Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.

Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of “industrialization” of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential. IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.

Metabolome-microbiome signatures in the fermented beverage, Kombucha.

Traditional fermented foods are of major importance with respect to the socio-economic growth, food security, nutrition, and health of African consumers. In several African countries, traditional fermentation processes provide a means of food preservation, improving the shelf life and adding to the nutrients in the food products. As with any fermented foods, the associated food microbiota is of great importance and interest. Recent studies on the microbiome of African fermented foods using high-throughput DNA sequencing techniques have revealed the presence of diverse microbial populations of fundamental, technological, and commercial interest that could be harnessed to further improve health, food safety, and quality. This review provides an overview of African fermented foods, their microbiota, and the health-promoting potential of these foods and microbes.

A changing microbiome has been linked to biological aging in mice and humans, suggesting a possible role of gut flora in pathogenic aging phenotypes. Many bat species have exceptional longevity given their body size and some can live up to ten times longer than expected with little signs of aging. This study explores the anal microbiome of the exceptionally long-lived Myotis myotis bat, investigating bacterial composition in both adult and juvenile bats to determine if the microbiome changes with age in a wild, long-lived non-model organism, using non-lethal sampling. The anal microbiome was sequenced using metabarcoding in more than 50 individuals, finding no significant difference between the composition of juvenile and adult bats, suggesting that age-related microbial shifts previously observed in other mammals may not be present in Myotis myotis. Functional gene categories, inferred from metabarcoding data, expressed in the M. myotis microbiome were categorized identifying pathways involved in metabolism, DNA repair and oxidative phosphorylation. We highlight an abundance of ‘Proteobacteria’ relative to other mammals, with similar patterns compared to other bat microbiomes. Our results suggest that M. myotis may have a relatively stable, unchanging microbiome playing a role in their extended ‘health spans’ with the advancement of age, and suggest a potential link between microbiome and sustained, powered flight.

15Fermented foods have been the focus of ever greater interest as a consequence of purported health 16 benefits. Indeed, it has been suggested that the consumption of these foods that help to address the 17 negative consequences of 'industrialization' of the human gut microbiota in Western society. 18 However, as the mechanisms via which the microbes in fermented foods improve health are not 19 understood, it is necessary to develop an understanding of the composition and functionality of the 20 fermented food microbiota to better harness desirable traits. Here we considerably expand the 21 understanding of fermented food microbiomes by employing shotgun metagenomic sequencing to 22 provide a comprehensive insight into the microbial composition, diversity and functional potential 23 (including antimicrobial resistance, carbohydrate-degrading and health-associated gene content) of 24 a diverse range of 58 fermented foods from artisanal producers from around the Globe. Food type, 25i.e., dairy-, sugar-or brine-type fermented foods, was to be the primary driver of microbial 26 composition, with dairy foods found to have the lowest microbial diversity. From the combined 27 dataset, 127 high quality metagenome-assembled genomes (MAGs), including 10 MAGs 28 representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Lactobacillus, 29Leuconostoc and Rouxiella, were generated. Potential health promoting attributes were more 30 common in fermented foods than non-fermented equivalents, with waterkefirs, sauerkrauts and 31 kvasses containing the greatest numbers of potentially health-associated gene clusters (PHAGCs). 32Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented 33 foods to date, and yields novel information regarding their relative health-promoting potential. 34 Importance 35Fermented foods are regaining popularity in Western society due in part to an appreciation of the 36 potential for fermented food microbiota to positively impact on health. Many previous studies have 37 studied fermented microbiota using classical culture-based microbiological methods, older 38 molecular techniques or, where deeper analyses have been performed, have involved a relatively 39 3 small number of one specific food type. Here, we have used a state-of-the-art shotgun metagenomic 40 approach to investigate 58 different fermented foods of different type and origin. Through this 41 analysis, we were able to identify the differences in the microbiota across these foods, the factors 42 that drove their microbial composition, and the relative potential functional benefits of these 43 microbes. The information provided here will provide significant opportunities for the further 44 optimisation of fermented food production and the harnessing of their health promoting potential. 45 128 Lactic Acid Bacteria dominate Brine Foods 129The brine-type foods tested comprised 26 plant substrate-derived foods fermented in a saline 130 solution. Unlike both dairy-and sugar-type ferm...

Molecular technologies including high-throughput sequencing have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities has generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment—especially diet and nutrition—in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and to a lesser extent, live microbes into the human gut. Here we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarise the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.

Canastra cheese is the most well-known artisanal cheese produced in Brazil. Although its production includes a step to remove fungi from the cheese surface, in recent years some cheesemakers have preserved the autochthonous fungi grown during ripening due to an interest in the sensory characteristics attributed to these microorganisms. In this work, the mycobiota of artisanal cheeses produced in the Canastra region was characterized based on ITS marker gene analysis. A total of 96 artisanal cheeses from 16 different farms across 9 cities were collected during two different periods (dry and wet seasons). The Canastra cheese mycobiota was significantly impacted by the season, the city of production and the farm but altitude did not affect the fungal community of the cheeses analyzed. Debaryomyces prosopidis was most abundant in the majority of samples across both seasons. During the wet season, Trichosporon asahii, Kluyveromyces lactis and Fusarium solani were the next most abundant species, followed by Torulaspora delbrueckii and Acremonium citrinum. These results highlight the importance of manufacturing practices and seasonality on the fungal composition of Canastra cheeses. These insights are particularly important in light of recent new regulation in Brazil, removing previous obstacles for surface fungi to persist on cheese. These new regulations will allow new approaches to cheese production, and ultimately, novel products.