A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods

Background: The lactic acid bacterium Lactobacillus rhamnosus GG is the most studied probiotic bacterium with proven health benefits upon oral intake, including the alleviation of diarrhea. The mission of the Yoba for Life foundation is to provide impoverished communities in Africa increased access to Lactobacillus rhamnosus GG under the name Lactobacillus rhamnosus yoba 2012, world's first generic probiotic strain. We have been able to overcome the strain's limitations to grow in food matrices like milk, by formulating a dried starter consortium with Streptococcus thermophilus that enables the propagation of both strains in milk and other food matrices. The affordable seed culture is used by people in resource-poor communities. Results: We used S. thermophilus C106 as an adjuvant culture for the propagation of L. rhamnosus yoba 2012 in a variety of fermented foods up to concentrations, because of its endogenous proteolytic activity, ability to degrade lactose and other synergistic effects. Subsequently, L. rhamnosus could reach final titers of 1E+09 CFU ml(-1), which is sufficient to comply with the recommended daily dose for probiotics. The specific metabolic interactions between the two strains were derived from the full genome sequences of L. rhamnosus GG and S. thermophilus C106. The piliation of the L. rhamnosus yoba 2012, required for epithelial adhesion and inflammatory signaling in the human host, was stable during growth in milk for two rounds of fermentation. Sachets prepared with the two strains, yoba 2012 and C106, retained viability for at least 2 years. Conclusions: A stable dried seed culture has been developed which facilitates local and low-cost production of a wide range of fermented foods that subsequently act as delivery vehicles for beneficial bacteria to communities in east Africa.Peer reviewe

Metabolische Oszillationen in Hefe

Wenn Hefe in einer kontinuierlichen Kultur wächst, kommt es zu einer spontanen Synchronisation der Zellen resultierend in einer stabilen respiratorischen Oszillation. Sowohl weite Teile des Transkriptoms als auch des Metaboloms oszillieren in klaren Phasenbeziehungen zu dieser respiratorischen Aktivität. In dieser Arbeit wird das Phänomen sowohl von theoretischer als auch experimenteller Seite untersucht. Es wird die Dynamik des Lipidoms analysiert und gezeigt, dass dieses ebenfalls oszillatorisches Verhalten aufweist. Dabei gibt es eine Gruppe an Lipiden, die ihre höchsten Konzentrationen in der Phase hoher Sauerstoffaufnahme zeigt und eine andere Gruppe in der Phase niedriger Sauerstoffaufnahme. Zudem werden vier Szenarien betrachtet, die in biochemischen Netzwerken zu Oszillationen führen können. Es wäre möglich, dass es sich um einen rein mechanistischen Effekt ohne eine unmittelbare Funktion - beruhend auf einer negativen Rückkopplung und einer intrinsischen Zeitverzögerung - handelt. Weiterhin könnten diese Oszillationen die sich ändernen physiologischen Anforderungen eines Prozesses, der in einer gegebenen Ordnung abzulaufen hat, widerspiegeln. Unter Verwendung von Minimalsystemen und in-silico Evolution wird gezeigt, dass Oszillationen zu einem Fitnessvorteil auf Einzelzellebene führen können. Dieser beruht zum einen darauf, dass Oszillationen eine zeitliche Trennung der Produktion toxischer Nebenprodukte von der Produktion der durch sie geschädigten Komponenten ermöglicht. Zum anderen erlaubt oszillatorisches Verhalten das Ablaufen von Reaktionen in dem für sie jeweils günstigsten Reaktionsmilieu. Basierend auf den experimentell bestimmten Austauschraten für Glucose, O2 und CO2 wird mittels FBA untersucht, wie sich die optimalen Syntheseraten von Biomasse und die Vorläufer selbiger über den Zyklus hinweg ändern. Die Ergebnisse deuten auf eine Trennung von Biosynthese und Stressantwort hin, was eine mögliche Funktion dieser Zyklen darstellen könnte.When grown in continuous culture, budding yeast tend to autosynchronize resulting in a stable respiratory oscillation. Thereby, respiration toggles between high and low oxygen uptake rates. In parallel with this toggling, most facets of cellular physiology oscillate with distinct phase relationships e.g the transcriptome and metabolome. In this work, the phenomenon is examined from a theoretical as well as an experimental point of view. It can be shown that also the lipidome is oscillatory whereby one group of lipids peaks in the phase of high oxygen uptake and the second group of lipids in the phase of low oxygen uptake. Furthermore, four scenarios are presented that might lead to oscillatory dynamics in biochemical networks: Oscillation might occur due to a negative feedback and an intrinsic time delay without bearing a certain function. They could further reflect the changing physiological requirements of a process that has to be performed in a certain order. Using generic models and in-silico evolution, it can be shown that oscillations can also be beneficial on a single cell level since they allow a temporal separation of the production of a toxic by-product and the synthesis of its target and also that reactions can occur in their respective favored reaction milieu. Using measured exchange rates for glucose, O2 and CO2 as constraints for FBA, it is examined how the optimal synthesis rates for biomass and its precursors vary over a cycle. The results suggest that there is a temporal separation of processes related to biosynthesis and stress response which might reflect a possible function of the yeast metabolic cycle

Selection for Cell Yield Does Not Reduce Overflow Metabolism in <i>Escherichia coli</i>

Overflow metabolism is ubiquitous in nature, and it is often considered inefficient because it leads to a relatively low biomass yield per consumed carbon. This metabolic strategy has been described as advantageous because it supports high growth rates during nutrient competition. Here, we experimentally evolved bacteria without nutrient competition by repeatedly growing and mixing millions of parallel batch cultures of Escherichia coli. Each culture originated from a water-in-oil emulsion droplet seeded with a single cell. Unexpectedly we found that overflow metabolism (acetate production) did not change. Instead, the numerical cell yield during the consumption of the accumulated acetate increased as a consequence of a reduction in cell size. Our experiments and a mathematical model show that fast growth and overflow metabolism, followed by the consumption of the overflow metabolite, can lead to a higher numerical cell yield and therefore a higher fitness compared with full respiration of the substrate. This provides an evolutionary scenario where overflow metabolism can be favorable even in the absence of nutrient competition

The dynamics of cellular energetics during continuous yeast culture

A plethora of data is accumulating from high throughput methods on metabolites, coenzymes, proteins, and nucleic acids and their interactions as well as the signalling and regulatory functions and pathways of the cellular network. The frozen moment viewed in a single discrete time sample requires frequent repetition and updating before any appreciation of the dynamics of component interaction becomes possible. Even then in a sample derived from a cell population, time-averaging of processes and events that occur in out-of-phase individuals blur the detailed complexity of single cell organization. Continuously-grown cultures of yeast can become spontaneously self-synchronized, thereby enabling resolution of far more detailed temporal structure. Continuous on-line monitoring by rapidly responding sensors (O2 electrode and membrane-inlet mass spectrometry for O2, CO2 and H2S; direct fluorimetry for NAD(P)H and flavins) gives dynamic information from time-scales of minutes to hours. Supplemented with capillary electophoresis and gas chromatography mass spectrometry and transcriptomics the predominantly oscillatory behaviour of network components becomes evident, with a 40 min cycle between a phase of increased respiration (oxidative phase) and decreased respiration (reductive phase). Highly pervasive, this ultradian clock provides a coordinating function that links mitochondrial energetics and redox balance to transcriptional regulation, mitochondrial structure and organelle remodelling, DNA duplication and cell division events. Ultimately, this leads to a global partitioning of anabolism and catabolism and the enzymes involved, mediated by a relatively simple ATP feedback loop on chromatin architecture

Finding functional differences between species in a microbial community: Case studies in wine fermentation and Kefir culture

Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own properties as well as those of the other species. Here, we apply a computational approach, which uses only genomic and metagenomic information and functional annotation of genes, to find properties that distinguish a species from others in the community, as well as to follow individual species in a community. We analyzed isolated and sequenced strains from a kefir community, and metagenomes from wine fermentations. We demonstrate how the distinguishing properties of an organism lead to experimentally testable hypotheses concerning the niche and the interactions with other species. We observe, for example, that L. kefiranofaciens, a dominant organism in kefir, stands out among the Lactobacilli because it potentially has more amino acid auxotrophies. Using metagenomic analysis of industrial wine fermentations we investigate the role of an inoculated L. plantarum in malolactic fermentation. We observed that L. plantarum thrives better on white than on red wine fermentations and has the largest number of phosphotransferase system among the bacteria observed in the wine communities. Also, L. plantarum together with Pantoea, Erwinia, Asaia, Gluconobacter, and Komagataeibacter genera had the highest number of genes involved in biosynthesis of amino acids

MOESM2 of A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods

Additional file 2: Figure S2. Protocol for the production of fermented milk from the seed culture. Front and backside of the sachets designed for African dairy producers. The protocol on the backside indicates two rounds of fermentation: round 1 from the dried bacterial powder (1 g per l) to fermented milk. round 2: from 1 l fermented milk to 50-100 l fermented milk