Fungal spoilage of foods represents a major cause of concern for food manufacturers. The use of lactic acid bacteria (LAB) to alleviate fungal decay of foods and feeds is a promising solution. The ...study and application of antifungal LAB has received a surge of interest in recent years. Significant progress has been reported on the isolation and characterization of antimycotic compounds, which include various organic acids, cyclic dipeptides and fatty acids, while various food-based applications of these antifungal LAB have been described in literature. This review summarizes the current knowledge on antifungal LAB, their bioactive metabolites, applications in food systems and interactions with their target fungi.
•We explore the upsurge in studies discerning the antifungal attributes of LAB.•The biochemical nature of antifungal compounds derived from LAB is described.•Standardization of isolation and purification methods is required for such compounds.•The application of anti-fungal LAB in foods and feeds as preservative cultures.•Defining the interactions of anti-fungal LAB and their target fungi.
Abstract
Bacteriophages (or phages) represent a persistent threat to the success and reliability of food fermentation processes. Recent reports of phages that infect Streptococcus thermophilus have ...highlighted the diversification of phages of this species. Phages of S. thermophilus typically exhibit a narrow range, a feature that is suggestive of diverse receptor moieties being presented on the cell surface of the host. Cell wall polysaccharides, including rhamnose-glucose polysaccharides and exopolysaccharides have been implicated as being involved in the initial interactions with several phages of this species. Following internalization of the phage genome, the host presents several defences, including CRISPR-Cas and restriction and modification systems to limit phage proliferation. This review provides a current and holistic view of the interactions of phages and their S. thermophilus host cells and how this has influenced the diversity and evolution of both entities.
This review provides an overview of the current knowledge of interactions and co-evolution of Streptococcus thermophilus and its infecting phages.
The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The ...establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
Bifidobacteria represent one of the dominant microbial groups that occur in the gut of various animals, being particularly prevalent during the suckling period of humans and other mammals. Their ...ability to compete with other gut bacteria is largely attributed to their saccharolytic features. Comparative and functional genomic as well as transcriptomic analyses have revealed the genetic background that underpins the overall saccharolytic phenotype for each of the 47 bifidobacterial (sub)species representing the genus Bifidobacterium, while also generating insightful information regarding carbohydrate resource sharing and cross-feeding among bifidobacteria. The abundance of bifidobacterial saccharolytic features in human microbiomes supports the notion that metabolic accessibility to dietary and/or host-derived glycans is a potent evolutionary force that has shaped the bifidobacterial genome.
Stress Physiology of Lactic Acid Bacteria Papadimitriou, Konstantinos; Alegría, Ángel; Bron, Peter A ...
Microbiology and molecular biology reviews,
09/2016, Letnik:
80, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Lactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the ...technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g., Lactococcus lactis), probiotic (e.g., several Lactobacillus spp.), and pathogenic (e.g., Enterococcus and Streptococcus spp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the "stressome" of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance.
Live bacteria (such as probiotics) have long been used to modulate gut microbiota and human physiology, but their colonization is mostly transient. Conceptual understanding of the ecological ...principles as they apply to exogenously introduced microbes in gut ecosystems is lacking. We find that, when orally administered to humans, Bifidobacterium longum AH1206 stably persists in the gut of 30% of individuals for at least 6 months without causing gastrointestinal symptoms or impacting the composition of the resident gut microbiota. AH1206 engraftment was associated with low abundance of resident B. longum and underrepresentation of specific carbohydrate utilization genes in the pre-treatment microbiome. Thus, phylogenetic limiting and resource availability are two factors that control the niche opportunity for AH1206 colonization. These findings suggest that bacterial species and functional genes absent in the gut microbiome of individual humans can be reestablished, providing opportunities for precise and personalized microbiome reconstitution.
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•Orally administered B. longum AH1206 persisted in the gut of 30% of humans for 6 months•AH1206 engraftment did not alter resident microbiota composition or cause GI symptoms•Lower levels of B. longum in the pre-treatment microbiome predict AH1206 persistence•Underrepresentation of carbohydrate-utilization genes is linked to AH1206 persistence
Understanding the principles underlying long-term bacterial colonization in humans will be crucial to the success of microbiome-based therapies. Maldonado-Gómez et al. show that an orally administered bacterial strain persists long-term in a subset of individuals. Engraftment depended on individualized features of the pre-treatment microbiome, likely representing a niche opportunity.
Abstract
A number of bacterial species are found in high abundance in the faeces of healthy breast-fed infants, an occurrence that is understood to be, at least in part, due to the ability of these ...bacteria to metabolize human milk oligosaccharides (HMOs). HMOs are the third most abundant component of human milk after lactose and lipids, and represent complex sugars which possess unique structural diversity and are resistant to infant gastrointestinal digestion. Thus, these sugars reach the infant distal intestine intact, thereby serving as a fermentable substrate for specific intestinal microbes, including Firmicutes, Proteobacteria, and especially infant-associated Bifidobacterium spp. which help to shape the infant gut microbiome. Bacteria utilising HMOs are equipped with genes associated with their degradation and a number of carbohydrate-active enzymes known as glycoside hydrolase enzymes have been identified in the infant gut, which supports this hypothesis. The resulting degraded HMOs can also be used as growth substrates for other infant gut bacteria present in a microbe-microbe interaction known as ‘cross-feeding’. This review describes the current knowledge on HMO metabolism by particular infant gut-associated bacteria, many of which are currently used as commercial probiotics, including the distinct strategies employed by individual species for HMO utilisation.
This review describes the current knowledge on HMO metabolism by a range of infant gut-associated bacteria, many of which are currently used as commercial probiotics, including the distinct strategies employed by individual species for HMO utilisation.
Vaginotypes of the human vaginal microbiome Mancabelli, Leonardo; Tarracchini, Chiara; Milani, Christian ...
Environmental microbiology,
March 2021, 2021-Mar, 2021-03-00, 20210301, Letnik:
23, Številka:
3
Journal Article
Recenzirano
Summary
The human vaginal environment harbours a community of bacteria that plays an important role in maintaining vaginal health and in protecting this environment from various urogenital ...infections. This bacterial population, also known as vaginal microbiota, has been demonstrated to be dominated by members of the Lactobacillus genus. Several studies employing 16S rRNA gene‐based amplicon sequencing have classified the vaginal microbiota into five distinct community state types (CSTs) or vaginotypes. To deepen our understanding of the vaginal microbiota we performed an in‐depth meta‐analysis of 1312 publicly available datasets concerning healthy vaginal microbiome information obtained by metagenomics sequencing. The analysis confirmed the predominance of taxa belonging to the Lactobacillus genus, followed by members of the genera Gardnerella, Vibrio and Atopobium. Moreover, the statistical robustness offered by this meta‐analysis allowed us to disentangle the species‐level composition of dominant and accessory taxa constituting each vaginotype and to revisit and refine the previously proposed CST classification. In addition, a functional characterization of the metagenomic datasets revealed particular genetic features associated with each assigned vaginotype.
Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. ...In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina.
In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol.
Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.
The biosynthetic machinery for cell wall polysaccharide (CWPS) production in lactococci is encoded by a large gene cluster, designated cwps. This locus displays considerable variation among ...lactococcal genomes, previously prompting a classification into three distinct genotypes (A–C). In the present study, the cwps loci of 107 lactococcal strains were compared, revealing the presence of a fourth cwps genotype (type D). Lactococcal CWPSs are comprised of two saccharidic structures: a peptidoglycan‐embedded rhamnan backbone polymer to which a surface‐exposed, poly/oligosaccharidic side‐chain is covalently linked. Chemical structures of the side‐chain of seven lactococcal strains were elucidated, highlighting their diverse and strain‐specific nature. Furthermore, a link between cwps genotype and chemical structure was derived based on the number of glycosyltransferase‐encoding genes in the cwps cluster and the presence of conserved genes encoding the presumed priming glycosyltransferase. This facilitates predictions of several structural features of lactococcal CWPSs including (a) whether the CWPS possesses short oligo/polysaccharide side‐chains, (b) the number of component monosaccharides in a given CWPS structure, (c) the order of monosaccharide incorporation into the repeating units of the side‐chain (for C‐type strains), (d) the presence of Galf and phosphodiester bonds in the side‐chain, and (e) the presence of glycerol phosphate substituents in the side‐chain.
The chemical structures of cell wall polysaccharides (CWPS) of seven distinct lactococcal strains were elucidated. Comparative genome analysis of the gene clusters that encode these structures of 107 lactococcal strains has led to the identification of four distinct genotypes that correlates to distinct chemical structures. The combined genome and structural data allow predictions of characteristics of lactococcal CWPS based on sequence information, while a model for the biosynthetic pathway of the CWPS of the prototypical B‐type strain IL1403 is proposed.
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