Summary In completely insular microbial communities, evolution of community structure cannot be shaped by the immigration of new members. In addition, when those communities are run in steady state, the influence of environmental factors on their assembly is reduced. Therefore, one would expect similar community structures under steady‐state conditions. Yet, in parallel setups, variability does occur. To reveal ecological mechanisms behind this phenomenon, five parallel reactors were studied at the single‐cell level for about 100 generations and community structure variations were quantified by ecological measures. Whether community variability can be controlled was tested by implementing soft temperature stressors as potential synchronizers. The low slope of the lognormal rank‐order abundance curves indicated a predominance of neutral mechanisms, i.e., where species identity plays no role. Variations in abundance ranks of subcommunities and increase in inter‐community pairwise β‐diversity over time support this. Niche differentiation was also observed, as indicated by steeper geometric‐like rank‐order abundance curves and increased numbers of correlations between abiotic and biotic parameters during initial adaptation and after disturbances. Still, neutral forces dominated community assembly. Our findings suggest that complex microbial communities in insular steady‐state environments can be difficult to synchronize and maintained in their original or desired structure, as they are non‐equilibrium systems.

Microbial communities drive many processes which affect human well-being directly, as in the human microbiome, or indirectly, as in natural environments or in biotechnological applications. Due to their complexity, their dynamics over time is difficult to monitor, and current sequence-based approaches are limited with respect to the temporal resolution. However, in order to eventually control microbial community dynamics, monitoring schemes of high temporal resolution are required. Flow cytometry provides single-cell-based data in the required temporal resolution, and we here use such data to compute stability properties as easy to interpret univariate indicators of microbial community dynamics. Such monitoring tools will allow for a fast, continuous, and cost-effective screening of stability states of microbiomes. Applicable to various environments, including bioreactors, surface water, and the human body, it will contribute to the development of control schemes to manipulate microbial community structures and performances.

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To further define requirements for embryo development without the assistance of complex media, serum, or coculture, the effects of 5% and 20% O2 concentrations, superoxide dismutase (SOD) (experiment 1), and taurine (experiment 2) were tested in a single culture medium (KSOM modified with 2.5 mM HEPES). Bovine embryos were produced in vitro maturation (IVM) and in vitro fertilization (IVF) of oocytes. After fertilization, embryos were cultured in 5% O2:5% CO2:90% N2 at 30 degrees C for the first 40-44 h; then embryos with 4 to 8 cells were cultured in different treatments for another 6 days. Percentage development subsequently was based on this number. In experiment 1, more blastocysts were produced in 5% O2:5% CO2:90% N2 (37%) than in 20% O2:5% CO2:75% N2 (18%; p < 0.01). Blastocyst development with 0, 300, and 600 U/ml of SOD, respectively, was 26%, 26%, and 30% (p > 0.05). In experiment 2, more blastocysts were formed in 5% O2 (39%) than in 95% air (30%; p < 0.05). Also, with 20% O2 and 0, 7, and 14 mM taurine in the medium, blastocyst formation was 18%, 35%, and 36% (p < 0.05). However, in 5% O2, 7 and 14 mM taurine was not beneficial (p = 0.99), as 39% blastocysts were formed with no taurine. In conclusion, results from both experiments demonstrated that 5% O2 was superior to 20% O2 for development of IVM/IVF bovine embryos. SOD had no effect in either 5% or 20% O2. However, 7 mM and 14 mM taurine counteracted the negative effect of 20% O2.(ABSTRACT TRUNCATED AT 250 WORDS)

The concentration of NaCl should not be higher than 95 mM and the total osmolarity of the medium should be between 250 and 270 mosmol.

Many functions in host-microbiota interactions are potentially influenced by intestinal transit times, but little is known about the effects of altered transition times on the composition and functionality of gut microbiota. To analyze these effects, we cultivated the model community SIHUMIx in bioreactors in order to determine the effects of varying transit times (TT) on the community structure and function. After five days of continuous cultivation, we investigated the influence of different medium TT of 12 h, 24 h, and 48 h. For profiling the microbial community, we applied flow cytometric fingerprinting and revealed changes in the community structure of SIHUMIx during the change of TT, which were not associated with changes in species abundances. For pinpointing metabolic alterations, we applied metaproteomics and metabolomics and found, along with shortening the TT, a slight decrease in glycan biosynthesis, carbohydrate, and amino acid metabolism and, furthermore, a reduction in butyrate, methyl butyrate, isobutyrate, valerate, and isovalerate concentrations. Specifically, B. thetaiotaomicron was identified to be affected in terms of butyrate metabolism. However, communities could recover to the original state afterward. This study shows that SIHUMIx showed high structural stability when TT changed-even four-fold. Resistance values remained high, which suggests that TTs did not interfere with the structure of the community to a certain degree.

Diverse intestinal microbiota is frequently used in in vitro bioreactor models to study the effects of diet, chemical contaminations, or medication. However, the reproducible cultivation of fecal microbiota is challenging and the resultant communities behave highly dynamic. To approach the issue of reproducibility in in vitro models, we established an intestinal microbiota model community of reduced complexity, SIHUMIx, as a valuable model for in vitro use. The development of the SIHUMIx community was monitored over time with methods covering the cellular and the molecular level. We used microbial flow cytometry, intact protein profiling and terminal restriction fragment length polymorphism analysis to assess community structure. In parallel, we analyzed the functional level by targeted analysis of short-chain fatty acids and untargeted metabolomics. The stability properties constancy, resistance, and resilience were approached both on the structural and functional level of the community. We show that the SIHUMIx community is highly reproducible and constant since day 5 of cultivation. Furthermore, SIHUMIx has the ability to resist and recover from a pulsed perturbation, with changes in community structure recovered earlier than functional changes. Since community structure and function changed divergently, both levels need to be monitored at the same time to gain a full overview of the community development. All five methods are highly suitable to follow the community dynamics of SIHUMIx and indicated stability on day five. This makes SIHUMIx a suitable in vitro model to investigate the effects of e.g. medical, chemical, or dietary interventions.

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