Capsular polysaccharide inhibits adhesion of Bifidobacterium longum 105-A to enterocyte-like Caco-2 cells and phagocytosis by macrophages

An improved temperature-sensitive shuttle vector system for scarless gene deletion in human-gut-associated Bifidobacterium species

Bifidobacterium is a prevalent bacterial taxon in the human gut that comprises over 10 (sub)species. Previous studies suggest that these species use evolutionarily distinct strategies for symbiosis with their hosts. However, the underlying species-specific mechanisms remain unclear due to the lack of efficient gene knockout systems applicable across different species. Here, we developed improved temperature-sensitive shuttle vectors by introducing Ser139Trp into the replication protein RepB. We then used temperature-sensitive plasmids to construct a double-crossover-mediated scarless gene deletion system. The system was employed for targeted gene deletion in Bifidobacterium longum subsp. longum, B. longum subsp. infantis, Bifidobacterium breve, Bifidobacterium adolescentis, Bifidobacterium kashiwanohense, and Bifidobacterium pseudocatenulatum. Deletion of genes involved in capsular polysaccharide biosynthesis, aromatic lactic acid production, and sugar utilization resulted in the expected phenotypic changes in the respective (sub)species. The temperature-sensitive plasmids developed in this study will aid in deciphering the evolutionary traits of the human-gut-associated Bifidobacterium species.

Taxonomic and phenotypic analysis of bifidobacteria isolated from IBD patients as potential probiotic strains

BACKGROUND

Inflammatory Bowel Diseases (IBD) are a major public health issue with unclear aetiology. Changes in the composition and functionality of the intestinal microbiota are associated with these pathologies, including the depletion of strict anaerobes such as Feacalibacterium prausnitzii. Less evidence is observed for depletion in other anaerobes, among which bifidobacteria. This study characterized the taxonomic and functional diversity of bifidobacteria isolated from the human intestinal microbiota in active and non-active IBD patients by a culturomics approach and evaluated if these bifidobacteria might be used as probiotics for gut health.

RESULTS

A total of 341 bifidobacteria were isolated from the intestinal microbiota of IBD patients (52 Crohn's disease and 26 ulcerative colitis patients), with a high proportion of Bifidobacterium dentium strains (28% of isolated bifidobacteria). In ulcerative colitis, the major species identified was B. dentium (39% of isolated bifidobacteria), in active and non-active ulcerative colitis. In Crohn's disease, B. adolescentis was the major species isolated from non-active patients (40%), while similar amounts of B. dentium and B. adolescentis were found in active Crohn's disease patients. The relative abundance of B. dentium was increased with age, both in Crohn's disease and ulcerative colitis and active and non-active IBD patients. Antibacterial capacities of bifidobacteria isolated from non-active ulcerative colitis against Escherichia coli LF82 and Salmonella enterica ATCC 14028 were observed more often compared to strains isolated from active ulcerative colitis. Finally, B. longum were retained as strains with the highest probiotic potential as they were the major strains presenting exopolysaccharide synthesis, antibacterial activity, and anti-inflammatory capacities. Antimicrobial activity and EPS synthesis were further correlated to the presence of antimicrobial and EPS gene clusters by in silico analysis.

CONCLUSIONS

Different bifidobacterial taxonomic profiles were identified in the microbiota of IBD patients. The most abundant species were B. dentium, mainly associated to the microbiota of ulcerative colitis patients and B. adolescentis, in the intestinal microbiota of Crohn's disease patients. Additionally, the relative abundance of B. dentium significantly increased with age. Furthermore, this study evidenced that bifidobacteria with probiotic potential (antipathogenic activity, exopolysaccharide production and anti-inflammatory activity), especially B. longum strains, can be isolated from the intestinal microbiota of both active and non-active Crohn's disease and ulcerative colitis patients.

Bacterial capsules: Occurrence, mechanism, and function

In environments characterized by extended multi-stress conditions, pathogens develop a variety of immune escape mechanisms to enhance their ability to infect the host. The capsules, polymers that bacteria secrete near their cell wall, participates in numerous bacterial life processes and plays a crucial role in resisting host immune attacks and adapting to their niche. Here, we discuss the relationship between capsules and bacterial virulence, summarizing the molecular mechanisms of capsular regulation and pathogenesis to provide new insights into the research on the pathogenesis of pathogenic bacteria.

Human milk oligosaccharides combine with Bifidobacterium longum to form the "golden shield" of the infant intestine: metabolic strategies, health effects, and mechanisms of action

Human milk oligosaccharides (HMOs) are the third most important nutrient in human milk and are the gold standard for infant nutrition. Due to the lack of an enzyme system capable of utilizing HMOs in the infant intestine, HMOs cannot be directly utilized. Instead, they function as natural prebiotics, participating in the establishment of the intestinal microbiota as a "bifidus factor." A crucial colonizer of the early intestine is Bifidobacterium longum (B. longum), particularly its subspecies B. longum subsp. infantis, which is the most active consumer of HMOs. However, due to the structural diversity of HMOs and the specificity of B. longum strains, studies on their synergy are limited. An in-depth investigation into the mechanisms of HMO utilization by B. longum is essential for applying both as synbiotics to promote early intestinal development in infants. This review describes the colonization advantages of B. longum in the infant intestinal tract and its metabolic strategies for HMOs. It also summarizes recent studies on the effect and mechanism of B. longum and HMOs in infant intestinal development directly or indirectly through the action of metabolites. In conclusion, further structural analysis of HMOs and a deeper understanding of the interactions between B. longum and HMOs, as well as clinical trials, are necessary to lay the foundation for future practical applications as synbiotics.

Milk phospholipids protect Bifidobacterium longum subsp. infantis during in vitro digestion and enhance polysaccharide production

Bifidobacterium longum subsp. infantis is associated with the gut microbiota of breast-fed infants. Bifidobacterium infantis promotes intestinal barrier and immune function through several proposed mechanisms, including interactions between their surface polysaccharides, the host, and other gut microorganisms. Dairy foods and ingredients are some of the most conspicuous food-based niches for this species and may provide benefits for their delivery and efficacy in the gut. Milk phospholipid (MPL)-rich ingredients have been increasingly recognized for their versatile benefits to health, including interactions with the gut microbiota and intestinal cells. Therefore, our objective was to investigate the capacity for MPL to promote survival of B. infantis during simulated digestion and to modulate bacterial polysaccharide production. To achieve these aims, B. infantis was incubated with or without 0.5% MPL in de Man, Rogosa, and Sharpe (MRS) media at 37°C under anaerobiosis. Survival across the oral, gastric, and intestinal phases using in vitro digestion was measured using plate count, along with adhesion to goblet-like intestinal cells. MPL increased B. infantis survival at the end of the intestinal phase by at least 7% and decreased adhesion to intestinal cells. The bacterial surface characteristics, which may contribute to these effects, were assessed by ζ-potential, changes in surface proteins using comparative proteomics, and production of bound polysaccharides. MPL decreased the surface charge of the bifidobacteria from -17 to -24 mV and increased a 50 kDa protein (3-fold) that appears to be involved in protection from stress. The production of bound polysaccharides was measured using FTIR, HPLC, and TEM imaging. These techniques all suggest an increase in bound polysaccharide production at least 1.7-fold in the presence of MPL. Our results show that MPL treatment increases B. infantis survival during simulated digestion, induces a stress resistance surface protein, and yields greater bound polysaccharide production, suggesting its use as a functional ingredient to enhance probiotic and postbiotic effects.

Effects of N-succinyl-chitosan coating on properties of astaxanthin-loaded PEG-liposomes: Environmental stability, antioxidant/antibacterial activities, and in vitro release

Astaxanthin (AST) has outstanding antioxidant and anti-inflammation bioactivities, but the low biocompatibility and stability limit its application in foods. In this study, N-succinyl-chitosan (NSC)-coated AST polyethylene glycol (PEG)-liposomes were constructed to enhance the biocompatibility, stability, and intestinal-targeted migration of AST. The AST NSC/PEG-liposomes were uniform in size, had larger particles, greater encapsulation efficiency, and better storage, pH, and temperature stability than the AST PEG-liposomes. AST NSC/PEG-liposomes exerted stronger antibacterial and antioxidant activities against Escherichia coli and Staphylococcus aureus than AST PEG-liposomes. The NSC coating not only protects AST PEG-liposomes from gastric acid but also prolongs the retention and sustained release of AST NSC/PEG-liposomes depending on the intestinal pH. Moreover, caco-2 cellular uptake studies showed that AST NSC/PEG-liposomes had higher cellular uptake efficiency than AST PEG-liposomes. And AST NSC/PEG-liposomes were taken up by caco-2 cells through clathrin mediated endocytic, macrophage pathways and paracellular transport pathway. These results further proved that AST NSC/PEG-liposomes delayed the release and promoted the intestinal absorption of AST. Hence, AST PEG-liposomes coated with NSC could potentially be used as an efficient delivery system for therapeutic AST.

Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait

The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.

Probiotic Yoghurt Made from Milk of Ewes Fed a Diet Supplemented with Spirulina platensis or Fish Oil

Purpose

Yoghurt is a widely consumed dairy product around the world. It has healing properties and characteristics that are important for human health. Our goal was to see how using ewes' milk fed Spirulina platensis (SP) or fish oil (FO)-supplemented diets affected the chemical, physical, and nutritional properties of yoghurt, as well as the activity and survival of starter and probiotic bacteria during storage.

Methods

The collected milk from each ewe group was preheated to 65 °C and homogenized in a laboratory homogenizer, then heated to 90 °C for 5 min, cooled to 42 °C, and divided into two equal portions. The first portion was inoculated with 2.0% mixed starter culture (Lactobacillus bulgaricus and Streptococcus thermophilus, 1:1), whereas the second was inoculated with 2% mixed starter culture and 1% Bifidobacterium longum as a probiotic bacteria.

Results

SP yoghurt had the highest levels of short chain-FA, medium chain-FA, mostly C10:0, and long chain-FA, namely C16:0, C18:2 and the lowest levels of C18:0 and C18:1, followed by FO yoghurt. The addition of SP or FO to ewes' diets resulted in yoghurt with higher viable counts of L. bulgaricus and S. thermophilus, which were still >107 cfu/g at the end of storage, as well as a higher level of acetaldehyde content (P<0.05) as a flavor compound, than the control (C) yoghurt. The viscosity of SP yoghurt was higher than that of FO and C yoghurt; the difference was not significant. The addition of B. longum, a probiotic bacteria, to all yoghurt samples, improved antioxidant activities, particularly against ABTS• radicals, but reduced SP yoghurt viscosity. When B. longum was added, acetaldehyde content increased from 39.91, 90.47, and 129.31 μmol/100g in C, FA, and SP yoghurts to 46.67, 135.55, and 144.1 μmol/100g in probiotic C, FA, and SP yoghurts, respectively. There was no significant difference in sensory qualities among all the yoghurt samples during all storage periods.

Conclusions

Supplementing the ewes' diets with Spirulina platensis or fish oil can change the fatty acid composition of the resulting yoghurt. The starter culture's activity, flavor compounds, and some chemical, physical, and antioxidant properties of milk produced from these diets can all be improved, particularly in yoghurt treated with probiotic bacteria (B. longum).

A programmable encapsulation system improves delivery of therapeutic bacteria in mice

Living bacteria therapies have been proposed as an alternative approach to treating a broad array of cancers. In this study, we developed a genetically encoded microbial encapsulation system with tunable and dynamic expression of surface capsular polysaccharides that enhances systemic delivery. Based on a small RNA screen of capsular biosynthesis pathways, we constructed inducible synthetic gene circuits that regulate bacterial encapsulation in Escherichia coli Nissle 1917. These bacteria are capable of temporarily evading immune attack, whereas subsequent loss of encapsulation results in effective clearance in vivo. This dynamic delivery strategy enabled a ten-fold increase in maximum tolerated dose of bacteria and improved anti-tumor efficacy in murine models of cancer. Furthermore, in situ encapsulation increased the fraction of microbial translocation among mouse tumors, leading to efficacy in distal tumors. The programmable encapsulation system promises to enhance the therapeutic utility of living engineered bacteria for cancer.

Transient capsule induction allows engineered bacteria to evade initial immune surveillance in a colorectal cancer model.

Roles of the Cell Surface Architecture of Bacteroides and Bifidobacterium in the Gut Colonization

There are numerous bacteria reside within the mammalian gastrointestinal tract. Among the intestinal bacteria, Akkermansia, Bacteroides, Bifidobacterium, and Ruminococcus closely interact with the intestinal mucus layer and are, therefore, known as mucosal bacteria. Mucosal bacteria use host or dietary glycans for colonization via adhesion, allowing access to the carbon source that the host’s nutrients provide. Cell wall or membrane proteins, polysaccharides, and extracellular vesicles facilitate these mucosal bacteria-host interactions. Recent studies revealed that the physiological properties of Bacteroides and Bifidobacterium significantly change in the presence of co-existing symbiotic bacteria or markedly differ with the spatial distribution in the mucosal niche. These recently discovered strategic colonization processes are important for understanding the survival of bacteria in the gut. In this review, first, we introduce the experimental models used to study host-bacteria interactions, and then, we highlight the latest discoveries on the colonization properties of mucosal bacteria, focusing on the roles of the cell surface architecture regarding Bacteroides and Bifidobacterium.

Exploring the Genomic Diversity and Antimicrobial Susceptibility of Bifidobacterium pseudocatenulatum in a Vietnamese Population

Bifidobacterium pseudocatenulatum is a member of the human gut microbiota, and specific variants of B. pseudocatenulatum have been associated with health benefits such as improving gut integrity and reducing inflammatory responses. Here, we aimed to assess the genomic diversity and predicted metabolic profiles of B. pseudocatenulatum cells found colonizing the gut of healthy Vietnamese adults and children. We found that the population of B. pseudocatenulatum from each individual was distinct and highly diverse, with intraclonal variation attributed largely to a gain or loss of carbohydrate-utilizing enzymes. The B. pseudocatenulatum genomes were enriched with glycosyl hydrolases predicted to target plant-based nondigestible carbohydrates (GH13, GH43) but not host-derived glycans. Notably, the exopolysaccharide biosynthesis region from organisms isolated from healthy children showed extensive genetic diversity and was subject to a high degree of genetic modification. Antimicrobial susceptibility profiling revealed that the Vietnamese B. pseudocatenulatum cells were uniformly susceptible to beta-lactams but exhibited variable resistance to azithromycin, tetracycline, ciprofloxacin, and metronidazole. The genomic presence of ermX and tet variants conferred resistance against azithromycin and tetracycline, respectively; ciprofloxacin resistance was associated with a mutation(s) in the quinolone resistance-determining region (GyrA, S115, and/or D119). Our work provides the first detailed genomic and antimicrobial resistance characterization of B. pseudocatenulatum found in the Vietnamese population, which can be exploited for the rational design of probiotics. IMPORTANCE Bifidobacterium pseudocatenulatum is a beneficial member of the human gut microbiota. The organism can modulate inflammation and has probiotic potential, but its characteristics are largely strain dependent and associated with distinct genomic and biochemical features. Population-specific beneficial microbes represent a promising avenue for the development of potential probiotics, as they may exhibit a more suitable profile in the target population. This study investigates the underexplored diversity of B. pseudocatenulatum in Vietnam and provides more understanding of its genomic diversity, metabolic potential, and antimicrobial susceptibility. Such data from indigenous populations are essential for selecting probiotic candidates that can be accelerated into further preclinical and clinical investigations.

Bifidobacterium breve Exopolysaccharide Blocks Dendritic Cell Maturation and Activation of CD4+ T Cells

Exopolysaccharide (EPS) is a bacterial extracellular carbohydrate moiety which has been associated with immunomodulatory activity and host protective effects of several gut commensal bacteria. Bifidobacterium breve are early colonizers of the human gastrointestinal tract (GIT) but the role of EPS in mediating their effects on the host has not been investigated for many strains. Here, we characterized EPS production by a panel of human B. breve isolates and investigated the effect of EPS status on host immune responses using human and murine cell culture-based assay systems. We report that B. breve EPS production is heterogenous across strains and that immune responses in human THP-1 monocytes are strain-specific, but not EPS status-specific. Using wild type and isogenic EPS deficient mutants of B. breve strains UCC2003 and JCM7017 we show that EPS had strain-specific divergent effects on cytokine responses from murine bone marrow derived macrophages (BMDMs) and dendritic cells (BMDCs). The B. breve UCC2003 EPS negative (EPS^–) strain increased expression of cytokine genes (Tnfa, Il6, Il12a, and Il23a) relative to untreated BMDCs and BMDCs treated with wild type strain. B. breve UCC2003 and JCM7017 EPS^– strains increased expression of dendritic cell (DC) activation and maturation marker genes (Cd80, Cd83, and Cd86) relative to untreated BMDCs. Consistent with this, BMDCs co-cultured with B. breve UCC2003 and JCM7017 EPS^– strains engineered to express OVA antigen activated OVA-specific OT-II CD4⁺ T-cells in a co-culture antigen-presentation assay while EPS proficient strains did not. Collectively, these data indicate that B. breve EPS proficient strains use EPS to prevent maturation of DCs and activation of antigen specific CD4⁺ T cells responses to B. breve. This study identifies a new immunomodulatory role for B. breve EPS and suggests it may be important for immune evasion of adaptive immunity by B. breve and contribute to host-microbe mutualism.

Probiotic Gastrointestinal Transit and Colonization After Oral Administration: A Long Journey

Orally administered probiotics encounter various challenges on their journey through the mouth, stomach, intestine and colon. The health benefits of probiotics are diminished mainly due to the substantial reduction of viable probiotic bacteria under the harsh conditions in the gastrointestinal tract and the colonization resistance caused by commensal bacteria. In this review, we illustrate the factors affecting probiotic viability and their mucoadhesive properties through their journey in the gastrointestinal tract, including a discussion on various mucosadhesion-related proteins on the probiotic cell surface which facilitate colonization.

Immune Suppression Induced by Gallibacterium anatis GtxA During Interaction with Chicken Macrophage-Like HD11 Cells

The RTX toxin GtxA expressed by Gallibacterium anatis biovar haemolytica has been proposed a major virulence factor during disease manifestations in the natural host, the chicken. To better understand the role of GtxA in the pathogenesis of G. anatis, we compared the GtxA expressing wildtype strain with its isogenic ∆gtxA mutant that was unable to express GtxA during exposure to chicken macrophage-like HD11 cells. From adhesion and invasion assays, we showed that GtxA appears to promote adhesion and invasion of HD11 cells. By using quantitative RT-PCR, we also demonstrated that the G. anatis expressing GtxA induced a mainly anti-inflammatory (IL-10) host cell response as opposed to the pro-inflammatory (IL-1β, IL-6 and TNF-α) response induced by the GtxA deletion mutant. Interestingly, these results, at least partly, resemble recent responses observed from spleen tissue of chickens infected with the same two bacterial strains. The effect of the GtxA toxin on the type of cell death was less clear. While GtxA clearly induced cell death, our efforts to characterize whether this was due to primarily necrosis or apoptosis through expression analysis of a broad range of apoptosis genes did not reveal clear answers.

Evaluation of Bifidobacteria and Lactobacillus Probiotics as Alternative Therapy for Salmonella typhimurium Infection in Broiler Chickens

Simple Summary

Salmonella is an important foodborne pathogen that represents a very critical threat to poultry industry worldwide. This study concerns an important aspect of human food and health problem by treating a common zoonotic bacterial disease in poultry industry. Owing to the increased resistance to antibiotics among Salmonellaenterica serotypes, we aimed to explore the beneficial effects of different probiotics strains as alternative sources of protection against infection in broiler chickens. Three probiotic strains Lactobacillus (Lacticaseibacillus) casei ATTC334, Bifidobacterium breve JCM1192 and Bifidobacterium infantis BL2416) improved body weight gain and prevented the deleterious effects and mortality induced by Salmonella infection in chicks through different mechanisms, including competitive exclusion and the promotion of cytokines’ release.

Abstract

Chicken Salmonella enterica serovars are enteric bacteria associated with massive public health risks and economic losses. There is a widespread antimicrobial resistance among S.enterica serotypes, and innovative solutions to antibiotic resistance are needed. We aimed to use probiotics to reduce antibiotic resistance and identify the major probiotic players that modify the early interactions between S.enterica and host cells. One-day-old cobb broiler chicks were challenged with S. typhimurium after oral inoculation with different probiotic strains for 3 days. The adherence of different probiotic strains to Caco-2 intestinal epithelial cells was studied in vitro. Lactobacillus (Lacticaseibacillus) casei ATTC334 and Bifidobacterium breve JCM1192 strains attached to Caco-2 cells stronger than B. infantis BL2416. L. casei ATTC334 and B. breve JCM1192 reduced S. typhimurium recovery from the cecal tonsils by competitive exclusion mechanism. Although B. infantis BL2416 bound poorly to Caco-2 epithelial cells, it reduced S. typhimurium recovery and increased IFN-γ and TNF-α production. L. casei ATTC334, B. breve JCM1192 and B. infantis BL2416 improved body weight gain and the food conversion rate in S. typhimurium-infected broilers. B. longum Ncc2785 neither attached to epithelial cells nor induced IFN-γ and TNF-α release and consequently did not prevent S. typhimurium colonization in broiler chickens. In conclusion, probiotics prevented the intestinal colonization of S. typhimurium in infected chickens by competitive exclusion or cytokine production mechanisms.

Immunomodulatory Roles of Polysaccharide Capsules in the Intestine

The interplay between the immune system and the microbiota in the human intestine dictates states of health vs. disease. Polysaccharide capsules are critical elements of bacteria that protect bacteria against environmental and host factors, including the host immune system. This review summarizes the mechanisms by which polysaccharide capsules from commensal and pathogenic bacteria in the gut microbiota modulate the innate and adaptive immune systems in the intestine. A deeper understanding of the roles of polysaccharide capsules in microbiota-immune interactions will provide a basis to harness their therapeutic potential to advance human health.

The distinction of CPR bacteria from other bacteria based on protein family content

Candidate phyla radiation (CPR) bacteria separate phylogenetically from other bacteria, but the organismal distribution of their protein families remains unclear. Here, we leveraged sequences from thousands of uncultivated organisms and identified protein families that co-occur in genomes, thus are likely foundational for lineage capacities. Protein family presence/absence patterns cluster CPR bacteria together, and away from all other bacteria and archaea, partly due to proteins without recognizable homology to proteins in other bacteria. Some are likely involved in cell-cell interactions and potentially important for episymbiotic lifestyles. The diversity of protein family combinations in CPR may exceed that of all other bacteria. Over the bacterial tree, protein family presence/absence patterns broadly recapitulate phylogenetic structure, suggesting persistence of core sets of proteins since lineage divergence. The CPR could have arisen in an episode of dramatic but heterogeneous genome reduction or from a protogenote community and co-evolved with other bacteria.

Recent studies have identified a large, phylogenetically distinct clade of bacteria, the candidate phyla radiation (CPR). Here, Méheust and colleagues analyze almost 3600 genomes to characterize the protein family content of CPR versus other bacteria and archaea.

Interactions of Surface Exopolysaccharides From Bifidobacterium and Lactobacillus Within the Intestinal Environment

Exopolysaccharides (EPS) are surface carbohydrate polymers present in most bacteria acting as a protective surface layer but also interacting with the surrounding environment. This review discusses the roles of EPS synthesized by strains of Lactobacillus and Bifidobacterium, many of them with probiotic characteristics, in the intestinal environment. Current knowledge on genetics and biosynthesis pathways of EPS in lactic acid bacteria and bifidobacteria, as well as the development of genetic tools, has created possibilities to elucidate the interplay between EPS and host intestinal mucosa. These include the microbiota that inhabits this ecological niche and the host cells. Several carbohydrate recognition receptors located in the intestinal epithelium could be involved in the interaction with bacterial EPS and modulation of immune response; however, little is known about the receptors recognizing EPS from lactobacilli or bifidobacteria and the triggered response. On the contrary, it has been clearly demonstrated that EPS play a relevant role in the persistence of the producing bacteria in the intestinal tract. Indeed, some authors postulate that some of the beneficial actions of EPS-producing probiotics could be related to the formation of a biofilm layer protecting the host against injury, for example by pathogens or their toxins. Nevertheless, the in vivo formation of biofilms by probiotics has not been proved to date. Finally, EPS produced by probiotic strains are also able to interact with the intestinal microbiota that populates the gut. In fact, some of these polymers can be used as carbohydrate fermentable source by some gut commensals thus being putatively involved in the release of bacterial metabolites that exert positive benefits for the host. In spite of the increasing knowledge about the role that these surface molecules play in the interaction of probiotic bacteria with the gut mucosal actors, both intestinal receptors and microbiota, the challenging issue is to demonstrate the functionality of EPS in vivo, which will open an avenue of opportunities for the application of EPS-producing probiotics to improve health.

Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.

Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens

Extracellular capsules constitute the outermost layer of many bacteria, are major virulence factors, and affect antimicrobial therapies. They have been used as epidemiological markers and recently became vaccination targets. Despite the efforts to biochemically serotype capsules in a few model pathogens, little is known of their taxonomic and environmental distribution. We developed, validated, and made available a computational tool, CapsuleFinder, to identify capsules in genomes. The analysis of over 2500 prokaryotic genomes, accessible in a database, revealed that ca. 50% of them—including Archaea—encode a capsule. The Wzx/Wzy-dependent capsular group was by far the most abundant. Surprisingly, a fifth of the genomes encode more than one capsule system—often from different groups—and their non-random co-occurrence suggests the existence of negative and positive epistatic interactions. To understand the role of multiple capsules, we queried more than 6700 metagenomes for the presence of species encoding capsules and showed that their distribution varied between environmental categories and, within the human microbiome, between body locations. Species encoding capsules, and especially those encoding multiple capsules, had larger environmental breadths than the other species. Accordingly, capsules were more frequent in environmental bacteria than in pathogens and, within the latter, they were more frequent among facultative pathogens. Nevertheless, capsules were frequent in clinical samples, and were usually associated with fast-growing bacteria with high infectious doses. Our results suggest that capsules increase the environmental range of bacteria and make them more resilient to environmental perturbations. Capsules might allow opportunistic pathogens to profit from empty ecological niches or environmental perturbations, such as those resulting from antibiotic therapy, to colonize the host. Capsule-associated virulence might thus be a by-product of environmental adaptation. Understanding the role of capsules in natural environments might enlighten their function in pathogenesis.

Extracellular capsules protect bacterial cells from external aggressions such as antibiotics or desiccation, but can also be targeted by vaccines. Since little was known about their frequency across Prokaryotes, we created and made freely available a computational tool, CapsuleFinder, to identify them from genomic data. Surprisingly, its use showed that many bacterial strains, especially those with the largest genomes, encode several capsules. The frequencies of the different combinations of capsule groups depended strongly on the phyla and the groups themselves, suggesting the existence of epistatic interactions between capsules. Bacteria encoding capsule systems were found in many natural environments, and were frequent in the human microbiome. In contrast to their frequent association with virulence, we found many more capsules in non-pathogens or facultative pathogens than among obligatory pathogens. We suggest that capsules increase the environmental breadth of bacteria thereby facilitating host colonization by opportunistic pathogens.