African countries. In addition, perspectives on harnessing the potentials of the technologically beneficial bacterial strains in fermented condiments in West Africa for enhanced food safety, quality and overall food security is presented.

Probiotic potential of Saccharomyces cerevisiae and Kluyveromyces marxianus isolated from West African spontaneously fermented cereal and milk products

The yeast species Saccharomyces cerevisiae and Kluyveromyces marxianus are associated with fermentation of West African indigenous foods. The aim of this study was to characterize potential probiotic properties of S. cerevisiae and K. marxianus isolates from the West African milk products lait caillé and nunu and a cereal-based product mawè. The strains (14 in total) were identified by 26S rRNA gene sequencing and characterized for survival at gastrointestinal stress (bile salts and low pH) and adhesion to Caco-2 intestinal epithelial cells. Selected yeast isolates were tested for their effect on the transepithelial electrical resistance (TEER), using the intestinal epithelial cell line Caco-2 and for maintenance of intracellular pH (pH_i ) during perfusion with gastrointestinal pH (3.5 and 6.5). All tested yeasts were able to grow in bile salts in a strain-dependent manner, exhibiting a maximum specific growth rate (μ_max ) of 0.58-1.50 h^-1 . At pH 2.5, slow growth was observed for the isolates from mawè (μ_max of 0.06-0.80 h^-1 ), whereas growth of yeasts from other sources was mostly inhibited. Yeast adhesion to Caco-2 cells was strain specific and varied between 8.0% and 36.2%. Selected strains of S. cerevisiae and K. marxianus were able to maintain the pH_i homeostasis at gastrointestinal pH and to increase TEER across the Caco-2 monolayers, indicating their potential to improve intestinal barrier functions. Based on overall results, strains of K. marxianus and S. cerevisiae from mawè exhibited the highest probiotic potential and might be recommended for further development as starter cultures in West African fermented products.

The quorum-sensing molecule 2-phenylethanol impaired conidial germination, hyphal membrane integrity and growth of Penicillium expansum and Penicillium nordicum

AIMS

The aim of the study was to investigate the antifungal effects of a quorum sensing-molecule, 2-phenylethanol, against the food spoilage moulds Penicillium expansum and Penicillium nordicum.

METHODS AND RESULTS

Conidial germination of the tested Penicillium spp. (three strains in total) were inhibited by treatments with 2-phenylethanol in a concentration-dependent manner. Germinated conidia was significantly reduced from 4·4-16·7% at 7·5 mmol l^-1 and completely inhibited at 15 mmol l^-1 2-phenylethanol. Integrity of conidial cell membranes was unaffected by 2-phenylethanol resulting in reversible inhibition pattern of germination. In contrast, membrane permeability of actively growing hyphae was severely compromised, showing 63·5 - 75·7% membrane damage upon treatment with 15 mmol l^-1 2-phenylethanol. The overall inhibitory effect of 2-phenylethanol on colony development and growth of P. expansum and P. nordicum was additionally confirmed.

CONCLUSIONS

2-phenylethanol inhibits conidial germination and growth of P. expansum and P. nordicum in a nonlethal, reversible and concentration-dependent manner.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study indicates that 2-phenylethanol can find potential application as an antifungal agent for biological control of moulds in the food industry.

Environmental heterogeneity of Staphylococcus species from alkaline fermented foods and associated toxins and antimicrobial resistance genetic elements

Different samples of three products including Bikalga and Soumbala from Burkina Faso (West Africa) and Ntoba Mbodi from Congo-Brazzaville (Central Africa) were evaluated. The bacteria (400) were phenotyped and genotypically characterized by Rep-PCR, PFGE, 16S rRNA and rpoB gene sequencing and spa typing. Their PFGE profiles were compared with those of 12,000 isolates in the Center for Disease Control (CDC, USA) database. They were screened for the production of enterotoxins, susceptibility to 19 antimicrobials, presence of 12 staphylococcal toxin and 38 AMR genes and the ability to transfer erythromycin and tetracycline resistance genes to Enterococcus faecalis JH2-2. Fifteen coagulase negative (CoNS) and positive (CoPS) species characterized by 25 Rep-PCR/PFGE clusters were identified: Staphylococcus arlettae, S. aureus, S. cohnii, S. epidermidis, S. gallinarum, S. haemolyticus, S. hominis, S. pasteuri, S. condimenti, S. piscifermentans, S. saprophyticus, S. sciuri, S. simulans, S. warneri and Macrococcus caseolyticus. Five species were specific to Soumbala, four to Bikalga and four to Ntoba Mbodi. Two clusters of S. gallinarum and three of S. sciuri were particular to Burkina Faso. The S. aureus isolates exhibited a spa type t355 and their PFGE profiles did not match any in the CDC database. Bacteria from the same cluster displayed similar AMR and toxin phenotypes and genotypes, whereas clusters peculiar to a product or a location generated distinct profiles. The toxin genes screened were not detected and the bacteria did not produce the staphylococcal enterotoxins A, B, C and D. AMR genes including blazA, cat501, dfr(A), dfr(G), mecA, mecA1, msr(A) and tet(K) were identified in CoNS and CoPS. Conjugation experiments produced JH2-2 isolates that acquired resistance to erythromycin and tetracycline, but no gene transfer was revealed by PCR. The investigation of the heterogeneity of Staphylococcus species from alkaline fermented foods, their relationship with clinical and environmental isolates and their safety in relation to antimicrobial resistance (AMR) and toxin production is anticipated to contribute to determining the importance of staphylococci in alkaline fermented foods, especially in relation to the safety of the consumers.

Occurrence and Importance of Yeasts in Indigenous Fermented Food and Beverages Produced in Sub-Saharan Africa

Indigenous fermented food and beverages represent a valuable cultural heritage in sub-Saharan Africa, having one of the richest selections of fermented food products in the world. In many of these indigenous spontaneously fermented food and beverages, yeasts are of significant importance. Several factors including raw materials, processing methods, hygienic conditions as well as the interactions between yeasts and other commensal microorganisms have been shown to influence yeast species diversity and successions. Both at species and strain levels, successions take place due to the continuous change in intrinsic and extrinsic growth factors. The selection pressure from the microbial stress factors leads to niche adaptation and both yeast species and strains with traits deviating from those generally acknowledged in current taxonomic keys, have been isolated from indigenous sub-Saharan African fermented food products. Yeasts are important for flavor development, impact shelf life, and nutritional value and do, in some cases, even provide host-beneficial effects. In order to sustain and upgrade these traditional fermented products, it is quite important to obtain detailed knowledge on the microorganisms involved in the fermentations, their growth requirements and interactions. While other publications have reported on the occurrence of prokaryotes in spontaneously fermented sub-Saharan food and beverages, the present review focuses on yeasts considering their current taxonomic position, relative occurrence and successions, interactions with other commensal microorganisms as well as beneficial effects and importance in human diet. Additionally, the risk of opportunistic yeasts is discussed.

Impact of botanical fermented foods on metabolic biomarkers and gut microbiota in adults with metabolic syndrome and type 2 diabetes: a systematic review protocol

INTRODUCTION

Dysfunctional gut microbiota is a common finding in patients with metabolic syndrome (MetS) and type 2 diabetes mellitus (T2DM). Recent clinical trials have assessed whether botanical fermented foods (BFFs) have beneficial effects on metabolic biomarkers, inflammatory markers and gut microbiota. The aim of this review is to critically evaluate all randomised controlled trials (RCTs) of BFF for evidence of impact on the outcome measures of these disease states.

METHODS AND ANALYSIS

Four electronic databases (Embase, MEDLINE, CENTRAL and Google Scholar) as well as the grey literature will be searched from inception to present without language or publication status restrictions applied. Eligible RCTs which have enrolled adult participants with T2DM, any MetS components or combinations of these components, treated prophylactically or therapeutically with any botanical fermented food intervention, compared with a control group (no intervention, placebo or active control) will be assessed. Primary outcomes are related to the target conditions, including metabolic biomarkers, inflammatory markers and gut microbiota composition/function. Using Covidence, two independent investigators will conduct title and abstract screening, followed by full-text screening to identify appropriate studies. Methodological quality of the trials will be assessed using the Cochrane risk of bias assessment tool. Findings will be summarised with a narrative synthesis of the differences between included studies. A meta-analysis will be conducted if sufficient data are obtained.

ETHICS AND DISSEMINATION

Ethical approval is not required as primary data will not be collected. Results will be disseminated through peer-reviewed publication, conference presentations and press.

PROSPERO REGISTRATION NUMBER

CRD42018117766.

Potential of Pectins to Beneficially Modulate the Gut Microbiota Depends on Their Structural Properties

Pectins are plant cell-wall polysaccharides which can be utilized by commensal bacteria in the gut, exhibiting beneficial properties for the host. Knowledge of the impact of pectins on intestinal bacterial communities is insufficient and limited to a few types of pectins. This study characterized the relationship between the structural properties of pectins and their potential to modulate composition and activity of the gut microbiota in a beneficial way. For this purpose we performed in vitro fermentations of nine structurally diverse pectins from citrus fruits and sugar beet, and a pectic derivative, rhamnogalacturonan I (RGI), using a TIM-2 colon model. The composition of microbiota during TIM-2 fermentations was assessed by 16S rRNA gene amplicon sequencing. Both general and pectin-specific changes were observed in relative abundances of numerous bacterial taxa in a time-dependent way. Bacterial populations associated with human health, such as Faecalibacterium prausnitzii, Coprococcus, Ruminococcus, Dorea, Blautia, Oscillospira, Sutterella, Bifidobacterium, Christensenellaceae, Prevotella copri, and Bacteroides spp. were either increased or decreased depending on the substrate, suggesting that these bacteria can be controlled using structurally different pectins. The main structural features linked to the pectin-mediated shifts in microbiota included degree of esterification, composition of neutral sugars, distribution of homogalacturonan and rhamnogalacturonan fractions, degree of branching, and the presence of amide groups. Cumulative production of the total short chain fatty acids and propionate was largest in fermentations of the high methoxyl pectins. Thus, this study indicates that microbial communities in the gut can be specifically modulated by pectins and identifies the features in pectin molecules linked to microbial alterations. This knowledge can be used to define preferred dietary pectins, targeting beneficial bacteria, and favoring more balanced microbiota communities in the gut.

Cheese brines from Danish dairies reveal a complex microbiota comprising several halotolerant bacteria and yeasts

The Danish Danbo cheese is a surface ripened semi-hard cheese, which before ripening is submerged in brine for up to 24 h. The brining is required in order to obtain the structural and organoleptic properties of the cheeses. Likewise, the content of NaCl in the cheese will influence especially the surface microbiota being of significant importance for flavour development and prevention of microbial spoilage. Even though the microbiota on cheese surfaces have been studied extensively, limited knowledge is available on the occurrence of microorganisms in cheese brine. The aim of the present study was to investigate by both culture-dependent and -independent techniques the brine microbiota in four Danish dairies producing Danbo cheese. The pH of the brines varied from 5.1 to 5.6 with a dry matter content from 20 to 27% (w/w). The content of lactate varied from 4.1 to 10.8 g/L and free amino acids from 65 to 224 mg/L. Bacteria were isolated on five different media with NaCl contents of 0.85-23.0% (w/v) NaCl. The highest count of 6.3 log CFU/mL was obtained on TSA added 4% (w/v) NaCl. For yeasts, the highest count was 3.7 log CFU/mL on MYGP added 8% (w/v) NaCl. A total of 31 bacterial and eight eukaryotic species were isolated including several halotolerant and/or halophilic species. Among bacteria, counts of ≥6.0 log CFU/mL were obtained for Tetragenococcus muriaticus and Psychrobacter celer, while counts between ≥4.5 and < 6.0 log CFU/mL were obtained for Lactococcus lactis, Staphylococcus equorum, Staphylococcus hominis, Chromohalobacter beijerinckii, Chromohalobacter japonicus and Microbacterium maritypicum. Among yeasts, counts of ≥3.5 log CFU/mL were only obtained for Debaryomyces hansenii. By amplicon-based high-throughput sequencing of 16S rRNA gene and ITS2 regions for bacteria and eukaryotes respectively, brines from the same dairy clustered together indicating the uniqueness of the dairy brine microbiota. To a great extent the results obtained by amplicon sequencing fitted with the culture-dependent technique though each of the two methodologies identified unique genera/species. Dairy brine handling procedures as e.g. microfiltration were found to influence the brine microbiota. The current study proves the occurrence of a specific dairy brine microbiota including several halotolerant and/or halophilic species most likely of sea salt origin. The importance of these species during especially the initial stages of cheese ripening and their influence on cheese quality and safety need to be investigated. Likewise, optimised brine handling procedures and microbial cultures are required to ensure an optimal brine microbiota.

Modulation of gut microbiota from obese individuals by in vitro fermentation of citrus pectin in combination with Bifidobacterium longum BB-46

This study aimed to evaluate the effects of three treatments, i.e., Bifidobacterium longum BB-46 (T1), B. longum BB-46 combined with the pectin (T2), and harsh extracted pectin from lemon (T3) on obesity-related microbiota using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). The effects of the treatments were assessed by the analysis of the intestinal microbial composition (using 16S rRNA gene amplicon sequencing) and the levels of short-chain fatty acids (SCFAs) and ammonium ions (NH₄⁺). Treatments T2 and T3 stimulated members of the Ruminococcaceae and Succinivibrionaceae families, which were positively correlated with an increase in butyric and acetic acids. Proteolytic bacteria were reduced by the two treatments, concurrently with a decrease in NH₄⁺. Treatment T1 stimulated the production of butyric acid in the simulated transverse and descending colon, reduction of NH₄⁺ as well as the growth of genera Lactobacillus, Megamonas, and members of Lachnospiracea. The results indicate that both B. longum BB-46 and pectin can modulate the obesity-related microbiota; however, when the pectin is combined with B. longum BB-46, the predominant effect of the pectin can be observed. This study showed that the citric pectin is able to stimulate butyrate-producing bacteria as well as genera related with anti-inflammatory effects. However, prospective clinical studies are necessary to evaluate the anti/pro-obesogenic and inflammatory effects of this pectin for future prevention of obesity.

Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa

Mawè is a West African spontaneous fermented cereal-based dough. Different types of mawè exist varying in type of cereal and/or production condition, with fermentations lasting 24-48 h. With the aim of obtaining a comprehensive understanding of the microbial ecology of mawè processing, a microbiological characterisation was performed for four mawè types, produced at eight sites in Benin. At the onset of the fermentations lactic acid bacteria (LAB) and yeast counts were on average 7.5 ± 1.03 and 4.8 ± 0.79 Log₁₀ cfu/g, which increased to 9.2 ± 0.38 and 7.4 ± 0.42 Log₁₀ cfu/g, respectively, at the end of the fermentations. LAB (n = 321) and yeasts (n = 298), isolated during the fermentations, were identified. The predominant LAB and yeast species were Lactobacillus fermentum and Pichia kudriavzevii, respectively, followed by Kluyveromyces marxianus, all present throughout the mawè fermentations. Further, microbial successions took place with Weissella confusa occurring mostly at the onset, while Pediococcus acidilactici and Saccharomyces cerevisiae were mainly associated with the end of the fermentations. Species diversity was influenced both by type of cereal and production condition. The dominating strain clusters of L. fermentum and P. kudriavzevii were ubiquitous and strain diversities were influenced by type of cereal and production site.