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Current Biology : CB May 2019Domestication refers to artificial selection and breeding of wild species to obtain cultivated variants that thrive in man-made niches and meet human or industrial... (Review)
Review
Domestication refers to artificial selection and breeding of wild species to obtain cultivated variants that thrive in man-made niches and meet human or industrial requirements. Several genotypic and phenotypic signatures of domestication have been described in crops, livestock and pets. However, domestication is not unique to plants and animals. Microbial diversity has also been shaped by the emergence of novel and highly specific man-made environments, like food and beverage fermentations. This allowed rapid adaptation and diversification of various microbes, such as certain Lactococcus, Lactobacillus, Oenococcus, Saccharomyces and Aspergillus species. During the domestication process, microbes gained the capacity to efficiently consume particular nutrients, cope with a multitude of industry-specific stress factors and produce desirable compounds, often at the cost of a reduction in fitness in their original, natural environments. Moreover, different lineages of the same species adapted to highly diverse niches, resulting in genetically and phenotypically distinct strains. In this Review, we discuss the basic principles of microbial domestication and describe how recent research is uncovering its genetic underpinnings.
Topics: Aspergillus; Domestication; Genetic Variation; Lactobacillus; Lactococcus; Oenococcus; Phenotype; Saccharomyces
PubMed: 31112692
DOI: 10.1016/j.cub.2019.04.025 -
International Journal of Systematic and... Mar 2022The genera , , , and , which formed the family , have recently been merged within the family . Using genome sequences for 47 of the 52 named species from these genera,...
Phylogenomic and comparative genomic analyses of species: identification of molecular signatures specific for the genera , and and proposal for a novel genus gen. nov.
The genera , , , and , which formed the family , have recently been merged within the family . Using genome sequences for 47 of the 52 named species from these genera, we report here comprehensive phylogenomic and comparative analyses on protein sequences from these species using multiple approaches. In a phylogenomic tree based on concatenated sequences of 498 core proteins from these five genera, and in a 16S rRNA gene tree, members of the genera , and formed distinct strongly supported clades. In contrast, species grouped into two distinct unrelated clades designated as the ‘ main clade’ and ‘ clade 2’. The presence of these clades is also seen in a matrix of pairwise average amino acid identity based on core protein sequences. In parallel, comparative genomic studies on protein sequences from genomes have identified 46 conserved signature indels (CSIs) in diverse proteins that are unique characteristics of the different observed species clades. Of these identified CSIs, five, five and 13 CSIs are uniquely present in members of the genera , and , respectively. We also report here six and five CSIs that are exclusively present in the species from the main clade and clade 2, respectively, providing independent evidence supporting their distinctness from each other. The remaining 12 identified CSIs are commonly shared by some or all of the species from the genera , and , clarifying their interrelationships. The identified CSIs provide novel and reliable means for the identification/circumscription of members of the genera , and as well as the two species clades in molecular terms. Based on the strong phylogenetic and molecular evidence presented here, we propose that the genus be limited to only the species from the a main clade, whereas the species forming clade 2 should be transferred to a new genus gen. nov.
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genomics; Leuconostoc; Leuconostocaceae; Oenococcus; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 35320068
DOI: 10.1099/ijsem.0.005284 -
Applied and Environmental Microbiology Oct 2018Fructophilic lactic acid bacteria (FLAB) are a recently discovered group, consisting of a few and species. Because of their unique characteristics, including poor... (Review)
Review
Fructophilic lactic acid bacteria (FLAB) are a recently discovered group, consisting of a few and species. Because of their unique characteristics, including poor growth on glucose and preference of oxygen, they are regarded as "unconventional" lactic acid bacteria (LAB). Their unusual growth characteristics are due to an incomplete gene encoding a bifunctional alcohol/acetaldehyde dehydrogenase (). This results in the imbalance of NAD/NADH and the requirement of additional electron acceptors to metabolize glucose. Oxygen, fructose, and pyruvate are used as electron acceptors. FLAB have significantly fewer genes for carbohydrate metabolism than other LAB, especially due to the lack of complete phosphotransferase system (PTS) transporters. They have been isolated from fructose-rich environments, including flowers, fruits, fermented fruits, and the guts of insects that feed on plants rich in fructose, and are separated into two groups on the basis of their habitats. One group is associated with flowers, grapes, wines, and insects, and the second group is associated with ripe fruits and fruit fermentations. Species associated with insects may play a role in the health of their host and are regarded as suitable vectors for paratransgenesis in honey bees. Besides their impact on insect health, FLAB may be promising candidates for the promotion of human health. Further studies are required to explore their beneficial properties in animals and humans and their applications in the food industry.
Topics: Alcohol Dehydrogenase; Aldehyde Oxidoreductases; Animals; Bacterial Proteins; Bees; Fermentation; Flowers; Fructose; Fruit; Glucose; Insecta; Lactobacillales; Lactobacillus; Leuconostocaceae; Phylogeny; Wine
PubMed: 30054367
DOI: 10.1128/AEM.01290-18 -
Applied Microbiology and Biotechnology Apr 2019Oenococcus oeni is the lactic acid bacteria species most commonly encountered in wine, where it develops after the alcoholic fermentation and achieves the malolactic... (Review)
Review
Oenococcus oeni is the lactic acid bacteria species most commonly encountered in wine, where it develops after the alcoholic fermentation and achieves the malolactic fermentation that is needed to improve the quality of most wines. O. oeni is abundant in the oenological environment as well as in apple cider and kombucha, whereas it is a minor species in the natural environment. Numerous studies have shown that there is a great diversity of strains in each wine region and in each product or type of wine. Recently, genomic studies have shed new light on the species diversity, population structure, and environmental distribution. They revealed that O. oeni has unique genomic features that have contributed to its fast evolution and adaptation to the enological environment. They have also unveiled the phylogenetic diversity and genomic properties of strains that develop in different regions or different products. This review explores the distribution of O. oeni and the diversity of strains in natural habitats.
Topics: Ecosystem; Evolution, Molecular; Fermentation; Genetic Variation; Genomics; Oenococcus; Phylogeny; Wine
PubMed: 30788540
DOI: 10.1007/s00253-019-09689-z -
Gut Microbes 2023Fermented foods demonstrate remarkable health benefits owing to probiotic bacteria or microproducts produced via bacterial fermentation. Fermented foods are produced by...
Fermented foods demonstrate remarkable health benefits owing to probiotic bacteria or microproducts produced via bacterial fermentation. Fermented foods are produced by the fermentative action of several lactic acid bacteria, including ; however, the exact mechanism of action of these foods remains unclear. Here, we observed that prebiotics associated with -produced exopolysaccharides (EPS) demonstrate substantial host metabolic benefits. -produced EPS is an indigestible α-glucan, and intake of the purified form of EPS improved glucose metabolism and energy homeostasis through EPS-derived gut microbial short-chain fatty acids, and changed gut microbial composition. Our findings reveal an important mechanism that accounts for the effects of diet, prebiotics, and probiotics on energy homeostasis and suggests an approach for preventing lifestyle-related diseases by targeting bacterial EPS.
Topics: Prebiotics; Leuconostoc mesenteroides; Gastrointestinal Microbiome; Probiotics; Lactobacillales; Bacteria; Fermentation
PubMed: 36604628
DOI: 10.1080/19490976.2022.2161271 -
Viruses Dec 2022The genus comprises four recognized species, and members have been found in different types of beverages, including wine, kefir, cider and kombucha. In this work, we...
The genus comprises four recognized species, and members have been found in different types of beverages, including wine, kefir, cider and kombucha. In this work, we implemented two complementary strategies to assess whether oenococcal hosts of different species and habitats were connected through their bacteriophages. First, we investigated the diversity of CRISPR-Cas systems using a genome-mining approach, and CRISPR-endowed strains were identified in three species. A census of the spacers from the four identified CRISPR-Cas loci showed that each spacer space was mostly dominated by species-specific sequences. Yet, we characterized a limited records of potentially recent and also ancient infections between and and phages of , suggesting that some related phages have interacted in diverse ways with their hosts over evolutionary time. Second, phage-host interaction analyses were performed experimentally with a diversified panel of phages and strains. None of the tested phages could infect strains across the species barrier. Yet, some infections occurred between phages and hosts from distinct beverages in the species.
Topics: Bacteriophages; Oenococcus; Clustered Regularly Interspaced Short Palindromic Repeats; Wine; Ecosystem; CRISPR-Cas Systems
PubMed: 36680056
DOI: 10.3390/v15010015 -
BMC Genomics Dec 2022Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation....
BACKGROUND
Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation. The impact in food science as well as the limited number of publicly available genomes prompted us to create pangenomes and perform genomic taxonomy analyses starting from de novo sequencing of the genomes of 37 L. gelidum/L. gasicomitatum strains from our culture collection. Our aim was also to evaluate the recently proposed change in taxonomy as well as to study the genomes of strains with different lifestyles in foods.
METHODS
We selected as diverse a set of strains as possible in terms of sources, previous genotyping results and geographical distribution, and included also 10 publicly available genomes in our analyses. We studied genomic taxonomy using pairwise average nucleotide identity (ANI) and calculation of digital DNA-DNA hybridisation (dDDH) scores. Phylogeny analyses were done using the core gene set of 1141 single-copy genes and a set of housekeeping genes commonly used for lactic acid bacteria. In addition, the pangenome and core genome sizes as well as some properties, such as acquired antimicrobial resistance (AMR), important due to the growth in foods, were analysed.
RESULTS
Genome relatedness indices and phylogenetic analyses supported the recently suggested classification that restores the taxonomic position of L. gelidum subsp. gasicomitatum back to the species level as L. gasicomitatum. Genome properties, such as size and coding potential, revealed limited intraspecies variation and showed no attribution to the source of isolation. The distribution of the unique genes between species and subspecies was not associated with the previously documented lifestyle in foods. None of the strains carried any acquired AMR genes or genes associated with any known form of virulence.
CONCLUSION
Genome-wide examination of strains confirms that the proposition to restore the taxonomic position of L. gasicomitatum is justified. It further confirms that the distribution and lifestyle of L. gelidum and L. gasicomitatum in foods have not been driven by the evolution of functional and phylogenetic diversification detectable at the genome level.
Topics: Phylogeny; Leuconostoc; DNA; Food Microbiology
PubMed: 36494615
DOI: 10.1186/s12864-022-09032-3 -
Food Research International (Ottawa,... Jan 2019The aim of this study was to investigate the impact of in situ produced exopolysaccharides (EPS) on the rheological and textural properties of fava bean protein... (Review)
Review
The aim of this study was to investigate the impact of in situ produced exopolysaccharides (EPS) on the rheological and textural properties of fava bean protein concentrate (FPC). EPS (dextrans) were produced from sucrose by two lactic acid bacteria (LAB). The acidification, rheology, and texture of FPC pastes fermented with Leuconostoc pseudomesenteroides DSM 20193 and Weissella confusa VTT E-143403 (E3403) were compared. A clear improvement in rheological and textural parameters was observed in sucrose-added pastes after fermentation, especially with W. confusa VTT E3403. Only moderate proteolysis of fava bean protein during fermentation was observed. The microstructure of the protein in FPC pastes, as observed by confocal laser scanning microscopy, revealed a less continuous and denser structure in EPS-abundant pastes. The beneficial structure formed during EPS-producing fermentation could not be mimicked by simply mixing FPC, isolated dextran, lactic acid, and acetic acid with water. These results emphasize the benefits of in situ produced EPS in connection with the LAB fermentation of legume protein-rich foods. Fermentation with EPS-producing LAB is a cost-effective and clean-labeled technology to obtain tailored textures, and it can further enhance the usability of legumes in novel foods.
Topics: Acetic Acid; Dextrans; Fabaceae; Fermentation; Hydrogen-Ion Concentration; Lactic Acid; Lactobacillales; Leuconostoc; Mannitol; Polysaccharides; Rheology; Sucrose; Vicia faba; Weissella
PubMed: 30599931
DOI: 10.1016/j.foodres.2018.08.054 -
Scientific Reports Nov 2020Although obesity is associated with numerous diseases, the risks of disease may depend on metabolic health. Associations between the gut microbiota, obesity, and...
Although obesity is associated with numerous diseases, the risks of disease may depend on metabolic health. Associations between the gut microbiota, obesity, and metabolic syndrome have been reported, but differences in microbiomes according to metabolic health in the obese population have not been explored in previous studies. Here, we investigated the composition of gut microbiota according to metabolic health status in obese and overweight subjects. A total of 747 overweight or obese adults were categorized by metabolic health status, and their fecal microbiota were profiled using 16S ribosomal RNA gene sequencing. We classified these adults into a metabolically healthy group (MH, N = 317) without any components of metabolic syndrome or a metabolically unhealthy group (MU, N = 430) defined as having at least one metabolic abnormality. The phylogenetic and non-phylogenetic alpha diversity for gut microbiota were lower in the MU group than the MH group, and there were significant differences in gut microbiota bacterial composition between the two groups. We found that the genus Oscillospira and the family Coriobacteriaceae were associated with good metabolic health in the overweight and obese populations. This is the first report to describe gut microbial diversity and composition in metabolically healthy and unhealthy overweight and obese individuals. Modulation of the gut microbiome may help prevent metabolic abnormalities in the obese population.
Topics: Actinobacteria; Adult; Body Mass Index; Female; Gastrointestinal Microbiome; Humans; Leuconostocaceae; Male; Middle Aged; Obesity; Overweight; RNA, Ribosomal, 16S
PubMed: 33173145
DOI: 10.1038/s41598-020-76474-8 -
Journal of Applied Microbiology Jul 2018Oenococcus oeni is the dominant species able to cope with a hostile environment of wines, comprising cumulative effects of low pH, high ethanol and SO content,... (Review)
Review
Oenococcus oeni is the dominant species able to cope with a hostile environment of wines, comprising cumulative effects of low pH, high ethanol and SO content, nonoptimal growth temperatures and growth inhibitory compounds. Ethanol tolerance is a crucial feature for the activity of O. oeni cells in wine because ethanol acts as a disordering agent of its cell membrane and negatively affects metabolic activity; it damages the membrane integrity, decreases cell viability and, as other stress conditions, delays the start of malolactic fermentation with a consequent alteration of wine quality. The cell wall, cytoplasmic membrane and metabolic pathways are the main sites involved in physiological changes aimed to ensure an adequate adaptive response to ethanol stress and to face the oxidative damage caused by increasing production of reactive oxygen species. Improving our understanding of the cellular impact of ethanol toxicity and how the cell responds to ethanol stress can facilitate the development of strategies to enhance microbial ethanol tolerance; this allows to perform a multidisciplinary endeavour requiring not only an ecological study of the spontaneous process but also the characterization of useful technological and physiological features of the predominant strains in order to select those with the highest potential for industrial applications.
Topics: Adaptation, Physiological; Cell Membrane; Cell Wall; Ethanol; Fermentation; Gene Expression Regulation, Bacterial; Metabolic Networks and Pathways; Oenococcus; Stress, Physiological; Wine
PubMed: 29377375
DOI: 10.1111/jam.13711