During the transformation of grapes to wine, wine fermentations are exposed to a large area of specialized equipment surfaces within wineries, which may serve as important reservoirs for two-way transfer of microbes between fermentations. However, the role of winery environments in shaping the microbiota of wine fermentations and vectoring wine spoilage organisms is poorly understood at the systems level. Microbial communities inhabiting all major equipment and surfaces in a pilot-scale winery were surveyed over the course of a single harvest to track the appearance of equipment microbiota before, during, and after grape harvest. Results demonstrate that under normal cleaning conditions winery surfaces harbor seasonally fluctuating populations of bacteria and fungi. Surface microbial communities were dependent on the production context at each site, shaped by technological practices, processing stage, and season. During harvest, grape- and fermentation-associated organisms populated most winery surfaces, acting as potential reservoirs for microbial transfer between fermentations. These surfaces harbored large populations of Saccharomyces cerevisiae and other yeasts prior to harvest, potentially serving as an important vector of these yeasts in wine fermentations. However, the majority of the surface communities before and after harvest comprised organisms with no known link to wine fermentations and a near-absence of spoilage-related organisms, suggesting that winery surfaces do not overtly vector wine spoilage microbes under normal operating conditions.

Sake (Japanese rice wine) production is a complex, multistage process in which fermentation is performed by a succession of mixed fungi and bacteria. This study employed high-throughput rRNA marker gene sequencing, quantitative PCR, and terminal restriction fragment length polymorphism to characterize the bacterial and fungal communities of spontaneous sake production from koji to product as well as brewery equipment surfaces. Results demonstrate a dynamic microbial succession, with koji and early moto fermentations dominated by Bacillus, Staphylococcus, and Aspergillus flavus var. oryzae, succeeded by Lactobacillus spp. and Saccharomyces cerevisiae later in the fermentations. The microbiota driving these fermentations were also prevalent in the production environment, illustrating the reservoirs and routes for microbial contact in this traditional food fermentation. Interrogating the microbial consortia of production environments in parallel with food products is a valuable approach for understanding the complete ecology of food production systems and can be applied to any food system, leading to enlightened perspectives for process control and food safety. Humans have employed food fermentation since time immemorial to improve the safety, stability, flavor, nutrition, and value of their agricultural products. Traditionally, these processes have been driven by indigenous fungi and bacteria originating in raw materials, in autochthonous starter cultures, or in the processing environment itself (1), organisms that are responsible for these beneficial transformative processes as well as for product spoilage (2, 3). While most modern fermented foods are inoculated with defined starter cultures, traditional, uninoculated products remain celebrated for their historical and cultural significances (4), and indigenous microbial activity is often considered to increase the flavor complexity of these foods (5). The advent of high-throughput sequencing technologies has enhanced our ability to investigate the role of microbial communities in food systems with greater scale and sensitivity than ever possible (4), connecting the transmission of microbial communities in food production and food processing environments to their impact on food products.Sake is the traditional, national alcoholic beverage of Japan. Sake is produced from rice through the saccharification of starch by Aspergillus flavus var. oryzae and subsequent alcoholic fermentation by Saccharomyces cerevisiae. Sake brewing involves a serial propagation process, beginning with koji, a solid culture consisting of rice and A. flavus var. oryzae (6) (Fig. 1). Polished, steamed rice is mixed with the dried spores of A. flavus var. oryzae and incubated for approximately 2 days. Koji is then pitched with more steamed rice, water, and yeast into the moto (seed mash) tank, an open mashing vessel, wherein fermentation occurs for 10 to 25 days. Next, the moto is moved to a larger vessel and mixed with increasing amounts of water, rice, and koji in three additions to form ...

Gut microbiome development affects infant health and postnatal physiology. The gut microbe assemblages of preterm infants have been reported to be different from that of healthy term infants. However, the patterns of ecosystem development and inter-individual differences remain poorly understood. We investigated hospitalised preterm infant gut microbiota development using 16S rRNA gene amplicons and the metabolic profiles of 268 stool samples obtained from 17 intensive care and 42 term infants to elucidate the dynamics and equilibria of the developing microbiota. Infant gut microbiota were predominated by Gram-positive cocci, Enterobacteriaceae or Bifidobacteriaceae, which showed sequential transitions to Bifidobacteriaceae-dominated microbiota. In neonatal intensive care unit preterm infants (NICU preterm infants), Staphylococcaceae abundance was higher immediately after birth than in healthy term infants, and Bifidobacteriaceae colonisation tended to be delayed. No specific NICU-cared infant enterotype-like cluster was observed, suggesting that the constrained environment only affected the pace of transition, but not infant gut microbiota equilibrium. Moreover, infants with Bifidobacteriaceae-dominated microbiota showed higher acetate concentrations and lower pH, which have been associated with host health. Our data provides an in-depth understanding of gut microbiota development in NICU preterm infants and complements earlier studies. Understanding the patterns and inter-individual differences of the preterm infant gut ecosystem is the first step towards controlling the risk of diseases in premature infants by targeting intestinal microbiota.