Biology subjects

Kothe, C. I.

Publications and source records attributed to Kothe, C. I..

7 recordsLinked to original sources

bioRxiv2025

Possible origins of kombucha in spontaneous fermentation

Although the microbial composition and functional attributes of kombucha have been extensively studied, the origins and mechanisms of the formation of their biofilm (Symbiotic Culture of Bacteria and Yeasts, or SCOBY) remain speculative. Based on historical reports and the concept of community coalescence, this study establishes a proof-of-concept, demonstrating how a kombucha-like biofilm can form spontaneously from microbes associated with plants, insects, and humans in a sweetened tea medium. Metagenomic analyses revealed microbial dynamics during fermentation, uncovering shifts in community composition driven by acetic acid bacteria, lactic acid bacteria, and yeasts. Comparative analyses with existing fermented beverages demonstrated microbial similarities to kombucha metagenomes. Pangenomic analyses focused on Fructobacillus evanidus, a species present in both the bee microbiome and our spontaneous fermentation. The MAGs of F. evanidus from the fermented beverage showed evidence of genetic streamlining, characterized by the loss of genes essential for survival in shifting and highly competitive environments, such as the bee gut, and adaptation to the more stable conditions of fermentation. This study offers insights into the origins of kombucha, integrating historical, microbiological, ecological and evolutionary perspectives to answer the question Is this a kombucha?, and gesturing toward further physical, chemical and sensory dimensions that could be explored.

microbiology↗

bioRxiv2024

Ripened plant-based cheese analogs in Europe: nutritional and microbial profiles

Plant-based cheese analogs have emerged as a novel global market trend driven by sustainability concerns for our planet. This study examines eleven soft ripened plant-based cheese analogs produced in Europe, primarily with bloomy rinds and cashew nuts as the main ingredient. First, we focused on exploring the macronutrients and salt content stated on the labels, as well a detailed fatty acid analysis of the samples. Compared to dairy cheeses, plant-based cheeses share similarities in lipid content, but their fatty acid profiles diverge significantly, with higher ratio of mono- and polyunsaturated fatty acids such as oleic and linoleic acids. We also investigated the microbiota of these analog products, employing a culture-dependent and -independent approaches. We identified a variety of microorganisms in the plant-based cheeses, with Lactococcus lactis and Leuconostoc mesenteroides being the dominant bacterial species, and Geotrichum candidum and Penicillium camemberti the dominant fungal species. Most of the species characterized are similar to those present in dairy cheeses, suggesting that they have been inoculated as culture starters to contribute to the sensorial acceptance of plant-based cheeses. However, we also identify several species that are possibly intrinsic to plant matrices or originate from the production environment, such as Pediococcus pentosaceus and Enterococcus spp. This coexistence of typical dairy-associated organisms with plant associated species highlights the potential microbial dynamics inherent in the production of plant-based cheese. These findings will contribute to a better understanding of plant-based cheese alternatives, enable the development of sustainable products, and pave the way for future research exploring the use of plant-based substrates in the production of cheese analogues.

microbiology↗

bioRxiv2024

MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics

SummaryFermented foods, which contain a diverse array of microbial metabolites and microbes, are increasingly recognized as potential mediators of human immune and metabolic health. While there is growing interest in characterizing the microbial landscape of fermented foods, current characterization methods typically rely on 16S rRNA sequencing or marker gene-based methods, which have low taxonomic resolution and cannot functionally characterize microbes. Here we describe MiFoDB-workflow, a metagenomics workflow for the identification of microbes associated with food fermentation based on a primary database of 675 genomes of bacteria, yeast, fungi, and common fermented food substrates. We constructed the database using metagenome-assembled genomes (MAGs) derived from metagenomic sequencing of 90 fermented foods, combined with previously-published fermented food-derived MAGs, and relevant genomes deposited in RefSeq and GenBank genomes. We demonstrate the utility of MiFoDB for high confidence genome identification, including discovery of previously uncharacterized species, strain tracking across related foods, and functional analysis in fermented foods of different substrates. The workflow streamlines high-confidence characterization of the diversity of the fermented food landscape including novel ferments, and allows strain-level tracking of microbes across time, substrates, and producers.

microbiology↗

bioRxiv2024

Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation

Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of S. epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.

microbiology↗

bioRxiv2024

Food Fermentation in Space Is Possible, Distinctive, and Beneficial

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 of Aspergillus 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 of Bacillus velezensis, a higher mutation rate of A. 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.

microbiology↗

bioRxiv2022

Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics

Brazilian artisanal cheeses date from the first Portuguese settlers and evolved via local factors, resulting in unique products that are now part of the patrimony and identity of different Brazilian regions. In this study, we combined several culture-independent approaches, including 16S/ITS metagenetics, assembly- and deep profiling-metagenomics to characterize the originality of the microbiota of five varieties of Brazilian artisanal cheeses from the South and Southeast regions of Brazil. Their core microbiota contained mainly lactic acid bacteria (LAB), of which Lactococcus lactis subsp. lactis was the most frequent, followed by Streptococcus thermophilus in the South region. Moreover, several samples from the Southeast region contained, as dominant LAB, two other food Streptococci belonging to a new species of the salivarius group and S. infantarius. Rinds of samples from the Southeast region were dominated by the halotolerant bacterium Corynebacterium variabile and the yeasts Diutina catenulata and, to a lesser extent, by Debaryomyces hansenii and Kodamaea ohmeri. Rinds from the South region contained mainly LAB due to their short ripening time, and the predominant yeast was D. hansenii. Phylogenomic analysis based on L. lactis metagenome-assembled genomes (MAGs) showed that most Brazilian strains are closely related and form a different clade from those whose genomes are available at this time, indicating that they belong to a specific group. Lastly, functional analysis showed that S. infantarius acquired a [~]26 kb DNA fragment from S. thermophilus starter strains that carry the LacSZ system, allowing fast lactose assimilation, an adaptation advantage for growth in milk. Finally, our study identified several areas of concern, such as the presence of somatic cell DNA and high levels of antibiotic resistance genes in several cheese microbiota, implying that the milk used was from diseased herds. Overall, the data from this study highlight the potential value of the traditional and artisanal cheese production network in Brazil, and provide a metagenomic-based scheme to help manage this resource safely.

microbiology↗

bioRxiv2020

Unraveling the world of halophilic and halotolerant bacteria in cheese by combining cultural, genomic and metagenomic approaches

Halophilic and halotolerant bacteria are generally assumed to live in natural environments, although they may also be found in foods such as cheese and seafood. These salt-loving bacteria have only been occasionally characterized in cheese, and studies on their ecological and technological functions are still scarce. We therefore selected 13 traditional cheeses in order to systematically characterize these microorganisms in their rinds via cultural, genomic and metagenomic methods. Using different salt-based media, we identified 35 strains with unique 16S rRNA and rpoB gene sequences, whose whole genome was sequenced. The most frequently isolated species are the halotolerant Gram-positive bacteria Brevibacterium aurantiacum (6) and Staphylococcus equorum (3), which are also frequently added as starters. Their genomic analyses confirm the high genetic diversity of B. aurantiacum and reveal the presence of two subspecies in S. equorum, as well as the genetic proximity of several cheese strains to bovine isolates. Additionally, we isolated 15 Gram-negative strains, potentially defining ten new species of halophilic cheese bacteria, in particular for the genera Halomonas and Psychrobacter. The use of these genomes as a reference to complement those existing in the databases allowed us to study the representativeness of 66 species of halophilic and halotolerant bacteria in 74 cheese rind metagenomes. The Gram-negative species are particularly abundant in a wide variety of cheeses with high moisture, such as washed-rind cheeses. Finally, analyses of co-occurrences reveal assemblies, including the frequent coexistence of several species of the same genus, forming moderately complex ecosystems with functional redundancies that probably ensure stable cheese development. IMPORTANCESalt is commonly added to food to avoid the growth of pathogens by lowering water activity, resulting in profound changes in the medium that lead to the development of particular ecosystems dominated by halophilic and halotolerant bacteria, communities that probably originate in the natural environment. In order to explore these communities that have been poorly studied in food up until now, we developed a combined approach that includes cultures, genomics and metagenomics to deconstruct these ecosystems in cheese rinds. This approach allowed us to isolate 26 different species, ten of which belong to still undescribed species that could be used as references to promote advances in functional studies of this particular world. The metagenomic scan of 74 cheese rind samples for the assembly of 66 halophilic and halotolerant species showed that these bacteria are widely distributed and form moderately complex ecosystems where related species coexist and probably jointly contribute to safe and efficient cheese development.

microbiology↗