Probiotic yogurt and milk supplemented with probiotics have been investigated for their role in 'low-grade' inflammation but evidence for their efficacy is inconclusive. This study explores the impact of probiotic yogurt on metabolic and inflammatory biomarkers, with a parallel study of gut microbiota dynamics. The randomised cross-over study was conducted in fourteen healthy, young men to test probiotic yogurt compared with milk acidified with 2 % d-(+)-glucono-δ-lactone during a 2-week intervention (400 g/d). Fasting assessments, a high-fat meal test (HFM) and microbiota analyses were used to assess the intervention effects. Baseline assessments for the HFM were carried out after a run-in during which normal milk was provided. No significant differences in the inflammatory response to the HFM were observed after probiotic yogurt compared with acidified milk intake; however, both products were associated with significant reductions in the inflammatory response to the HFM compared with the baseline tests (assessed by IL6, TNFα and chemokine ligand 5) (P<0·001). These observations were accompanied by significant changes in microbiota taxa, including decreased abundance of Bilophila wadsworthia after acidified milk (log 2-fold-change (FC)=-1·5, P adj=0·05) and probiotic yogurt intake (FC=-1·3, P adj=0·03), increased abundance of Bifidobacterium species after acidified milk intake (FC=1·4, P adj=0·04) and detection of Lactobacillus delbrueckii spp. bulgaricus (FC=7·0, P adj<0·01) and Streptococcus salivarius spp. thermophilus (FC=6·0, P adj<0·01) after probiotic yogurt intake. Probiotic yogurt and acidified milk similarly reduce postprandial inflammation that is associated with a HFM while inducing distinct changes in the gut microbiota of healthy men. These observations could be relevant for dietary treatments that target 'low-grade' inflammation.

Change History: September 2019 The title of the chapter has been adapted from Propionibacterium spp. to Propionibacterium spp. and Acidipropionibacterium spp., due to adaptions in the classification. The authorship has been expanded. Overall, the term "Emmental" has been replaced by the generic term "Swiss-type cheese". MT Fröhlich-Wyder and A Thierry revised the 'Introduction' section. U von Ah updated the 'Classification and Identification' section, described the new genus Acidipropionibacterium and Propionibacteriaceae family, added Table 1 as a new Table and updated Table 2 (from the Table 1 of the previous version). A Thierry and SM Deutsch revised and enriched the 'Morphology, Envelopes and Growth Conditions' section. M Turgay largely extended and updated the section 'Genetics', renamed into 'Genetic properties', from new complete genome sequence data, added Table 3 as a new Table, and updated Table 4 (from Table 2 of the previous version), replaced Table 3 by an extended section 'Genetic engineering' and added a section 'Immunity'. S Irmler restructured and enriched the section 'Metabolism' with short information on the biosynthesis of vitamin B12, trehalose, and pigment and additional information on the conversion of aspartate into succinate and modified Figure 1. G Jan updated and edited the section 'Adaptation to Stress'. MT Fröhlich-Wyder updated the section 'Use as Ripening Cultures in Cheese'. G Jan and H Falentin updated and edited the section 'Relation to Nutrition as Probiotics and Producers of Nutraceuticals'. HP Bachmann expanded the section 'Antimicrobial activities' into a section entitled 'Use as Protective Cultures' and updated Table 5 (from the Table 4 of the previous version). This is an update of A.

Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.

BackgroundAntimicrobial susceptibility testing of microorganisms is performed by either disc diffusion or broth dilution tests. In clinical use, the tests are often still performed manually although automated systems exist. Most systems, however, are based on turbidometric methods which have well-known drawbacks.ResultsIn this study we evaluated isothermal micro calorimetry (IMC) for the determination of minimal inhibitory concentrations (MICs) of 12 antibiotics for five micro-organisms. Here we present the data for the 12 antibiotics and two representative microorganisms E. coli (a Gram-) and S. aureus (a Gram+). IMC was able to determine the MICs correctly according to CLSI values. Since MICs require 24 hours, time was not reduced. However, IMC provided new additional data – a continuous record of heat-producing bacterial activity (e.g. growth) in calorimetry ampoules at subinhibitory antibiotic concentrations. Key features of the heatflow (P) and aggregate heat (Q) vs. time curves were identified (tdelay and ΔQ/Δt respectively). Antibiotics with similar modes of action proved to have similar effects on tdelay and/or ΔQ/Δt.ConclusionIMC can be a powerful tool for determining the effects of antibiotics on microorganisms in vitro. It easily provides accurate MICs – plus a potential means for analyzing and comparing the modes of action of antibiotics at subinhibitory concentrations. Also IMC is completely passive, so after evaluation, ampoule contents (media, bacteria, etc.) can be analyzed by any other method desired.