The impact of processing technology on microbial community composition and functional properties of Beninese maize ogi

Traditionally fermented maize starch, called ogi, is produced to prepare akpan, a yoghurt-like street food widely consumed in Benin. Current maize ogi production practices were compared to assess the impact of different processing technologies on the characteristics of the fermented product as a basis to determine best practices. Maize starch slurry samples were collected from processors in five municipalities in southern Benin and analysed before fermentation (starch samples) and after spontaneous fermentation (ogi samples). Four technological pathways for maize starch production were distinguished based on variations in the duration of steeping the grains, which ranged from 6 to 72 h, and whether or not kneading of the wet flour before filtration was practised. Six categories of maize ogi were derived from the four technology groups based on the duration of the fermentation, which lasted from 6 to 24 h. The average pH of maize starch varied from 3.2 to 5.3, with the lowest values for the two technology groups that also had the highest lactate concentrations (9-11.8 g/L). The six maize ogi categories had a pH ranging from 3.1 to 4.0. Viable plate counts of lactic acid bacteria were similar for maize starch samples and for ogi samples, whereas yeast counts showed clear differences. Members of the genera Limosilactobacillus, Lactobacillus, Weissella, Streptococcus and Ligilactobacillus, dominated the bacterial community in maize starch, and were also dominant in maize ogi. The members of the genera dominating the fungal community in maize starch were also dominant in maize ogi, except for Aspergillus and Stenocarpella spp., which decreased in relative abundance by fermentation. The highest total free essential amino acid concentration was 61.6 mg/L in maize starch and 98.7 mg/L in ogi. The main volatile organic compounds in maize starch samples were alcohols, esters, and carboxylic acids, which also prevailed in maize ogi samples. The results indicate that the characteristics of traditional maize ogi depend on the processing technologies used to produce the maize starch before the intentional fermentation into ogi, with no clear-cut connection with the production practices due to high variations between samples from the same technology groups. This revealed the importance of a standardized maize starch production process, which would benefit controlling the starch fermentation and the characteristics of maize ogi. Further research is needed to understand the hidden fermentation during maize starch production for determination of the best practices that support the production of quality maize ogi.

Dextran and levan exopolysaccharides from tempeh-associated lactic acid bacteria with bioactivity against enterotoxigenic Escherichia coli (ETEC)

Soybean tempeh contains bioactive carbohydrate that can reduce the severity of diarrhea by inhibiting enterotoxigenic Escherichia coli (ETEC) adhesion to mammalian epithelial cells. Lactic acid bacteria (LAB) are known to be present abundantly in soybean tempeh. Some LAB species can produce exopolysaccharides (EPS) with anti-adhesion bioactivity against ETEC but there has been no report of anti-adhesion bioactive EPS from tempeh-associated LAB. We isolated EPS-producing LAB from tempeh-related sources, identified them, unambiguously elucidated their EPS structure and assessed the bioactivity of their EPS against ETEC. Pediococcus pentosaceus TL, Leuconostoc mesenteroides WA and L. mesenteroides WN produced both dextran (α-1,6 linked glucan; >1000 kDa) and levan (β-2,6 linked fructan; 650-760 kDa) in varying amounts and Leuconostoc citreum TR produced gel-forming α-1,6-mixed linkage dextran (829 kDa). All four isolates produced EPS that could adhere to ETEC cells and inhibit auto-aggregation of ETEC. EPS-PpTL, EPS-LmWA and EPS-LmWN were more bioactive towards pig-associated ETEC K88 while EPS-LcTR was more bioactive against human-associated ETEC H10407. Our finding is the first to report on the bioactivity of dextran against ETEC. Tempeh is a promising source of LAB isolates that can produce bioactive EPS against ETEC adhesion and aggregation.

Development of novel natto using legumes produced in Europe

Natto is a traditional Japanese fermented product consisting of cooked soybeans fermented with Bacillus subtilis var. natto. We assessed three different B. subtilis strains and investigated their impact on product quality aspects, such as microbial quality, textural quality (poly-γ-glutamate strand formation), free amino acids (FAA), and volatile organic compounds (VOCs), but also the vitamin K1, K2 and B1 content, and presence of nattokinase. Using Bayesian contrast analysis, we conclude that the quality attributes were influenced by both the substrate and strain used, without significant differences in bacterial growth between strain or substrate. Overall, all the tested European legumes, except for brown beans, are adequate substrates to produce natto, with comparable or higher qualities compared to the traditional soy. Out of all the tested legumes, red lentils were the most optimal fermentation substrate. They were fermented most consistently, with high concentrations of vitamin K2, VOCs, FAA.

Impact of vitamin B12 on rhamnose metabolism, stress defense and in-vitro virulence of Listeria monocytogenes

Listeria monocytogenes is a facultative anaerobe which can cause a severe food-borne infection known as listeriosis. L. monocytogenes is capable of utilizing various nutrient sources including rhamnose, a naturally occurring deoxy sugar abundant in foods. L. monocytogenes can degrade rhamnose into lactate, acetate and 1,2-propanediol. Our previous study showed that addition of vitamin B12 stimulated anaerobic growth of L. monocytogenes on rhamnose due to the activation of bacterial microcompartments for 1,2-propanediol utilization (pdu BMC) with concomitant production of propionate and propanol. Notably, anaerobic 1,2-propanediol metabolism has been linked to virulence of enteric pathogens including Salmonella spp. and L. monocytogenes. In this study we investigated the impact of B12 and BMC activation on i) aerobic and anerobic growth of L. monocytogenes on rhamnose and ii) the level of virulence. We observed B12-induced pdu BMC activation and growth stimulation only in anaerobically grown cells. Comparative Caco-2 virulence assays showed that these pdu BMC-induced cells have significantly higher translocation efficiency compared to non-induced cells (anaerobic growth without B12; aerobic growth with or without B12), while adhesion and invasion capacity is similar for all cells. Comparative proteome analysis showed specific and overlapping responses linked to metabolic shifts, activation of stress defense proteins and virulence factors, with RNA polymerase sigma factor SigL, teichoic acid export ATP-binding protein TagH, DNA repair and protection proteins, RadA and DPS, and glutathione synthase GshAB, previously linked to activation of virulence response in L. monocytogenes, uniquely upregulated in anaerobically rhamnose grown pdu-induced cells. Our results shed light on possible effects of B12 on L. monocytogenes competitive fitness and virulence activation when utilizing rhamnose in anaerobic conditions encountered during transmission and the human intestine.

Lactococcus cell envelope proteases enable lactococcal growth in minimal growth media supplemented with high molecular weight proteins of plant and animal origin

Lactic acid bacteria (LAB) have evolved into fastidious microorganisms that require amino acids from environmental sources. Some LAB have cell envelope proteases (CEPs) that drive the proteolysis of high molecular weight proteins like casein in milk. CEP activity is typically studied using casein as the predominant substrate, even though CEPs can hydrolyze other protein sources. Plant protein hydrolysis by LAB has rarely been connected to the activity of specific CEPs. This study aims to show the activity of individual CEPs using LAB growth in a minimal growth medium supplemented with high molecular weight casein or potato proteins. Using Lactococcus cremoris MG1363 as isogenic background to express CEPs, we demonstrate that CEP activity is directly related to growth in the protein-supplemented minimal growth media. Proteolysis is analyzed based on the amino acid release, allowing a comparison of CEP activities and analysis of amino acid utilization by L. cremoris MG1363. This approach provides a basis to analyze CEP activity on plant-based protein substrates as casein alternatives and to compare activity of CEP homologs.

The stressostat: A novel approach in adaptive laboratory evolution to improve end-product resistance

End-product inhibition in pH-controlled batch cultures, is the major limiting factor for bacterial biomass formation in the starter culture industry as well as in many other biotechnological processes. Adaptive laboratory evolution (ALE) has emerged over the past decades as a powerful tool for phenotype optimization, but none of the existing ALE methods could select for improved end-product resistance. Therefore, we developed the stressostat (STress Resistance Evolution in Substrate Surplus) as a novel continuous ALE method. Stressostat cultivation applies end-product concentrations as constant evolutionary pressure on microorganisms in the presence of substrate surplus. In this study, we improved the lactate resistance of Lactococcus lactis FM03P in 35 days of stressostat cultivations. The lactate concentrations increased over time from 530 to 675 mM, indicating the successful selection for variants with improved lactate resistance. Thirty-four variants were isolated and grouped into four clusters based on their growth rates at high lactate concentrations. In the high-throughput screening without pH control, most isolated variants could grow at high lactate concentrations (870-928 mM), while the wild type was completely inhibited. The variants grew slower than wild type at low lactate media indicating possible evolutionary trade-off. However, in pH-controlled batch cultivations, most variants produced more biomass than the wild type. In conclusion, stressostat cultivation is a valuable method to obtain L. lactis variants with improved end-product resistance and further characterization is needed to elucidate underlying resistance mechanisms and potential industrial applications.

Strain diversity in Saccharomyces cerevisiae thiamine production capacity

Vitamin B1 , also known as thiamine, is an important vitamin that, besides its role in human health, is converted to meat aromas upon exposure to high temperatures. Therefore, it is relevant for the production of vegan meat-like flavours. In this study, we investigated 48 Saccharomyces cerevisiae strains for their thiamine production capacity by measuring the intracellular and extracellular vitamins produced in the thiamine-free minimal medium after 72 h of growth. We found approximately an 8.2-fold difference in overall thiamine yield between the highest and lowest-producing strains. While the highest thiamine yield was 254.6 nmol/L, the highest thiamine-specific productivity was 160.9 nmol/g DW. To assess whether extracellular thiamine was due to leakage caused by cell damage, we monitored membrane permeabilization using propidium iodide (PI) staining and flow cytometry. We found a good correlation between the percentage of extracellular thiamine and PI-stained cells (Spearman's ρ = 0.85). Finally, we compared S. cerevisiae CEN.PK113-7D (wild type [WT]) to three strains evolved in a thiamine-free medium for their thiamine production capacity. On average, we saw an increase in the amount of thiamine produced. One of the evolved strains had a 49% increase in intracellular thiamine-specific productivity and a biomass increase of 20% compared with the WT. This led to a total increase in thiamine yield of 60% in this strain, reaching 208 nmol/L. This study demonstrated that it is possible to achieve thiamine overproduction in S. cerevisiae via strain selection and adaptive laboratory evolution.

Influence of metabolic guilds on a temporal scale in an experimental fermented food derived microbial community

The influence of community diversity, which can be measured at the level of metabolic guilds, on community function is a central question in ecology. Particularly, the long-term temporal dynamic between a community's function and its diversity remains unclear. We investigated the influence of metabolic guild diversity on associated community function by propagating natural microbial communities from a traditionally fermented milk beverage diluted to various levels. Specifically, we assessed the influence of less abundant microbial types, such as yeast, on community functionality and bacterial community compositions over repeated propagation cycles amounting to ∼100 generations. The starting richness of metabolic guilds had a repeatable effect on bacterial community compositions, metabolic profiles, and acidity. The influence of a single metabolic guild, yeast in our study, played a dramatic role on function, but interestingly not on long-term species sorting trajectories of the remaining bacterial community. Our results together suggest an unexpected niche division between yeast and bacterial communities and evidence ecological selection on the microbial communities in our system.

Lytic bacteriophages affect the population dynamics of multi-strain microbial communities

Background: Lytic bacteriophages infect and lyse bacteria and, as a by-product, may affect diversity in microbial communities through selective predation on abundant bacterial strains. We used a complex dairy starter named Ur to investigate population dynamics of Lactococcus lactis, Lactococcus cremoris and Leuconostoc mesenteroides strains in terms of constant-diversity and periodic selection models. Methods: To mimic the starter Ur, we designed blends of 24 strains representing all eight previously identified genetic lineages in the starter culture. The blends were propagated by daily transfers in milk for over 500 generations in the presence or absence of a cocktail of lytic bacteriophages. The relative abundance of genetic lineages of L. lactis, L. cremoris and Lc. mesenteroides strains present in the complex blend, as well as phage presence, were monitored. Results: Control blends without phage predation showed decreased strain diversity, leading to a stable state due to the domination of the fittest strain(s) of a particular lineage according to periodic selection dynamics. However, in phage-challenged blends, predation caused a large shift in the microbial composition by killing the fittest and sensitive strains. Conclusion: It was demonstrated that phage-challenged blends maintained their diversity at the level of genetic lineages, thus providing experimental support for the constant-diversity dynamics model in a complex microbial community.

Technological variations, microbial diversity and quality characteristics of maize ogi used for akpan production in Benin

Fermented maize starch, called ogi in Benin, is used for preparing akpan, a traditional yoghurt-like food that contributes to the food and nutrition security of its consumers. Current ogi processing technologies used by two socio-cultural groups of Benin, namely the Fon and the Goun, and aspects of the quality of the fermented starches were studied to assess the current state-of-the-art, explore changes in key product characteristics over time and identify priorities for follow-up research to increase product quality and shelf life. A survey on processing technologies was conducted in five municipalities in south Benin and samples of maize starch were collected, which were analysed after the fermentation required to obtain ogi. Four processing technologies were identified, two from the Goun (G1, G2) and two from the Fon (F1, F2). The main difference between the four processing technologies was the steeping procedure used for the maize grains. The pH of the ogi samples ranged between 3.1 and 4.2, with the highest values for G1 samples, which also contained relatively higher concentrations of sucrose (0.05-0.3 g/L) than F1 samples (0.02-0.08 g/L), and lower citrate and lactate concentrations (0.2-0.3 and 5.6-16.9 g/L, respectively) than F2 samples (0.4-0.5 and 14-27.7 g/L, respectively). Fon samples collected in Abomey were particularly rich in volatile organic compounds and free essential amino acids. Members of the genera Lactobacillus (8.6-69.3%), Limosilactobacillus (5.4-79.1%), Streptococcus (0.6-59.3%) and Weissella (2.6-51.2%) dominated the bacterial microbiota of ogi with a significant abundance of Lactobacillus spp. in Goun samples. Sordariomycetes (10.6-81.9%) and Saccharomycetes (6.2-81.4%) dominated the fungal microbiota. The yeast community of ogi samples mainly consisted of the genera Diutina, Pichia, Kluyveromyces, Lachancea and unclassified members of the Dipodascaceae family. Hierarchical clustering of metabolic data showed similarities between samples from different technologies at a default threshold of 0.05. No obvious trend in the composition of the samples' microbial communities reflected the clusters observed for the metabolic characteristics. The results indicate that beyond the general impact of the use of Fon or Goun technologies on fermented maize starch, the individual contribution of processing practices warrants study, under controlled conditions, to determine the drivers of difference or similarity between maize ogi samples to further contribute to improving product quality and shelf life.

Quantitative Physiology and Proteome Adaptations of Bifidobacterium breve NRBB57 at Near-Zero Growth Rates

In natural environments, nutrients are usually scarce, causing microorganisms to grow slowly while staying metabolically active. These natural conditions can be simulated using retentostat cultivations. The present study describes the physiological and proteome adaptations of the probiotic Bifidobacterium breve NRBB57 from high (0.4 h-1) to near-zero growth rates. Lactose-limited retentostat cultivations were carried out for 21 days in which the bacterial growth rate progressively reduced to 0.00092 h-1, leading to a 3.4-fold reduction of the maintenance energy requirement. Lactose was mainly converted into acetate, formate, and ethanol at high growth rates, while in the retentostat, lactate production increased. Interestingly, the consumption of several amino acids (serine, aspartic acid, and glutamine/arginine) and glycerol increased over time in the retentostat. Morphological changes and viable but nonculturable cells were also observed in the retentostat. Proteomes were compared for all growth rates, revealing a downregulation of ribosomal proteins at near-zero growth rates and an upregulation of proteins involved in the catabolism of alternative energy sources. Finally, we observed induction of the stringent response and stress defense systems. Retentostat cultivations were proven useful to study the physiology of B. breve, mimicking the nutrient scarcity of its complex habitat, the human gut. IMPORTANCE In natural environments, nutrients are usually scarce, causing microorganisms to grow slowly while staying metabolically active. In this study we used retentostat cultivation to investigate how the probiotic Bifidobacterium breve adapts its physiology and proteome under severe nutrient limitation resulting in near-zero growth rates (<0.001 h-1). We showed that the nutrient limitation induced a multifaceted response including stress defense and stringent response, metabolic shifts, and the activation of novel alternative energy-producing pathways.

Dynamic genome-scale modeling of Saccharomyces cerevisiae unravels mechanisms for ester formation during alcoholic fermentation

Fermentation employing Saccharomyces cerevisiae has produced alcoholic beverages and bread for millennia. More recently, S. cerevisiae has been used to manufacture specific metabolites for the food, pharmaceutical, and cosmetic industries. Among the most important of these metabolites are compounds associated with desirable aromas and flavors, including higher alcohols and esters. Although the physiology of yeast has been well-studied, its metabolic modulation leading to aroma production in relevant industrial scenarios such as winemaking is still unclear. Here we ask what are the underlying metabolic mechanisms that explain the conserved and varying behavior of different yeasts regarding aroma formation under enological conditions? We employed dynamic flux balance analysis (dFBA) to answer this key question using the latest genome-scale metabolic model (GEM) of S. cerevisiae. The model revealed several conserved mechanisms among wine yeasts, for example, acetate ester formation is dependent on intracellular metabolic acetyl-CoA/CoA levels, and the formation of ethyl esters facilitates the removal of toxic fatty acids from cells using CoA. Species-specific mechanisms were also found, such as a preference for the shikimate pathway leading to more 2-phenylethanol production in the Opale strain as well as strain behavior varying notably during the carbohydrate accumulation phase and carbohydrate accumulation inducing redox restrictions during a later cell growth phase for strain Uvaferm. In conclusion, our new metabolic model of yeast under enological conditions revealed key metabolic mechanisms in wine yeasts, which will aid future research strategies to optimize their behavior in industrial settings.

Enhanced stress resistance of Bifidobacterium breve NRBB57 by induction of stress proteins at near-zero growth rates

Bifidobacterium breve is a common habitant of the human gut and is used as probiotic in functional foods. B. breve has to cope with multiple stress conditions encountered during processing and passage through the human gut, including high temperature, low pH and exposure to oxygen. Additionally, during industrial processing and in the gut, B. breve could encounter nutrient limitation resulting in reduced growth rates that can trigger adaptive stress responses. For this reason, it is important to develop culture methods that elicit resistance to multiple stresses (robustness) encountered by the bacteria. To investigate the impact of caloric restriction on robustness of the probiotic B. breve NRBB57, this strain was grown in lactose-limited chemostat cultures and in retentostat for 21 days, at growth rates ranging from 0.4 h^-1 to 0.00081 h^-1. Proteomes of cells harvested at different growth rates were correlated to acid, hydrogen peroxide and heat stress survival capacity. Comparative proteome analysis showed that retentostat-grown cells had significantly increased abundance of a variety of stress proteins involved in protein quality maintenance and DNA repair (DnaJ, Hsp90, FtsH, ClpB, ClpP1, ClpC, GroES, RuvB, RecA), as well as proteins involved in oxidative stress defence (peroxiredoxin, ferredoxin, thioredoxin peroxidase, glutaredoxin and thioredoxin reductase). Exposure to three different stress conditions, 45 °C, pH 3, and 10 mM H₂O₂, showed highest stress resistance of retentostat cells sampled at week 2 and week 3 grown at 0.0018 and 0.00081 h^-1. Our findings show that cultivation at near-zero growth rates induces higher abundance of stress defence proteins contributing to the robustness of B. breve NRBB57, thereby offering an approach that may support its production and functionality.

Microaerobic metabolism of lactate and propionate enhances vitamin B12 production in Propionibacterium freudenreichii

BACKGROUND

Propionibacterium freudenreichii is used in biotechnological applications to produce vitamin B₁₂. Although cultured mainly in anaerobic conditions, microaerobic conditions can greatly enhance biomass formation in P. freudenreichii. Since B₁₂ yields may be coupled to biomass formation, microaerobic conditions show great potential for increasing B₁₂ yields in P. freudenreichii.

RESULTS

Here we show biomass formation increases 2.7 times for P. freudenreichii grown in microaerobic conditions on lactate versus anaerobic conditions (1.87 g/L vs 0.70 g/L). Consumption of lactate in microaerobic conditions resulted first in production of pyruvate, propionate and acetate. When lactate was depleted, pyruvate and propionate were oxidised with a concomitant sixfold increase in the B₁₂ titer compared to anaerobic conditions, showing potential for propionate and pyruvate as carbon sources for B₁₂ production. Consequently, a fed-batch reactor with anaerobically precultured lactate-grown cells was fed propionate in microaerobic conditions resulting in biomass increase and production of B₁₂. Vitamin yields increased from 0.3 [Formula: see text] B₁₂ per mmol lactate in anaerobic conditions to 2.4 [Formula: see text] B₁₂ per mmol lactate and 8.4 [Formula: see text] B₁₂ per mmol propionate in microaerobic conditions. Yield per cell dry weight (CDW) increased from 41 [Formula: see text] per g CDW in anaerobic conditions on lactate to 92 [Formula: see text] per g CDW on lactate and 184 [Formula: see text] per g CDW on propionate in microaerobic conditions.

CONCLUSIONS

Here we have shown both B₁₂ yield per substrate and per CDW were highest on cells oxidising propionate in microaerobic conditions, showing the potential of propionate for biotechnological production of vitamin B₁₂ by P. freudenreichii.

A simple, sensitive, and specific method for the extraction and determination of thiamine and thiamine phosphate esters in fresh yeast biomass

Thiamine is an essential vitamin for most living organisms, of which yeasts are a rich nutritional source. In this study we developed a thiamine extraction and determination method to detect thiamine in fresh yeast biomass. The thiamine determination method combines the derivatization of thiamine to a highly fluorescent product, with chromatographic separation (HPLC) and fluorescence detection. The method specifically detects free thiamine (T), thiamine phosphate (TP), and thiamine pyrophosphate (TPP). It has a high sensitivity of 2 ng/ml for TPP and TP, and 1 ng/ml for T, excellent instrumental repeatability, and low day-to-day variation in retention time of the different phosphate forms. We demonstrated the robustness of the method by proving that the fluorescence signals of the derivatised samples are stable for at least 82 h after derivatization, and by showing that the final pH of the samples does not influence the fluorescent response. In addition, we developed and validated a thiamine extraction method consisting of beads beating the fresh yeast biomass in 0.1 M HCl using a lysing matrix composed of 0.1 mm silica spheres. The performance of this method was compared to extraction via heat treatment at 95 °C for 30 min, and a combination of beads beating and heat treatment carried out in different order. We demonstrated that thiamine extraction via beads beating is the only method that prevents the biologically active form thiamine pyrophosphate to be degraded to thiamine phosphate, therefore, the extraction method developed and described in this study is preferred when the different thiamine vitamers need to be detected in their actual proportions. The combination of the extraction via beads beating, the conversion of all vitamers to the thiochrome derivatives, and the separation of these compounds on the reversed phase HPLC with a fluorescence detector, yielded a sensitive, specific, repeatable, and robust method for extraction and determination of vitamin B₁ in fresh yeast biomass.

The growth-survival trade-off is hard-wired in the Lactococcus lactis gene regulation network

Most microbes reside in oligotrophic environments for extended periods of time, requiring survival strategies that maintain proliferative capacity. We demonstrate that the non-spore-forming Lactococcus lactis KF147 progressively activates the expression of stress-associated functions in response to the declining growth rate elicited by prolonged retentostat cultivation, which coincides with up to 10⁴ -fold increased stress tolerance. Our findings provide a quantified view of the transcription and stress-tolerance adaptations underlying the growth-survival trade-off in L. lactis, and exemplify the hard-wiring of this trade-off in the lactococcal gene regulation network.

Physiological Roles of Short-Chain and Long-Chain Menaquinones (Vitamin K2) in Lactococcus cremoris

Lactococcus cremoris and L. lactis are well known for their occurrence and applications in dairy fermentations, but their niche extends to a range of natural and food production environments. L. cremoris and L. lactis produce MKs (vitamin K2), mainly as the long-chain forms represented by MK-9 and MK-8, and a detectable number of short-chain forms represented by MK-3. The physiological significance of the different MK forms in the lifestyle of these bacterial species has not been investigated extensively. In this study, we used L. cremoris MG1363 to construct mutants producing different MK profiles by deletion of genes encoding (i) a menaquinone-specific isochorismate synthase, (ii) a geranyltranstransferase, and (iii) a prenyl diphosphate synthase. These gene deletions resulted in (i) a non-MK producer (ΔmenF), (ii) a presumed MK-1 producer (ΔispA), and (iii) an MK-3 producer (Δllmg_0196), respectively. By examining the phenotypes of the MG1363 wildtype strain and respective mutants, including biomass accumulation, stationary phase survival, oxygen consumption, primary metabolites, azo dye/copper reduction, and proteomes, under aerobic, anaerobic, and respiration-permissive conditions, we could infer that short-chain MKs like MK-1 and MK-3 are preferred to mediate extracellular electron transfer and reaction with extracellular oxygen, while the long-chain MKs like MK-9 and MK-8 are more efficient in aerobic respiratory electron transport chain. The different electron transfer routes mediated by short-chain and long-chain MKs likely support growth and survival of L. cremoris in a range of (transiently) anaerobic and aerobic niches including food fermentations, highlighting the physiological significance of diverse MKs in L. cremoris.

Extracellular vesicle formation in Lactococcus lactis is stimulated by prophage-encoded holin-lysin system

Gram-positive bacterial extracellular membrane vesicles (EVs) have been drawing more attention in recent years. However, mechanistic insights are still lacking on how EVs are released through the cell walls in Gram-positive bacteria. In this study, we characterized underlying mechanisms of EV production and provide evidence for a role of prophage activation in EV release using the Gram-positive bacterium Lactococcus lactis as a model. By applying a standard EV isolation procedure, we observed the presence of EVs in the culture supernatant of a lysogenic L. lactis strain FM-YL11, for which the prophage-inducing condition led to an over 10-fold increase in EV production in comparison with the non-inducing condition. In contrast, the prophage-encoded holin-lysin knockout mutant YL11ΔHLH and the prophage-cured mutant FM-YL12 produced constantly low levels of EVs. Under the prophage-inducing condition, FM-YL11 did not show massive cell lysis. Defective phage particles were found to be released in and associated with holin-lysin-induced EVs from FM-YL11, as demonstrated by transmission electron microscopic images, flow cytometry and proteomics analysis. Findings from this study further generalized the EV-producing phenotype to Gram-positive L. lactis, and provide additional insights into the EV production mechanism involving prophage-encoded holin-lysin system. The knowledge on bacterial EV production can be applied to all Gram-positive bacteria and other lactic acid bacteria with important roles in fermentations and probiotic formulations, to enable desired release and delivery of cellular components with nutritional values or probiotic effects.

Validation of skeletal muscle mass assessment at the level of the third cervical vertebra in patients with head and neck cancer

BACKGROUND

Low skeletal muscle mass (SMM) is associated with adverse outcomes. SMM is often assessed at the third lumbar vertebra (L3) on abdominal imaging. Abdominal imaging is not routinely performed in patients with head and neck cancer (HNC). We aim to validate SMM measurement at the level of the third cervical vertebra (C3) on head and neck imaging.

MATERIAL AND METHODS

Patients with pre-treatment whole-body computed tomography (CT) between 2010 and 2018 were included. Cross-sectional muscle area (CSMA) was manually delineated at the level of C3 and L3. Correlation coefficients and intraclass correlation coefficients (ICCs) were calculated. Cohen's kappa was used to assess the reliability of identifying a patient with low SMM.

RESULTS

Two hundred patients were included. Correlation between CSMA at the level of C3 and L3 was good (r = 0.75, p < 0.01). Using a multivariate formula to estimate CSMA at L3, including gender, age, and weight, correlation improved (r = 0.82, p < 0.01). The agreement between estimated and actual CSMA at L3 was good (ICC 0.78, p < 0.01). There was moderate agreement in the identification of patients with low SMM based on the estimated lumbar skeletal muscle mass index (LSMI) and actual LSMI (Cohen's κ: 0.57, 95%CI 0.45-0.69).

CONCLUSIONS

CSMA at C3 correlates well with CSMA at L3. There is moderate agreement in the identification of patients with low SMM based on the estimated lumbar SMI (based on measurement at C3) and actual LSMI.

Lactococcus lactis Mutants Obtained From Laboratory Evolution Showed Elevated Vitamin K2 Content and Enhanced Resistance to Oxidative Stress

Vitamin K2 is an important vitamin for human health. Vitamin K2 enrichment in the human diet is possible by using vitamin K2-producing bacteria such as Lactococcus lactis in food fermentations. Based on previous observations that aerated cultivation conditions improved vitamin K2 content in L. lactis, we performed laboratory evolution on L. lactis MG1363 by cultivating this strain in a shake flask in a sequential propagation regime with transfers to a fresh medium every 72h. After 100 generations of propagation, we selected three evolved strains that showed improved stationary phase survival in oxygenated conditions. In comparison to the original strain MG1363, the evolved strains showed 50-110% increased vitamin K2 content and exhibited high resistance against hydrogen peroxide-induced oxidative stress. Genome sequencing of the evolved strains revealed common mutations in the genes ldh and gapB. Proteomics analysis revealed overproduction of glyceraldehyde 3-phosphate dehydrogenase (GapA), universal stress protein A2 (UspA2), and formamidopyrimidine-DNA glycosylase (MutM) under aerated conditions in evolved strains, proteins with putative functions in redox reactions, universal stress response, and DNA damage repair, all of which could contribute to the enhanced oxidative stress resistance. The mechanisms underlying elevated vitamin K2 content in the evolved strains remain to be elucidated. Two out of the three evolved strains performed similar to the original strain MG1363 in terms of growth and acidification of culture media. In conclusion, this study demonstrated a natural selection approach without genetic manipulations to obtain vitamin K2 overproducers that are highly relevant for food applications and contributed to the understanding of oxidative stress resistance in L. lactis.

Metabolic flux sampling predicts strain-dependent differences related to aroma production among commercial wine yeasts

BACKGROUND

Metabolomics coupled with genome-scale metabolic modeling approaches have been employed recently to quantitatively analyze the physiological states of various organisms, including Saccharomyces cerevisiae. Although yeast physiology in laboratory strains is well-studied, the metabolic states under industrially relevant scenarios such as winemaking are still not sufficiently understood, especially as there is considerable variation in metabolism between commercial strains. To study the potential causes of strain-dependent variation in the production of volatile compounds during enological conditions, random flux sampling and statistical methods were used, along with experimental extracellular metabolite flux data to characterize the differences in predicted intracellular metabolic states between strains.

RESULTS

It was observed that four selected commercial wine yeast strains (Elixir, Opale, R2, and Uvaferm) produced variable amounts of key volatile organic compounds (VOCs). Principal component analysis was performed on extracellular metabolite data from the strains at three time points of cell cultivation (24, 58, and 144 h). Separation of the strains was observed at all three time points. Furthermore, Uvaferm at 24 h, for instance, was most associated with propanol and ethyl hexanoate. R2 was found to be associated with ethyl acetate and Opale could be associated with isobutanol while Elixir was most associated with phenylethanol and phenylethyl acetate. Constraint-based modeling (CBM) was employed using the latest genome-scale metabolic model of yeast (Yeast8) and random flux sampling was performed with experimentally derived fluxes at various stages of growth as constraints for the model. The flux sampling simulations allowed us to characterize intracellular metabolic flux states and illustrate the key parts of metabolism that likely determine the observed strain differences. Flux sampling determined that Uvaferm and Elixir are similar while R2 and Opale exhibited the highest degree of differences in the Ehrlich pathway and carbon metabolism, thereby causing strain-specific variation in VOC production. The model predictions also established the top 20 fluxes that relate to phenotypic strain variation (e.g. at 24 h). These fluxes indicated that Opale had a higher median flux for pyruvate decarboxylase reactions compared with the other strains. Conversely, R2 which was lower in all VOCs, had higher median fluxes going toward central metabolism. For Elixir and Uvaferm, the differences in metabolism were most evident in fluxes pertaining to transaminase and hexokinase associated reactions. The applied analysis of metabolic divergence unveiled strain-specific differences in yeast metabolism linked to fusel alcohol and ester production.

CONCLUSIONS

Overall, this approach proved useful in elucidating key reactions in amino acid, carbon, and glycerophospholipid metabolism which suggest genetic divergence in activity in metabolic subsystems among these wine strains related to the observed differences in VOC formation. The findings in this study could steer more focused research endeavors in developing or selecting optimal aroma-producing yeast stains for winemaking and other types of alcoholic fermentations.

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used.

Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity

Genetic background and environmental conditions affect the production of sensory impact compounds by Saccharomyces cerevisiae. The relative importance of the strain-specific metabolic capabilities for the production of volatile organic compounds (VOCs) remains unclear. We investigated which amino acids contribute to VOC production and whether amino acid-VOC relations are conserved among yeast strains. Amino acid consumption and production of VOCs during grape juice fermentation was investigated using four commercial wine yeast strains: Elixir, Opale, R2, and Uvaferm. Principal component analysis of the VOC data demonstrated that Uvaferm correlated with ethyl acetate and ethyl hexanoate production, R2 negatively correlated with the acetate esters, and Opale positively correlated with fusel alcohols. Biomass formation was similar for all strains, pointing to metabolic differences in the utilization of nutrients to form VOCs. Partial least-squares linear regression showed that total aroma production is a function of nitrogen utilization (R2 = 0.87). We found that glycine, tyrosine, leucine, and lysine utilization were positively correlated with fusel alcohols and acetate esters. Mechanistic modeling of the yeast metabolic network via parsimonious flux balance analysis and flux enrichment analysis revealed enzymes with crucial roles, such as transaminases and decarboxylases. Our work provides insights in VOC production in wine yeasts. IMPORTANCE Saccharomyces cerevisiae is widely used in grape juice fermentation to produce wines. Along with the genetic background, the nitrogen in the environment in which S. cerevisiae grows impacts its regulation of metabolism. Also, commercial S. cerevisiae strains exhibit immense diversity in their formation of aromas, and a desirable aroma bouquet is an essential characteristic for wines. Since nitrogen affects aroma formation in wines, it is essential to know the extent of this connection and how it leads to strain-dependent aroma profiles in wines. We evaluated the differences in the production of key aroma compounds among four commercial wine strains. Moreover, we analyzed the role of nitrogen utilization on the formation of various aroma compounds. This work illustrates the unique aroma-producing differences among industrial yeast strains and suggests more intricate, nitrogen-associated routes influencing those aroma-producing differences.

Propionibacterium freudenreichii thrives in microaerobic conditions by complete oxidation of lactate to CO2

In this study we show increased biomass formation for four species of food-grade propionic acid bacteria (Acidipropionibacterium acidipropionici, Acidipropionibacterium jensenii, Acidipropionibacterium thoenii and Propionibacterium freudenreichii) when exposed to oxygen, implicating functional respiratory systems. Using an optimal microaerobic condition, P. freudenreichii DSM 20271 consumed lactate to produce propionate and acetate initially. When lactate was depleted propionate was oxidized to acetate. We propose to name the switch from propionate production to consumption in microaerobic conditions the 'propionate switch'. When propionate was depleted the 'acetate switch' occurred, resulting in complete consumption of acetate. Both growth rate on lactate (0.100 versus 0.078 h-1 ) and biomass yield (20.5 versus 8.6 g* mol-1 lactate) increased compared to anaerobic conditions. Proteome analysis revealed that the abundance of proteins involved in the aerobic and anaerobic electron transport chains and major metabolic pathways did not significantly differ between anaerobic and microaerobic conditions. This implicates that P. freudenreichii is prepared for utilizing O2 when it comes available in anaerobic conditions. The ecological niche of propionic acid bacteria can conceivably be extended to environments with oxygen gradients from oxic to anoxic, so-called microoxic environments, as found in the rumen, gut and soils, where they can thrive by utilizing low concentrations of oxygen.

Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization of Propionibacterium freudenreichii

Bacterial microcompartments (BMCs) are proteinaceous prokaryotic organelles that enable the utilization of substrates such as 1,2-propanediol and ethanolamine. BMCs are mostly linked to the survival of particular pathogenic bacteria by providing a growth advantage through utilization of 1,2-propanediol and ethanolamine which are abundantly present in the human gut. Although a 1,2-propanediol utilization cluster was found in the probiotic bacterium Propionibacterium freudenreichii, BMC-mediated metabolism of 1,2-propanediol has not been demonstrated experimentally in P. freudenreichii. In this study we show that P. freudenreichii DSM 20271 metabolizes 1,2-propanediol in anaerobic conditions to propionate and 1-propanol. Furthermore, 1,2-propanediol induced the formation of BMCs, which were visualized by transmission electron microscopy and resembled BMCs found in other bacteria. Proteomic analysis of 1,2-propanediol grown cells compared to L-lactate grown cells showed significant upregulation of proteins involved in propanediol-utilization (pdu-cluster), DNA repair mechanisms and BMC shell proteins while proteins involved in oxidative phosphorylation were down-regulated. 1,2-Propanediol utilizing cells actively produced vitamin B₁₂ (cobalamin) in similar amounts as cells growing on L-lactate. The ability to metabolize 1,2-propanediol may have implications for human gut colonization and modulation, and can potentially aid in delivering propionate and vitamin B₁₂in situ.

Lifestyle, metabolism and environmental adaptation in Lactococcus lactis

Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights into the species L. lactis, including the resolution of the genetic basis of its subspecies division, as well as the control mechanisms involved in the fine-tuning of growth rate and energy metabolism. In addition, it has enabled novel approaches to study lactococcal lifestyle adaptations to the dairy application environment, including its adjustment to near-zero growth rates that are particularly relevant in the context of cheese ripening. This review highlights various insights in these areas and exemplifies the strength of combining experimental evolution with functional genomics and bacterial physiology research to expand our fundamental understanding of the L. lactis lifestyle under different environmental conditions.

Microbial population dynamics during traditional production of Mabisi, a spontaneous fermented milk product from Zambia: a field trial

Mabisi is a fermented milk product, traditionally produced in a calabash by uncontrolled fermentation. Due to high costs and a reduced availability of calabashes, nowadays plastic containers are also used for Mabisi production. However, the effect of this change in production practice on the properties of the product has not been documented. Therefore, we aimed at determining the effect of fermentation vessels and types of back-slopping on acidification and microbial communities during fermentation. A series of fifteen experiments using two types of fermentation vessels (plastic buckets and calabashes) in combination with different types of back-slopping (no back-slopping, passive back-slopping, and active back-slopping) were set up at a field site in rural Zambia. In each of the fifteen fermentations we analysed acidification rate of traditional Mabisi fermentation and bacterial diversity over time. No significant difference was found in terms of microbial diversity during and at the end of fermentation between fermentations performed in buckets or previously used calabashes. Bacterial communities in general decreased in diversity over time, where the drop in pH correlated with a decrease in Shannon Index. In case of active back-slopping, the pH drop started right after inoculation while in the no back-slopping and passive back-slopping fermentations, there was a clear lag phase before acidification started. All experimental series resulted in a microbial community dominated by Lactococcus lactis and a Shannon Index, as a measure for diversity, between 0.6 and 2.0. The use of plastic buckets for Mabisi fermentation can be a valuable alternative to the use of calabashes as this study showed no biological and physico-chemical differences between Mabisi resulting from both fermentation vessels, although the reason for perceived differences should be further investigated.

Composition and Diversity of Natural Bacterial Communities in Mabisi, a Traditionally Fermented Milk

Many traditionally fermented milk products such as mabisi involve spontaneous fermentation, which can result in bacterial community composition variation due to selection pressure. The aim of this study was to determine the composition of bacterial communities in the different types of mabisi produced across Zambia and identify the factors that influence their composition. Samples of mabisi were collected across the country, and analyzed for pH and bacterial communities using 16S rRNA amplicon sequencing. We found that the bacterial community composition was dominated by members of two phyla, i.e., Firmicutes and Proteobacteria, from which the top 10 most abundant genera were Lactococcus, Lactobacillus, Streptococcus, Enterobacter, Citrobacter, Klebsiella, Kluyvera, Buttiauxella, Aeromonas, and Acinetobacter. The most dominant genus was Lactococcus, which was present in all types of mabisi produced from all regions. The mabisi products from traditional mabisi production regions (TMPRs) were dominated by lactic acid bacteria (LAB) whereas products from non-TMPRs were dominated by non-LAB species. Tonga mabisi, the most popular type of mabisi produced in non-TMPRs, had the most complex and diverse bacterial community composition compared to the other types, which included barotse, backslopping, creamy, and thick-tonga mabisi. Other factors that influenced bacterial community composition were geographical location, fermentation duration and pH while the type of fermentation container and producer did not. This study provides new insights that can be applied in starter culture development as well as microbial functionality studies.

Visualizing the invisible: class excursions to ignite children's enthusiasm for microbes

We have recently argued that, because microbes have pervasive - often vital - influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology-literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513-1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public-health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well-being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of 'germs' and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination-capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision-making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology-centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre-occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom.

Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota

The important role for the human small intestinal microbiota in health and disease has been widely acknowledged. However, the difficulties encountered in accessing the small intestine in a non-invasive way in healthy subjects have limited the possibilities to study its microbiota. In this study, a dynamic in vitro model that simulates the human ileum was developed, including its microbiota. Ileostomy effluent and fecal inocula were employed to cultivate microbial communities within the in vitro model. Microbial stability was repetitively achieved after 10 days of model operation with bacterial concentrations reaching on average 107 to 108 16S rRNA copy numbers/ml. High diversities similar to those observed in in vivo ileum samples were achieved at steady state using both fecal and ileostomy effluent inocula. Functional stability based on Short Chain Fatty Acid concentrations was reached after 10 days of operation using fecal inocula, but was not reached with ileostomy effluent as inoculum. Principal Components and cluster analysis of the phylogenetic profiles revealed that in vitro samples at steady state clustered closest to two samples obtained from the terminal ileum of healthy individuals, independent of the inoculum used, demonstrating that the in vitro microbiota at steady state resembles that of the human ileum.

Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization Stimulates Anaerobic Growth of Listeria monocytogenes EGDe

Bacterial microcompartments (BMCs) are proteinaceous organelles that optimize specific metabolic pathways referred to as metabolosomes involving transient production of toxic volatile metabolites such as aldehydes. Previous bioinformatics analysis predicted the presence of BMCs in 23 bacterial phyla including foodborne pathogens and a link with gene clusters for the utilization of host-derived substrates such as 1,2-propanediol utilization, i.e., the Pdu cluster. Although, transcriptional regulation of the Pdu cluster and its role in Listeria monocytogenes virulence in animal models have recently been reported, the experimental identification and the physiological role of BMCs in L. monocytogenes is still unexplored. Here, we ask whether BMCs could enable utilization of 1,2-propanediol (Pd) in L. monocytogenes under anaerobic conditions. Using L. monocytogenes EGDe as a model strain, we could demonstrate efficient utilization of Pd with concomitant production of 1-propanol and propionate after 24 h of anaerobic growth, while the utilization was significantly reduced in aerobic conditions. In line with this, expression of genes encoding predicted shell proteins and the signature enzyme propanediol dehydratase is upregulated more than 20-fold in cells anaerobically grown in Pdu-induced versus non-induced control conditions. Additional proteomics analysis confirmed the presence of BMC shell proteins and Pdu enzymes in cells that show active degradation of Pd. Furthermore, using transmission electron microscopy, BMC structures have been detected in these cells linking gene expression, protein composition, and BMCs to activation of the Pdu cluster in anaerobic growth of L. monocytogenes. Studies in defined minimal medium with Pd as an energy source showed a significant increase in cell numbers, indicating that Pdu and the predicted generation of ATP in the conversion of propionyl-phosphate to the end product propionate can support anaerobic growth of L. monocytogenes. Our findings may suggest a role for BMC-dependent utilization of Pd in L. monocytogenes growth, transmission, and interaction with the human host.

Long-chain vitamin K2 production in Lactococcus lactis is influenced by temperature, carbon source, aeration and mode of energy metabolism

Background

Vitamin K2 (menaquinone, MK-n) is a lipid-soluble vitamin that functions as a carboxylase co-factor for maturation of proteins involved in many vital physiological processes in humans. Notably, long-chain vitamin K2 is produced by bacteria, including some species and strains belonging to the group of lactic acid bacteria (LAB) that play important roles in food fermentation processes. This study was performed to gain insights into the natural long-chain vitamin K2 production capacity of LAB and the factors influencing vitamin K2 production during cultivation, providing a basis for biotechnological production of vitamin K2 and in situ fortification of this vitamin in food products.

Results

We observed that six selected Lactococcus lactis strains produced MK-5 to MK-10, with MK-8 and MK-9 as the major MK variant. Significant diversities between strains were observed in terms of specific concentrations and titres of vitamin K2. L. lactis ssp. cremoris MG1363 was selected for more detailed studies of the impact of selected carbon sources tested under different growth conditions [i.e. static fermentation (oxygen absent, heme absent); aerobic fermentation (oxygen present, heme absent) and aerobic respiration (oxygen present, heme present)] on vitamin K2 production in M17 media. Aerobic fermentation with fructose as a carbon source resulted in the highest specific concentration of vitamin K2: 3.7-fold increase compared to static fermentation with glucose, whereas aerobic respiration with trehalose resulted in the highest titre: 5.2-fold increase compared to static fermentation with glucose. When the same strain was applied to quark fermentation, we consistently observed that altered carbon source (fructose) and aerobic cultivation of the pre-culture resulted in efficient vitamin K2 fortification in the quark product.

Conclusions

With this study we demonstrate that certain LAB strains can be employed for efficient production of long-chain vitamin K2. Strain selection and optimisation of growth conditions offer a viable strategy towards natural vitamin K2 enrichment of fermented foods, and to improved biotechnological vitamin K2 production processes.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1179-9) contains supplementary material, which is available to authorized users.

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal

Spontaneously fermented food products contain a complex, natural microbial community with potential probiotic activity. The addition of a health-promoting, probiotic bacterium to these products ensures the delivery of that probiotic activity to consumers. Here, we assess the microbial community of a traditional Senegalese milk product produced by spontaneous fermentation, called lait caillé. We produced the lait caillé in a traditional way and added a probiotic starter containing Lactobacillus rhamnosus yoba 2012 to the traditional process. We found various species that are known for their ability to ferment milk, including species from the genera Lactobacillus, Acetobacter, Lactococcus, and Streptococcus. Our results show that the addition of L. rhamnosus to the inoculum, can result in detectable levels of this strain in the final product, ranging between 0.2 and 1 percent of the total bacterial population. Subsequent rounds of fermentation using passive back-slopping without the addition of new L. rhamnosus led to a loss of this strain from the community of fermenting bacteria. Our results suggest that the addition of probiotic strains at every fermentation cycle can enrich the existing complex communities of traditionally fermented lait caillé while traditional bacterial strains remain dominant in the bacterial communities.

Application of a partial cell recycling chemostat for continuous production of aroma compounds at near-zero growth rates

Objective

The partial cell recycling chemostat is a modification of the chemostat in which cells are partially recycled towards the bioreactor. This allows using dilution rates higher than the maximum growth rate resulting in higher biomass concentrations and increased process rates. In this study, we demonstrate with a single observation that this system can also be used to study microorganisms at near-zero growth rates and as production system for compounds specific for slow growth, such as those typical for ripened cheese.

Results

Lactococcus lactis FM03-V2 was cultivated at growth rates between 0.0025 and 0.025 h⁻¹. Detailed analysis of produced aroma compounds revealed that levels of particular compounds were clearly affected by the growth rate within the studied range demonstrating that we can steer the aroma production by controlling the growth rate. With this approach, we also experimentally validated that the maintenance coefficient of this dairy strain decreased at near-zero growth rates (6.4-fold). An exponentially decreasing maintenance coefficient was included in the growth model, enabling accurate prediction of biomass accumulation in the partial cell recycling chemostat. This study demonstrates the potential of partial cell recycling chemostat both as aroma production system at near-zero growth rates and as unique research tool.

Electronic supplementary material

The online version of this article (10.1186/s13104-019-4213-4) contains supplementary material, which is available to authorized users.

Robust sampling and preservation of DNA for microbial community profiling in field experiments

Objective

Stabilising samples of microbial communities for DNA extraction without access to laboratory equipment can be a challenging task. In this paper we propose a method using filter paper disks for the preservation of DNA from diverse microbial communities which are found in a fermented milk product.

Results

Small adaptations to the DNA extraction method used for liquid fermented milk delivered DNA of sufficient amounts and quality to be used for later analyses, e.g. full community 16S amplicon sequencing. The microbial community structure obtained via the filter paper method showed sufficient resemblance to the structure obtain via the traditional DNA extraction from the liquid milk sample. This method can therefore successfully be used to analyse diverse microbial communities from fermented milk products from remote areas.

Electronic supplementary material

The online version of this article (10.1186/s13104-019-4187-2) contains supplementary material, which is available to authorized users.

Aroma formation in retentostat co-cultures of Lactococcus lactis and Leuconostoc mesenteroides

Lactococcus lactis subsp. lactis biovar diacetylactis and Leuconostoc mesenteroides are considered to be the main aroma producers in Dutch-type cheeses. Both species of lactic acid bacteria were grown in retentostat mono- and co-cultures to investigate their interaction at near-zero growth rates and to determine if co-cultivation enhances the aroma complexity compared to single species performance. During retentostat mono-cultures, the growth rates of both species decreased to less than 0.001 h^-1 and a large fraction of the cells became viable but not culturable. Compared to Lc. mesenteroides, L. lactis reached a 3.4-fold higher biomass concentration caused by i) a higher ATP yield on substrate, ii) a higher biomass yield on ATP and iii) a lower maintenance requirement (m_ATP). Dynamic models estimated that the m_ATP of both species decreased approximately 7-fold at near-zero growth rates compared to high growth rates. Extension of these models by assuming equal substrate distribution resulted in excellent prediction of the biomass accumulation in retentostat co-cultures with L. lactis dominating (100:1) as observed in ripened cheese. Despite its low abundance (∼1%), Lc. mesenteroides contributed to aroma production in co-cultures as indicated by the presence of all 5 specific Lc. mesenteroides compounds. This study provides insights in the production of cheese aroma compounds outside the cheese matrix by co-cultures of L. lactis and Lc. mesenteroides, which could be used as food supplements in dairy or non-dairy products.

Interobserver agreement of skeletal muscle mass measurement on head and neck CT imaging at the level of the third cervical vertebra

OBJECTIVES

Skeletal muscle mass (SMM) is most often assessed in cancer patients on abdominal computed tomography (CT) imaging at the level of the third lumbar vertebra (L3). Abdominal CT imaging is not routinely performed in head and neck cancer (HNC) patients. Recently, a novel method to assess SMM on a single transversal CT slice at the level of the third cervical vertebra (C3) was published. The objective of this study was to assess the robustness of this novel C3 measurement method in terms of interobserver agreement.

PATIENTS AND METHODS

Patients diagnosed with locally advanced head and neck squamous cell carcinoma (LA-HNSCC) at our center between 2007 and 2011 were evaluated. Fifty-four patients with were randomly selected for analysis. Six observers independently measured the cross-sectional muscle area (CSMA) at the level of C3 using a predefined, written protocol as instruction. Interobserver agreement was assessed using intraclass correlation coefficients (ICCs), a Bland-Altman plot and Fleiss' kappa (κ).

RESULTS

The agreement in vertebra selection between all observers was excellent (Fleiss' κ: 0.96). There was a substantial agreement between all observers in single slice selection (Fleiss' κ: 0.61). For all CSMA measurements, ICCs were excellent (0.763-0.969; all p < 0.001). The Bland-Altman plot showed good agreement between measurements, with narrow limits of agreement.

CONCLUSION

Interobserver agreement for SMM measurement at the level of C3 was excellent. Assessment of SMM at the level of C3 is easy and robust and can performed on routinely available imaging in HNC patients.

Delivery of genome editing tools by bacterial extracellular vesicles

Here we propose to use bacterial cells as factories that generate EVs harboring both the RNP complex (or any other CRISPR-mediated tool) and a specific ligand molecule. The ligand would allow specific binding of EVs to cells with the matching receptors, adding a level of specificity to the delivery, hence stimulating precise genome editing.

Contribution of Eat1 and Other Alcohol Acyltransferases to Ester Production in Saccharomyces cerevisiae

Esters are essential for the flavor and aroma of fermented products, and are mainly produced by alcohol acyl transferases (AATs). A recently discovered AAT family named Eat (Ethanol acetyltransferase) contributes to ethyl acetate synthesis in yeast. However, its effect on the synthesis of other esters is unknown. In this study, the role of the Eat family in ester synthesis was compared to that of other Saccharomyces cerevisiae AATs (Atf1p, Atf2p, Eht1p, and Eeb1p) in silico and in vivo. A genomic study in a collection of industrial S. cerevisiae strains showed that variation of the primary sequence of the AATs did not correlate with ester production. Fifteen members of the EAT family from nine yeast species were overexpressed in S. cerevisiae CEN.PK2-1D and were able to increase the production of acetate and propanoate esters. The role of Eat1p was then studied in more detail in S. cerevisiae CEN.PK2-1D by deleting EAT1 in various combinations with other known S. cerevisiae AATs. Between 6 and 11 esters were produced under three cultivation conditions. Contrary to our expectations, a strain where all known AATs were disrupted could still produce, e.g., ethyl acetate and isoamyl acetate. This study has expanded our understanding of ester synthesis in yeast but also showed that some unknown ester-producing mechanisms still exist.