Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation

Sooresh, Maanasa Mudoor; Willing, Benjamin P.; Bourrie, Benjamin C. T.

doi:10.3390/foods12030673

Cited by 13 publications

(6 citation statements)

References 115 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Enterobacterales, mainly represented by members of the Enterobacteriaceae family, are commonly found via metagenomic approaches in fermented vegetables (Thierry et al, 2023). They are associated with many raw materials and are common in the initial phases of various spontaneous food fermentations including vegetables (Kłapeć et al, 2016;Mudoor Sooresh et al, 2023).…”

Section: Lactic Acid Bacteria Dominated the Microbial Community Of Mo...mentioning

confidence: 99%

Microbial communities of a variety of 75 homemade fermented vegetables

Thierry,

Madec,

Chuat

et al. 2023

Front. Microbiol.

View full text Add to dashboard Cite

Fermentation is an ancient practice of food preservation. Fermented vegetables are popular in Eastern European and Asian countries. They have received a growing interest in Western countries, where they are mainly manufactured at domestic and artisanal scales and poorly characterized. Our aim was to investigate the microbial communities and the safety of French homemade fermented vegetables, in the frame of a citizen science project. Fermented vegetables and the data associated with their manufacture were collected from citizens and characterized for pH, NaCl concentration, and microbiology by culturomics and 16S DNA metabarcoding analysis. Lactic acid bacteria (LAB) and yeast isolates were identified by 16S rRNA gene sequencing and D1/D2 domains of the large subunit of the rRNA gene, respectively. The 75 collected samples contained 23 types of vegetables, mainly cabbage, followed by carrots and beets, and many mixtures of vegetables. They were 2 weeks to 4 years old, and their median pH was 3.56, except for two samples with a pH over 4.5. LAB represented the dominant viable bacteria. LAB concentrations ranged from non-detectable values to 8.7 log colony-forming units (CFU)/g and only depended on the age of the samples, with the highest most frequently observed in the youngest samples (<100 days). The 93 LAB isolates identified belonged to 23 species, the two mains being Lactiplantibacillus pentosus/plantarum and Levilactobacillus brevis. The other microbial groups enumerated (total aerobic bacteria, halotolerant bacteria, Gram-negative bacteria, and acetic acid bacteria) generally showed lower concentrations compared to LAB concentrations. No pathogenic bacteria were detected. Viable yeasts were observed in nearly half the samples, at concentrations reaching up to 8.0 log CFU/g. The 33 yeast clones identified belonged to 16 species. Bacterial metabarcoding showed two main orders, namely, Lactobacillales (i.e., LAB, 79% of abundance, 177 of the 398 total ASVs) and Enterobacterales (19% of abundance, 191 ASVs). Fifteen LAB genera were identified, with Lactiplantibacillus and Levilactobacillus as the most abundant, with 41 and 12% of total reads, respectively. Enterobacterales members were mainly represented by Enterobacteriaceae and Yersiniaceae. This study is the first wide description of the microbiota of a large variety of homemade fermented vegetables and documents their safety.

show abstract

Section: Lactic Acid Bacteria Dominated the Microbial Community Of Mo...mentioning

confidence: 99%

Microbial communities of a variety of 75 homemade fermented vegetables

Thierry,

Madec,

Chuat

et al. 2023

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…A fourth home-made sauerkraut (Sample 4) showed little resemblance to other sauerkrauts and had high proportions of Enterobacter spp. and Klebsiella taxa but limited LAB, possibly resulting from contamination and a shorter fermentation time [39] (Table S15). The three commercial sauerkrauts presented some variability; two were dominated by different Lactiplantibacillus taxa and had relatively high proportions of L. brevis and either Leuconostoc sp.…”

Section: Sauerkrautmentioning

confidence: 99%

“…Sequencing methods are also limited in the regard that it is not possible to distinguish living from dead microbes, which could be a reason for why we detected some unexpected or uncommon bacteria in the fermented foods, e.g., common intestinal bacteria. While it is not possible (and sometimes not preferable as in the case of spontaneous fermentation) to completely avoid contamination from the environment (raw materials, equipment, and environment [39]), proper hand hygiene and cleanliness of the workspace and utensils can reduce some unwanted contamination [3]. Whilst generally considered safe to consume, fermented foods are not exempt from food-borne pathogens, and we measured high proportions of intestinal bacteria (Enterobacter and Klebsiella) in a home-made sauerkraut.…”

Section: Final Remarksmentioning

confidence: 99%

Characterization of the Bacterial Composition of 47 Fermented Foods in Sweden

Palmnäs-Bédard,

de Santa Izabel,

Dicksved

et al. 2023

Foods

View full text Add to dashboard Cite

Fermentation has long been utilized to preserve and enhance the flavor and nutritional value of foods. Recently, fermented foods have gained popularity, reaching new consumer groups due to perceived health benefits. However, the microbial composition of many fermented foods re-mains unknown. Here, we characterized the bacterial composition, diversity, and richness of 47 fermented foods available in Sweden, including kombucha, water kefir, milk kefir, yogurt, plant-based yogurt alternatives, kimchi, sauerkraut, and fermented vegetables. Via 16S rRNA gene sequencing, we identified 2497 bacteria (amplicon sequence variants). The bacterial composition was strongly associated with the type of fermented food, and lactic acid bacteria and/or acetic acid bacteria dominated most samples. However, each fermented food had a unique composition, with kombucha and water kefir having the highest diversity across and within samples. Few bacteria were abundant in multiple foods and food groups. These were Streptococcus thermophilus in yogurts and plant-based yoghurts; Lactococcus lactis in milk kefirs and one water kefir; and Lactiplantibacillus plantarum in kimchi, sauerkraut, and fermented cucumber. The broad range of fermented foods included in this study and their diverse bacterial communities warrant further investigation into the implications of microbial compositions for product traits and potential impact on human health.

show abstract

“…While almost every culture past and present has some form of fermentation tradition, fermentation practice has not yet entered the space environment. Since the fermentation process is shaped by its environment (19) new flavors and microbial communities may emerge as fermented foods migrate to outer space. This new research direction builds on the recent explosion of scientific interest in studying the microbiome of the ISS (20)(21)(22)(23)(24) and the human microbiome in space (25).…”

Section: Introductionmentioning

confidence: 99%

Food Fermentation in Space Is Possible, Distinctive, and Beneficial

Coblentz,

Evans,

Kothe

et al. 2024

Preprint

View full text Add to dashboard Cite

Space exploration is expanding, which demands new technologies and enables new scientific questions. Food, as a bridge between disciplines, can bring these fundamental and applied goals together. Here we investigate whether food fermentation in space is possible, and if so, how it compares with fermentation on Earth. We fermented a miso, a traditional Japanese condiment, on the International Space Station over 30 days, and compared it with two earthbound controls. Using a specially-built environmental sensing box, we gathered metadata for temperature, relative humidity, pressure, and radiation. We analyzed the three misos with shotgun metagenomics to investigate the microbial communities’ composition and safety; whole genome sequencing to investigate the mutation rate ofAspergillus oryzae; untargeted metabolomics to quantify aromatic compounds, amino acids and organic acids; colorimetry to quantify color; and sensory analysis to describe the misos’ flavours and quantify liking and sensory difference. Across these datasets, we found that overall, the space miso is recognizable as a miso, suggesting fermentation in space is possible. We also found certain differences in the space miso: specifically the presence ofBacillus velezensis, a higher mutation rate ofA. oryzae, higher attributions of ‘roasted’ and ‘nutty’ flavours, and the most different sensory impression. Taken together, these observations suggest unique features of the space environment—what we might call ‘space terroir’—which could be harnessed to create more flavorful, nourishing foods for long-term space missions and to address fundamental questions about the biology of novel environments.Significance StatementOur study presents, to our knowledge, the first time a food product has been fermented in space. We demonstrate that fermentation in space is possible with safe and successful results, a proof of concept that offers fermentation as a new tool for space research and future long-term space exploration missions. We also document how the space environment shapes the fermentation process in unique ways, suggesting a ‘space terroir’. These findings on the feasibility and novelty of fermentation in space open up directions for further multidisciplinary research across science, health, systems design, and society and culture.

show abstract

Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation

Cited by 13 publications

References 115 publications

Microbial communities of a variety of 75 homemade fermented vegetables

Microbial communities of a variety of 75 homemade fermented vegetables

Characterization of the Bacterial Composition of 47 Fermented Foods in Sweden

Food Fermentation in Space Is Possible, Distinctive, and Beneficial

Contact Info

Product

Resources

About