Species dynamics in natural bacterial communities over multiple rounds of propagation.

Our experimental work illustrates how microbial ecosystems can be shaped by selective pressures over long-term ecological time scales. Natural microbial ecosystems generally consist of various co-existing species, where community composition describes the frequency at which species or types are present. Overall functionality of the system is achieved by interacting species. Upon short-term selection, for instance by transfer to a novel environment, community composition and functionality may change in a process referred to as species sorting. Various factors, such as initial community composition and selective pressures from the environment, may influence this change. Mabisi is a traditional fermented food from Zambia that naturally contains a bacterial community of around twenty unique bacterial types. We used six comparable but different natural bacterial Mabisi communities, each split into five identical replicates, for 16 propagation cycles in a novel, common laboratory environment. Composition of the bacterial communities changed upon propagation. The influence of four main factors on community composition, i.e. initial composition (history), impact of the environment (adaptation), changes due to interaction between species and random processes (chance) in species dynamics, was tested using maximum likelihood ratios. Initial community composition seemed to determine the change in community composition, followed by random processes. Interestingly, we observed convergence at the level of ecosystem functionality, which was measured as profiles of metabolic output. This suggests different combinations of species or types can achieve similar eco-system functionality.

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.

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.

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.

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.