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ABSTRACT: The study of the complex relationships between milk metagenomics and milk composition and cheese-making efficiency as affected by indoor farming and summer highland grazing was the aim of the present work. The experimental design considered monthly sampling (over 5 mo) of the milk produced by 12 Brown Swiss cows divided into 2 groups: the first remained on a lowland indoor farm from June to October, and the second was moved to highland pastures in July and then returned to the lowland farm in September. The resulting 60 milk samples (2 kg each) were used to analyze milk composition, milk coagulation, curd firming, and syneresis processes, and to make individual model cheeses to measure cheese yields and nutrient recoveries in the cheese. After DNA extraction and Illumina Miseq sequencing, milk microbiota amplicons were also processed by means of an open-source pipeline called Quantitative Insights Into Microbial Ecology (Qiime2, version 2018.2; https://qiime2.org). Out of a total of 44 taxa analyzed, 13 bacterial taxa were considered important for the dairy industry (lactic acid bacteria, LAB, 5 taxa; and spoilage bacteria, 4) and for human (other probiotics, 2) and animal health (pathogenic bacteria, 2). The results revealed the transhumant group of cows transferred to summer highland pastures showed an increase in almost all the LAB taxa, bifidobacteria, and propionibacteria, and a reduction in spoilage taxa. All the metagenomic changes disappeared when the transhumant cows were moved back to the permanent indoor farm. The relationships between 17 microbial traits and 30 compositional and technological milk traits were investigated through analysis of correlation and latent explanatory factor analysis. Eight latent factors were identified, explaining 75.3% of the total variance, 2 of which were mainly based on microbial traits: pro-dairy bacteria (14% of total variance, improving during summer pasturing) and pathogenic bacteria (6.0% of total variance). Some bacterial traits contributed to other compositional-technological latent factors (gelation, udder health, and caseins).

This study aimed at investigating the potential of a novel functional herbal tea to act as the carrier for the probiotic Bacillus coagulans GanedenBC30. Spores markedly survived to infusion treatments and the simulation of the gastrointestinal transit only slightly affected the survival, which was 94.8 ± 2.8%. An in-depth investigation using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) which incorporated mucin-covered microcosms was performed. Q-PCR with targeted primers demonstrated that the probiotic quickly colonized mucosal compartments and still persisted after 4 days of wash out. As estimated by plate count combined with 16S rRNA sequencing, B. coagulans GanedenBC30 showed almost the same behavior in luminal compartments both during herbal tea intake and wash out. By summing the luminal and mucosal values and referring to whole volume of colon bioreactors, the content of viable cells of B. coagulans GanedenBC30 was largely above the probiotic threshold.