Role of extracellular transaldolase from Bifidobacterium bifidum in mucin adhesion and aggregation

Proteomic Analysis of Caco-2 Cells Disrupted by EcN 1917-Derived OMVs Reveals Molecular Information on Bacteria-Mediated Cancer Cell Migration

Escherichia coli Nissle 1917 (EcN 1917) exhibits distinct tumor-targeting activity, and early studies demonstrated that outer membrane vesicles (OMVs) mediate bacteria-host interactions. To decipher the molecular mechanism underlying the interaction between EcN 1917 and host cells via OMV-mediated communication, we investigated the phenotypic changes in Caco-2 cells perturbed by EcN 1917-derived OMVs and constructed proteomic maps of the EcN 1917-derived OMV components and OMV-perturbed host cells. Our findings revealed that the size of the EcN 1917-derived OMV proteome increased 4-fold. Treatment with EcN 1917-derived OMVs altered the proteomic and phosphoproteomic profiles of host cells. Importantly, for the first time, we found that treatment with EcN 1917-derived OMVs inhibited cancer cell migration by suppressing the expression of ANXA9. In addition, phosphoproteomic data suggested that the ErbB pathway may be involved in OMV-mediated cell migration. Taken together, our study provides valuable data for further investigations of OMV-mediated bacteria-host interactions and offers great insights into the underlying mechanism of probiotic-assisted colorectal cancer therapy.

Mucus production, host-microbiome interactions, hormone sensitivity, and innate immune responses modeled in human cervix chips

Modulation of the cervix by steroid hormones and commensal microbiome play a central role in the health of the female reproductive tract. Here we describe organ-on-a-chip (Organ Chip) models that recreate the human cervical epithelial-stromal interface with a functional epithelial barrier and production of mucus with biochemical and hormone-responsive properties similar to living cervix. When Cervix Chips are populated with optimal healthy versus dysbiotic microbial communities (dominated by Lactobacillus crispatus and Gardnerella vaginalis, respectively), significant differences in tissue innate immune responses, barrier function, cell viability, proteome, and mucus composition are observed that are similar to those seen in vivo. Thus, human Cervix Organ Chips represent physiologically relevant in vitro models to study cervix physiology and host-microbiome interactions, and hence may be used as a preclinical testbed for development of therapeutic interventions to enhance women's health.

A Review of the Mechanisms of Bacterial Colonization of the Mammal Gut

A healthy animal intestine hosts a diverse population of bacteria in a symbiotic relationship. These bacteria utilize nutrients in the host's intestinal environment for growth and reproduction. In return, they assist the host in digesting and metabolizing nutrients, fortifying the intestinal barrier, defending against potential pathogens, and maintaining gut health. Bacterial colonization is a crucial aspect of this interaction between bacteria and the intestine and involves the attachment of bacteria to intestinal mucus or epithelial cells through nonspecific or specific interactions. This process primarily relies on adhesins. The binding of bacterial adhesins to host receptors is a prerequisite for the long-term colonization of bacteria and serves as the foundation for the pathogenicity of pathogenic bacteria. Intervening in the adhesion and colonization of bacteria in animal intestines may offer an effective approach to treating gastrointestinal diseases and preventing pathogenic infections. Therefore, this paper reviews the situation and mechanisms of bacterial colonization, the colonization characteristics of various bacteria, and the factors influencing bacterial colonization. The aim of this study was to serve as a reference for further research on bacteria-gut interactions and improving animal gut health.

Comparative proteomics reveals the antibiotic resistance and virulence of Cronobacter isolated from powdered infant formula and its processing environment

Cronobacter species are opportunistic foodborne pathogens that can cause neonatal meningitis, sepsis, and necrotizing enterocolitis. In this genus, certain level strains have high mortality to infant (Cronobacter sakazakii and Cronobacter malonaticus) and antibiotic tolerance. Cronobacter has strong environmental tolerance (acid resistance, high temperature resistance, UV resistance, antibiotic resistance, etc.) and can survive in a variety of environments. It has been isolated in various production environments and products in several countries. However, the relationships between Cronobacter antibiotic tolerance and virulence remain unclear, especially at the molecular level. In this study, 96 strains of Cronobacter were isolated from powdered infant formula and its processing environment and screened for antibiotic tolerance, and proteomic maps of the representative strains of Cronobacter with antibiotic tolerance were generated by analyzing proteomics data using multiple techniques to identify protein that are implicated in Cronobacter virulence and antibiotic resistance. The increase in antibiotic tolerance of Cronobacter had a certain increase in the production of enterotoxin and hemolysin. Only triple tolerated Cronobacter sakazakii decreased the utilization of sialic acid. A total of 16,131 intracellular proteins were detected in eight representative strains, and different proteomes were present in strains with different antibiotic tolerance, including 56 virulence-related proteins. Multiple virulence proteins regulated by unknown genes were also found in the eight isolated representative strains.

HMO-primed bifidobacteria exhibit enhanced ability to adhere to intestinal epithelial cells

The ability of gut commensals to adhere to the intestinal epithelium can play a key role in influencing the composition of the gut microbiota. Bifidobacteria are associated with a multitude of health benefits and are one of the most widely used probiotics for humans. Enhanced bifidobacterial adhesion may increase host-microbe, microbe-nutrient, and/or microbe-microbe interactions, thereby enabling consolidated health benefits to the host. The objective of this study was to determine the ability of human milk oligosaccharides (HMOs) to enhance bifidobacterial intestinal adhesion in vitro. This study assessed the colonisation-promoting effects of HMOs on four commercial infant-associated Bifidobacterium strains (two B. longum subsp. infantis strains, B. breve and B. bifidum). HT29-MTX cells were used as an in vitro intestinal model for bacterial adhesion. Short-term exposure of four commercial infant-associated Bifidobacterium strains to HMOs derived from breastmilk substantially increased the adherence (up to 47%) of these probiotic strains. Interestingly, when strains were incubated with HMOs as a four-strain combination, the number of viable bacteria adhering to intestinal cells increased by >90%. Proteomic analysis of this multi-strain bifidobacterial mixture revealed that the increased adherence resulting from exposure to HMOs was associated with notable increases in the abundance of sortase-dependent pili and glycosyl hydrolases matched to Bifidobacterium bifidum. This study suggests that HMOs may prime infant gut-associated Bifidobacterium for colonisation to intestinal epithelial cells by influencing the expression of various colonization factors.

Identification and evaluation of probiotic potential of Bifidobacterium breve AHC3 isolated from chicken intestines and its effect on necrotizing enterocolitis (NEC) in newborn SD rats

Necrotizing enterocolitis (NEC) is a severe intestinal disease of the newborn infants, associated with high morbidity and mortality. It has been reported that Bifidobacterium could protect the intestinal barrier function and reduce the risk of NEC. This study aimed to evaluate the probiotic potential of Bifidobacterium strains isolated from the chicken intestines and its effect on necrotizing enterocolitis in newborn SD rats. Out of 32 isolates, B. breve AHC3 not only exhibited excellent probiotic potential, including tolerance to artificial simulated gastric conditions, adhesion to HT-29 cells, antioxidant capacity and antibacterial activity, but also possessed reliable safety. Additionally, NEC model was established to further investigate the effect of B. breve AHC3 on necrotizing enterocolitis in newborn SD rats. It was illustrated that administration of B. breve AHC3 significantly not only reduced the incidence of NEC (from 81.25% to 34.38%) (P< 0.05), but also alleviated the severity of ileal injury (P< 0.05). Compared with NEC model, B. breve AHC3 could significantly decrease the level of proinflammatory factor TNF-α (P< 0.05) and increase the level of antiinflammatory factor IL-10 (P< 0.05) in the ileum of NEC rats. Through the intervention of B. breve AHC3, the gray value of inducible nitric oxide synthase (iNOS) in intestinal tissue of NEC rats was significantly reduced (P< 0.05). It was indicated that B. breve AHC3 exhibited prominent probiotic potential and reliable safety. In the neonatal SD rat model of NEC, B. breve AHC3 had an available protective effect on the intestinal injury of NEC, which might be related to reducing the inflammatory reaction in the ileum and inhibiting the expression of iNOS in intestinal tissue cells. B. breve AHC3 could be used as a potential treatment for human NEC.

Bifidobacterium and the intestinal mucus layer

Bifidobacterium species are integral members of the human gut microbiota and these microbes have significant interactions with the intestinal mucus layer. This review delves into Bifidobacterium-mucus dynamics, shedding light on the multifaceted nature of this relationship. We cover conserved features of Bifidobacterium-mucus interactions, such as mucus adhesion and positive regulation of goblet cell and mucus production, as well as species and strain-specific attributes of mucus degradation. For each interface, we explore the molecular mechanisms underlying these interactions and their potential implications for human health. Notably, we emphasize the ability of Bifidobacterium species to positively influence the mucus layer, shedding light on its potential as a mucin-builder and a therapeutic agent for diseases associated with disrupted mucus barriers. By elucidating the complex interplay between Bifidobacterium and intestinal mucus, we aim to contribute to a deeper understanding of the gut microbiota-host interface and pave the way for novel therapeutic strategies.

Intestinal mucus and their glycans: A habitat for thriving microbiota

The colon mucus layer is organized with an inner colon mucus layer that is impenetrable to bacteria and an outer mucus layer that is expanded to allow microbiota colonization. A major component of mucus is MUC2, a glycoprotein that is extensively decorated, especially with O-glycans. In the intestine, goblet cells are specialized in controlling glycosylation and making mucus. Some microbiota members are known to encode multiple proteins that are predicted to bind and/or cleave mucin glycans. The interactions between commensal microbiota and host mucins drive intestinal colonization, while at the same time, the microbiota can utilize the glycans on mucins and affect the colonic mucus properties. This review will examine this interaction between commensal microbes and intestinal mucins and discuss how this interplay affects health and disease.

Screening for potential novel probiotic Levilactobacillus brevis RAMULAB52 with antihyperglycemic property from fermented Carica papaya L

Probiotics are live microorganisms with various health benefits when consumed in appropriate amounts. Fermented foods are a rich source of these beneficial organisms. This study aimed to investigate the probiotic potential of lactic acid bacteria (LAB) isolated from fermented papaya (Carica papaya L.) through in vitro methods. The LAB strains were thoroughly characterized, considering their morphological, physiological, fermentative, biochemical, and molecular properties. The LAB strain's adherence and resistance to gastrointestinal conditions, as well as its antibacterial and antioxidant capabilities, were examined. Moreover, the strains were tested for susceptibility against specific antibiotics, and safety evaluations encompassed the hemolytic assay and DNase activity. The supernatant of the LAB isolate underwent organic acid profiling (LCMS). The primary objective of this study was to assess the inhibitory activity of α-amylase and α-glucosidase enzymes, both in vitro and in silico. Gram-positive strains that were catalase-negative and carbohydrate fermenting were selected for further analysis. The LAB isolate exhibited resistance to acid bile (0.3% and 1%), phenol (0.1% and 0.4%), and simulated gastrointestinal juice (pH 3-8). It demonstrated potent antibacterial and antioxidant abilities and resistance to kanamycin, vancomycin, and methicillin. The LAB strain showed autoaggregation (83%) and adhesion to chicken crop epithelial cells, buccal epithelial cells, and HT-29 cells. Safety assessments indicated no evidence of hemolysis or DNA degradation, confirming the safety of the LAB isolates. The isolate's identity was confirmed using the 16S rRNA sequence. The LAB strain Levilactobacillus brevis RAMULAB52, derived from fermented papaya, exhibited promising probiotic properties. Moreover, the isolate demonstrated significant inhibition of α-amylase (86.97%) and α-glucosidase (75.87%) enzymes. In silico studies uncovered that hydroxycitric acid, one of the organic acids derived from the isolate, interacted with crucial amino acid residues of the target enzymes. Specifically, hydroxycitric acid formed hydrogen bonds with key amino acid residues, such as GLU233 and ASP197 in α-amylase, and ASN241, ARG312, GLU304, SER308, HIS279, PRO309, and PHE311 in α-glucosidase. In conclusion, Levilactobacillus brevis RAMULAB52, isolated from fermented papaya, possesses promising probiotic properties and exhibits potential as an effective remedy for diabetes. Its resistance to gastrointestinal conditions, antibacterial and antioxidant abilities, adhesion to different cell types, and significant inhibition of target enzymes make it a valuable candidate for further research and potential application in the field of probiotics and diabetes management.

Sharing of Moonlighting Proteins Mediates the Symbiotic Relationship among Intestinal Commensals

The human gastrointestinal tract is inhabited by trillions of symbiotic bacteria that form a complex ecological community and influence human physiology. Symbiotic nutrient sharing and nutrient competition are the most studied relationships in gut commensals, whereas the interactions underlying homeostasis and community maintenance are not fully understood. Here, we provide insights into a new symbiotic relationship wherein the sharing of secreted cytoplasmic proteins, called "moonlighting proteins," between two heterologous bacterial strains (Bifidobacterium longum and Bacteroides thetaiotaomicron) was observed to affect the adhesion of bacteria to mucins. B. longum and B. thetaiotaomicron were cocultured using a membrane-filter system, and in this system the cocultured B. thetaiotaomicron cells showed greater adhesion to mucins compared to that shown by monoculture cells. Proteomic analysis showed the presence of 13 B. longum-derived cytoplasmic proteins on the surface of B. thetaiotaomicron. Moreover, incubation of B. thetaiotaomicron with the recombinant proteins GroEL and elongation factor Tu (EF-Tu)-two well-known mucin-adhesive moonlighting proteins of B. longum-led to an increase in the adhesion of B. thetaiotaomicron to mucins, a result attributed to the localization of these proteins on the B. thetaiotaomicron cell surface. Furthermore, the recombinant EF-Tu and GroEL proteins were observed to bind to the cell surface of several other bacterial species; however, the binding was species dependent. The present findings indicate a symbiotic relationship mediated by the sharing of moonlighting proteins among specific strains of B. longum and B. thetaiotaomicron. IMPORTANCE The adhesion of intestinal bacteria to the mucus layer is an important colonization strategy in the gut environment. Generally, the bacterial adhesion process is a characteristic feature of the individual cell surface-associated adhesion factors secreted by a particular bacterium. In this study, coculture experiments between Bifidobacterium and Bacteroides show that the secreted moonlighting proteins adhere to the cell surface of coexisting bacteria and alter the adhesiveness of the bacteria to mucins. This finding indicates that the moonlighting proteins act as adhesion factors for not only homologous strains but also for coexisting heterologous strains. The presence of a coexisting bacterium in the environment can significantly alter the mucin-adhesive properties of another bacterium. The findings from this study contribute to a better understanding of the colonization properties of gut bacteria through the discovery of a new symbiotic relationship between them.

Structural analysis and prebiotic activity of exopolysaccharide produced by probiotic strain Bifidobacterium bifidum EPS DA-LAIM

Exopolysaccharide (EPS)-producing Bifidobacterium bifidum EPS DA-LAIM was isolated from healthy human feces, the structure of purified EPS from the strain was analyzed, and its prebiotic activity was evaluated. The EPS from B. bifidum EPS DA-LAIM is a glucomannan-type heteropolysaccharide with a molecular weight of 407-1007 kDa, and its structure comprises 2-mannosyl, 6-mannosyl, and 2,6-mannosyl residues. The purified EPS promoted the growth of representative lactic acid bacteria and bifidobacterial strains. Bifidobacterium bifidum EPS DA-LAIM increased nitric oxide production in RAW 264.7 macrophage cells, indicating its immunostimulatory activity. Bifidobacterium bifidum EPS DA-LAIM also exhibited high gastrointestinal tract tolerance, gut adhesion ability, and antioxidant activity. These results suggest that EPS from B. bifidum EPS DA-LAIM is a potentially useful prebiotic material, and B. bifidum EPS DA-LAIM could be applied as a probiotic candidate.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01213-w.

Gut bacterial extracellular vesicles: important players in regulating intestinal microenvironment

Intestinal microenvironment dysbiosis is one of the major causes of diseases, such as obesity, diabetes, inflammatory bowel disease, and colon cancer. Microbiota-based strategies have excellent clinical potential in the treatment of repetitive and refractory diseases; however, the underlying regulatory mechanisms remain elusive. Identification of the internal regulatory mechanism of the gut microbiome and the interaction mechanisms involving bacteria-host is essential to achieve precise control of the gut microbiome and obtain effective clinical data. Gut bacteria-derived extracellular vesicles (GBEVs) are lipid bilayer nanoparticles secreted by the gut microbiota and are considered key players in bacteria-bacteria and bacteria-host communication. This review focusses on the role of GBEVs in gut microbiota interactions and bacteria-host communication, and the potential clinical applications of GBEVs.

Enteric VIP-producing neurons maintain gut microbiota homeostasis through regulating epithelium fucosylation

Interactions between the enteric nervous system (ENS) and intestinal epithelium are thought to play a vital role in intestinal homeostasis. How the ENS monitors the frontier with commensal and pathogenic microbes while maintaining epithelial function remains unclear. Here, by combining subdiaphragmatic vagotomy with transcriptomics, chemogenetic strategy, and coculture of enteric neuron-intestinal organoid, we show that enteric neurons expressing VIP shape the α1,2-fucosylation of intestinal epithelial cells (IECs). Mechanistically, neuropeptide VIP activates fut2 expression via the Erk1/2-c-Fos pathway through the VIPR1 receptor on IECs. We further demonstrate that perturbation of enteric neurons leads to gut dysbiosis through α1,2-fucosylation in the steady state and results in increased susceptibility to alcohol-associated liver disease (ALD). This was attributed to an imbalance between beneficial Bifidobacterium and opportunistic pathogenic Enterococcus faecalis in ALD. In addition, Bifidobacterium α1,2-fucosidase may promote Bifidobacterium adhesion to the mucosal surface, which restricts Enterococcus faecalis overgrowth and prevents ALD progression.

Gastrointestinal Microbiome and Multiple Health Outcomes: Umbrella Review

In recent years, there has been growing concern about the impact of the gastrointestinal microbiome on human health outcomes. To clarify the evidence for a link between the gastrointestinal microbiome and a variety of health outcomes in humans, we conducted an all-encompassing review of meta-analyses and systematic reviews that included 195 meta-analyses containing 950 unique health outcomes. The gastrointestinal microbiome is related to mortality, gastrointestinal disease, immune and metabolic outcomes, neurological and psychiatric outcomes, maternal and infant outcomes, and other outcomes. Existing interventions for intestinal microbiota (such as probiotics, fecal microbiota transplant, etc.) are generally safe and beneficial to a variety of human health outcomes, but the quality of evidence is not high, and more detailed and well-designed randomized controlled trials are necessary.

Screening of Antibacterial Efficacy of Chitosan Encapsulated Probiotics (Lactococcus lactis and Lactobacillus curvattus) against Clinical Bacterial Pathogens

Probiotics frontier in depressing the clinical bacterial pathogens to avoid multidrug resistance phenomenon. The present study aimed to determine the antibacterial efficiency of chitosan encapsulated probiotics isolated from buffalo milk samples against clinical bacterial pathogens. The Agar well method was used for antibacterial activity. Lactococcus lactis (A) and Lactobacillus curvattus (B) were isolated from fresh buffalo milk samples, identified via culturing media, Gram's staining, biochemical tests, and antibiogram analysis. Encapsulation of probiotics was carried out using chitosan and was characterized via a scanning electron microscope. Antibiogram analysis elicit that L. lactis culture (A1) was highly sensitive to chloramphenicol (17.66±0.47 mm), tobramycin (15.33±0.47 mm), and ciprofloxacin (12.33±0.47 mm) and resistant against tetracycline, Penicillin G, Erythromycin, Amoxycillin, Ceftriaxone, Cephalothin, and Cephradine, while L. curvattus culture (B1) was affected by Ceftriaxone (18.67±0.47 mm), Amoxycillin (14.33±0.94 mm), Cephalothin (13.67±0.47 mm), Erythromycin (13.33±0.47 mm), Penicillin G (12.67±0.47 mm), Cephradine (10.33±0.47 mm), and Chloramphenicol (9.67±0.47 mm) and resistant against tetracycline, Tobramycin, and Ciprofloxacin. Antibacterial efficacy of non-encapsulated probiotic cultures was significant and maximum inhibition of bacterial were recorded compared to their cellular components. SEM of encapsulated probiotics revealed that they were successfully covered with a chitosan protective layer and could be effective as bio-preservatives due to being slowly released at the target site. The current study concluded that L. lactis, L. curvattus, and their cellular components have a significant bactericidal effect against infectious pathogens and could be used as a potential therapeutic drug against infectious diseases.

How Gut Microbiota Are Shaped by Pattern Recognition Receptors in Colitis and Colorectal Cancer

Simple Summary

The pathogenesis of intestinal inflammatory disorders such as colitis and colorectal cancer is complicated and dysregulation of gut microbiota is considered an important contributing factor. Inflammation is often initiated by the activation of pattern recognition receptors. However, the relationship between these innate immune receptors and gut microbiota is not fully understood. Here, we show that pattern recognition receptors not only recognize pathogens and initiate inflammatory signal transduction to induce immune responses, but also influence the composition of intestinal microorganisms, thus affecting the development of intestinal inflammation and cancer through various mechanisms. This suggests that the modification of innate immune receptors and relevant molecules could be therapeutic targets for the treatment of colitis and colorectal cancer by regulating gut microbiota.

Abstract

Disorders of gut microbiota have been closely linked to the occurrence of various intestinal diseases including colitis and colorectal cancer (CRC). Specifically, the production of beneficial bacteria and intestinal metabolites may slow the development of some intestinal diseases. Recently, it has been proposed that pattern recognition receptors (PRRs) not only recognize pathogens and initiate inflammatory signal transduction to induce immune responses but also influence the composition of intestinal microorganisms. However, the mechanisms through which PRRs regulate gut microbiota in the setting of colitis and CRC have rarely been systematically reviewed. Therefore, in this paper, we summarize recent advances in our understanding of how PRRs shape gut microbiota and how this influences the development of colitis and CRC.

Genome-wide siRNA screening reveals several host receptors for the binding of human gut commensal Bifidobacterium bifidum

Bifidobacterium spp. are abundant gut commensals, especially in breast-fed infants. Bifidobacteria are associated with many health-promoting effects including maintenance of epithelial barrier and integrity as well as immunomodulation. However, the protective mechanisms of bifidobacteria on intestinal epithelium at molecular level are poorly understood. In this study, we developed a high-throughput in vitro screening assay to explore binding receptors of intestinal epithelial cells for Bifidobacterium bifidum. Short interfering RNAs (siRNA) were used to silence expression of each gene in the Caco-2 cell line one by one. The screen yielded four cell surface proteins, SERPINB3, LGICZ1, PKD1 and PAQR6, which were identified as potential receptors as the siRNA knock-down of their expression decreased adhesion of B. bifidum to the cell line repeatedly during the three rounds of siRNA screening. Furthermore, blocking of these host cell proteins by specific antibodies decreased the binding of B. bifidum significantly to Caco-2 and HT29 cell lines. All these molecules are located on the surface of epithelial cells and three out of four, SERPINB3, PKD1 and PAQR6, are involved in the regulation of cellular processes related to proliferation, differentiation and apoptosis as well as inflammation and immunity. Our results provide leads to the first steps in the mechanistic cascade of B. bifidum-host interactions leading to regulatory effects in the epithelium and may partly explain how this commensal bacterium is able to promote intestinal homeostasis.

Strain-dependent effectivity, and protective role against enzymes of S-layers in Lactiplantibacillus plantarum strains

The present study investigated whether the surface layer (S-layer), which is known to have a varying effect from strain to strain on aggregation, adhesion ability, also has an effect on the resistance of bacteria to digestive enzymes, phenol, lysozymes. The effect of S-layers on the resistance against various enzymes, aggregation and adhesion abilities, and strain specificity were determined of eight Lactiplantibacillus plantarum strains. Strains were treated with 5 M lithium chloride (LiCl) to extract the S-layers, the presence of this layer in those microorganisms was demonstrated by polyacrylamide gel electrophoresis. Scanning electron microscopy was used to visualize the separation of the S-layer, which surrounds the microorganism, from the microorganism by the LiCl. The images were taken three times, once at the beginning, once 30 min later, and once at the end of this process, which took 2 h in total. The effect against enzymes varied depending on the strain, but it was determined that all the tested strains had a serious loss of viability against phenol in the absence of an S-layer. Lpb. plantarum DA100 showed a maximum decrease against gastrointestinal system enzymes after the LiCl (96.48 ± 0.03% before and 66.46 ± 0.01% after LiCl). Lpb. plantarum DA255 showed a significant decrease against lysozyme (99.11 ± 0.00% before and 62.80 ± 0.0% after LiCl). Removal of the S-layer greatly affected the adhesion ability of some strains, while for others there was hardly any change. The results showed that the role of the S-layer may be strain-specific, the rate of effect can vary. The primary function of S-layer proteins is thought to contribute to the adhesion ability of bacteria. There are limited studies that have reported the protective property of this layer against various enzymes, however, our results showed that S-layer could be one of the resistance strategies developed by bacteria against enzymes.

2'-Fucosyllactose promotes Lactobacillus rhamnosus KLDS 8001 to repair LPS-induced damage in Caco-2 cells

The aim of this study was to investigate the effect of 2'-fucosyllactose (2'-FL) on the repair of monolayer barrier damage in Caco-2 cells by Lactobacillus rhamnosus KLDS 8001 (KLDS 8001). The results showed that the addition of 2'-FL not only promoted the adhesion ability of KLDS 8001 to Caco-2 cells but also improved the anti-adhesive effect of pathogenic bacteria. Compared with 2'-FL or KLDS 8001 alone, 2'-FL+KLDS 8001 significantly reduced lipopolysaccharide (LPS)-induced malondialdehyde (MDA), lactate dehydrogenase (LDH) release, and cytokine (IL-1β, IL-6, and TNF-α) production. In addition, 2'-FL effectively promoted the transmembrane electrical resistance (TEER), cell viability, and cellular permeability of KLDS 8001 repaired damaged cells with dose-dependent properties. The mRNA and protein expression of Zonula Occludens-1 (ZO-1), Occludin, and Claudin-1 were also upregulated in the KLDS 8001 and 2'-FL co-treated treatment group. It was speculated that 2'-FL could effectively regulate the interaction between KLDS 8001 and intestinal epithelial cells to play a role in maintaining intestinal barrier function and avoiding pathogenic bacteria invasion. PRACTICAL APPLICATIONS: As the most widely used human milk oligosaccharides (HMOs), 2'-FL is vital for maintaining infant intestinal health. Our study found that the addition of 2'-FL promoted KLDS 8001 adhesion, anti-adhesion of pathogenic bacteria, anti-inflammatory capacity, repair of barrier damage, and tight junction protein expression, providing a new strategy to protect infant intestinal health and prevent various intestinal diseases.

Comparative proteomics and secretomics revealed virulence, and coresistance-related factors in non O1/O139 Vibrio cholerae recovered from 16 species of consumable aquatic animals

Vibrio cholerae can cause pandemic cholera in humans. The bacterium resides in aquatic environments worldwide. Identification of risk factors of V. cholerae in aquatic products is imperative for assuming food safety. In this study, we determined virulence-associated genes, cross-resistance between antibiotics and heavy metals, and genome fingerprinting profiles of non O1/O139 V. cholerae isolates (n = 20) recovered from 16 species of consumable aquatic animals. Secretomes and proteomes of V. cholerae with distinct genotypes and phenotypes were obtained by using two-dimensional gel electrophoresis (2D-GE) and/or liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques. Comparative secretomic analysis revealed 4 common and 45 differential extracellular proteins among 20 V. cholerae strains, including 13 virulence- and 8 resistance-associated proteins. A total of 21,972 intracellular proteins were identified, and comparative proteomic analysis revealed 215 common and 913 differential intracellular proteins, including 22 virulence- and 8 resistance-associated proteins. Additionally, different secretomes and proteomes were observed between V. cholerae isolates of fish and shellfish origins. A number of novel proteins with unknown function and strain-specific proteins were also discovered in the V. cholerae isolates. SIGNIFICANCE: V. cholerae can cause pandemic cholera in humans. The bacterium is distributed in aquatic environments worldwide. Identification of risk factors of V. cholerae in aquatic products is imperative for assuming food safety. Non-O1/O139 V. cholerae has been reported to cause sporadic cholera-like diarrhea and bacteremia diseases, which indicates virulence factors rather than the major cholera toxin (CT) exist. This study for the first time investigated proteomes and secretomes of non-O1/O139 V. cholerae originating from aquatic animals. This resulted in the identification of a number of virulence and coresistance-related factors, as well as novel proteins and strain-specific proteins in V. cholerae isolates recovered from 16 species of consumable aquatic animals. These results fill gaps for better understanding of pathogenesis and resistance of V. cholerae, and also support the increasing need for novel diagnosis and vaccine targets against the leading waterborne pathogen worldwide.

The Possible Link Between Manufacturing and Probiotic Efficacy; a Molecular Point of View on Bifidobacterium

Probiotics for food or supplement use have been studied in numerous clinical trials, addressing a broad variety of diseases, and conditions. However, discrepancies were observed in the clinical outcomes stemming from the use of lactobacillaceae and bifidobacteria strains. These differences are often attributed to variations in the clinical trial protocol like trial design, included target population, probiotic dosage, or outcome parameters measured. However, a contribution of the methods used to produce the live bioactive ingredients should not be neglected as a possible additional factor in the observed clinical outcome variations. It is well established that manufacturing conditions play a role in determining the survival and viability of probiotics, but much less is known about their influence on the probiotic molecular composition and functionality. In this review, we briefly summarize the evidence obtained for Lacticaseibacillus rhamnosus GG and Lactiplantibacillus plantarum WCFS1, highlighting that expression and presence of probiotic niche factor (NF) and/or effector molecules (EM) may be altered during production of those two well-characterized lactobacillaceae probiotic strains. Subsequently, we summarize in more depth what is the present state of knowledge about bifidobacterial probiotic NF and EM; how their expression may be modified by manufacturing related environmental factors and how that may affect their biological activity in the host. This review highlights the importance of gathering knowledge on probiotic NF and EM, to validate them as surrogate markers of probiotic functionality. We further propose that monitoring of validated NF and/or EM during production and/or in the final preparation could complement viable count assessments that are currently applied in industry. Overall, we suggest that implementation of molecular level quality controls (i.e., based on validated NF and EM), could provide mode of action based in vitro tests contributing to better control the health-promoting reliability of probiotic products.

Functional foods as a formulation ingredients in beverages: technological advancements and constraints

As a consequence of expanded science and technical research, the market perception of consumers has shifted from standard traditional to valuable foods, which are furthermore nutritional as well as healthier in today's world. This food concept, precisely referred to as functional, focuses on including probiotics, which enhance immune system activity, cognitive response, and overall health. This review primarily focuses on functional foods as functional additives in beverages and other food items that can regulate the human immune system and avert any possibility of contracting the infection. Many safety concerns must be resolved during their administration. Functional foods must have an adequate amount of specific probiotic strain(s) during their use and storage, as good viability is needed for optimum functionality of the probiotic. Thus, when developing novel functional food-based formulations, choosing a strain with strong technological properties is crucial. The present review focused on probiotics as an active ingredient in different beverage formulations and the exerting mechanism of action and fate of probiotics in the human body. Moreover, a comprehensive overview of the regulative and safety issues of probiotics-based foods and beverages formulations.

Evaluation of the Function of Probiotics, Emphasizing the Role of their Binding to the Intestinal Epithelium in the Stability and their Effects on the Immune System

Due to the importance of using cost-effective methods for therapeutic purposes, the function of probiotics as safe microorganisms and the study of their relevant functional mechanisms have recently been in the spotlight. Finding the mechanisms of attachment and stability and their beneficial effects on the immune system can be useful in identifying and increasing the therapeutic effects of probiotics. In this review, the functional mechanisms of probiotics were comprehensively investigated. Relevant articles were searched in scientific sources, documents, and databases, including PubMed, NCBI, Bactibace, OptiBac, and Bagel4. The most important functional mechanisms of probiotics and their effects on strengthening the epithelial barrier, competitive inhibition of pathogenic microorganisms, production of antimicrobials, binding and interaction with the host, and regulatory effects on the immune system were discussed.

In this regard, the attachment of probiotics to the epithelium is very important because the prerequisite for their proper functioning is to establish a proper connection to the epithelium. Therefore, more attention should be paid to the binding effect of probiotics, including sortase A, a significant factor involved in the expression of sortase-dependent proteins (SDP), on their surface as mediators of intestinal epithelial cell binding. In general, by investigating the functional mechanisms of probiotics, it was concluded that the mechanism by which probiotics regulate the immune system and adhesion capacity can directly and indirectly have preventive and therapeutic effects on a wide range of diseases. However, further study of these mechanisms requires extensive research on various aspects.

Critical roles of a housekeeping sortase of probiotic Bifidobacterium bifidum in bacterium-host cell crosstalk

Bifidobacterium bifidum YIT 10347 (BF-1) is adhesive in vitro. Here we studied the molecular aspects of the BF-1 adhesion process. We identified and characterized non-adhesive mutants and found that a class E housekeeping sortase was critical for the adhesion to mucin. These mutants were significantly less adhesive to GCIY cells than was the wild type (WT), which protected GCIY cells against acid treatment more than did a non-adhesive mutant. The non-adhesive mutants aberrantly accumulated precursors of putative sortase-dependent proteins (SDPs). Recombinant SDPs bound to mucin. Disruption of the housekeeping sortase influenced expression of SDPs and pilus components. Mutants defective in a pilin or in an SDP showed the same adhesion properties as WT. Therefore, multiple SDPs and pili seem to work cooperatively to achieve adhesion, and the housekeeping sortase is responsible for cell wall anchoring of its substrates to ensure their proper biological function.

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.

Potential applications of recombinant bifidobacterial proteins in the food industry, biomedicine, process innovation and glycobiology

Bifidobacterial proteins have been widely studied to elucidate the metabolic mechanisms of diet adaptation and survival of Bifidobacteria, among others. The use of heterologous expression systems to obtain proteins in sufficient quantities to be characterized has been essential in these studies. L. lactis and the same Bifidobacterium as expression systems highlight ways to corroborate some of the functions attributed to these proteins. The most studied proteins are enzymes related to carbohydrate metabolism, particularly glycosidases, due to their potential application in the synthesis of neoglycoconjugates, prebiotic neooligosaccharides, and active metabolites as well as their high specificity and efficiency in processing glycoconjugates. In this review, we classified the recombinant bifidobacterial proteins reported to date whose characterization has demonstrated their usefulness or their ability to produce a product of commercial interest for the food industry, biomedicine, process innovation and glycobiology. Future directions for their study are also discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-021-00957-1.

Targeting Probiotics in Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a progressive inflammatory disorder characterized by swollen joints, discomfort, tightness, bone degeneration and frailty. Genetic, agamogenetic and sex-specific variables, Prevotella, diet, oral health and gut microbiota imbalance are all likely causes of the onset or development of RA, perhaps the specific pathways remain unknown. Lactobacillus spp. probiotics are often utilized as relief or dietary supplements to treat bowel diseases, build a strong immune system and sustain the immune system. At present, the action mechanism of Lactobacillus spp. towards RA remains unknown. Therefore, researchers conclude the latest analysis to effectively comprehend the ultimate pathogenicity of rheumatoid arthritis, as well as the functions of probiotics, specifically Lactobacillus casei or Lactobacillus acidophilus, in the treatment of RA in therapeutic and diagnostic reports. RA is a chronic inflammation immunological illness wherein the gut microbiota is affected. Probiotics are organisms that can regulate gut microbiota, which may assist to relieve RA manifestations. Over the last two decades, there has been a surge in the use of probiotics. However, just a few research have considered the effect of probiotic administration on the treatment and prevention of arthritis. Randomized regulated experimental trials have shown that particular probiotics supplement has anti-inflammatory benefits, helps people with RA enhance daily activities and alleviates symptoms. As a result, utilizing probiotic microorganisms as therapeutics could be a potential possibility for arthritis treatment. This review highlights the known data on the therapeutic and preventative effects of probiotics in RA, as well as their interactions.

Mutual Preservation: A Review of Interactions Between Cervicovaginal Mucus and Microbiota

At mucosal surfaces throughout the body mucus and mucins regulate interactions between epithelia and both commensal and pathogenic bacteria. Although the microbes in the female genital tract have been linked to multiple reproductive health outcomes, the role of cervicovaginal mucus in regulating genital tract microbes is largely unexplored. Mucus-microbe interactions could support the predominance of specific bacterial species and, conversely, commensal bacteria can influence mucus properties and its influence on reproductive health. Herein, we discuss the current evidence for both synergistic and antagonistic interactions between cervicovaginal mucus and the female genital tract microbiome, and how an improved understanding of these relationships could significantly improve women’s health.

Probiotics, Prebiotics, and Synbiotics: Implications and Beneficial Effects against Irritable Bowel Syndrome

Irritable bowel syndrome (IBS) is still a common functional gastrointestinal disease that presents chronic abdominal symptoms but with a pathophysiology that is not yet fully elucidated. Moreover, the use of the synergistic combination of prebiotics and probiotics, known as synbiotics, for IBS therapy is still in the early stages. Advancements in technology led to determining the important role played by probiotics in IBS, whereas the present paper focuses on the detailed review of the various pathophysiologic mechanisms of action of probiotics, prebiotics, and synbiotics via multidisciplinary domains involving the gastroenterology (microbiota modulation, alteration of gut barrier function, visceral hypersensitivity, and gastrointestinal dysmotility) immunology (intestinal immunological modulation), and neurology (microbiota–gut–brain axis communication and co-morbidities) in mitigating the symptoms of IBS. In addition, this review synthesizes literature about the mechanisms involved in the beneficial effects of prebiotics and synbiotics for patients with IBS, discussing clinical studies testing the efficiency and outcomes of synbiotics used as therapy for IBS.

Adhesion mechanisms of Bifidobacterium animalis subsp. lactis JCM 10602 to dietary fiber

Adherence of probiotics to dietary fibers present in the intestinal tract may affect adhesion to intestinal epithelial cells. The properties of the adhesion of bifidobacteria to mucin or epithelial cells have been well studied; however, adhesion of bifidobacteria to dietary fiber has not been investigated. The adhesion ratio of six Bifidobacterium strains to cellulose and chitin was examined; among the strains, Bifidobacterium animalis subsp. lactis JCM 10602 showed high adherence to both cellulose and chitin, and two strains showed high adherence to only chitin. The ratios of adhesion of B. animalis to cellulose and chitin were positively and negatively correlated with ionic strength, respectively. These data suggest that hydrophobic and electrostatic interactions are involved in the adhesion to cellulose and chitin, respectively. The adhesion ratios of the cells in the late logarithmic phase to cellulose and chitin decreased by approximately 40% and 70% of the cells in the early logarithmic phase, respectively. Furthermore, the adhesion ratio to cellulose decreased with increasing bile concentration regardless of the culture phase of the cells. On the other hand, the adhesion ratio to chitin of cells in the early logarithmic phase decreased with increasing bile concentration; however, that of cells in the late logarithmic phase increased slightly, suggesting that adhesins differ depending on the culture phase. Our results indicated the importance of considering adhesion to both dietary fibers and the intestinal mucosa when using bifidobacteria as probiotics.

A Novel Major Pilin Subunit Protein FimM Is Involved in Adhesion of Bifidobacterium longum BBMN68 to Intestinal Epithelial Cells

Adhesion to the gastrointestinal tract is considered to be important for bifidobacteria to colonize the human gut and exert their probiotic effects. Some cell surface proteins of bifidobacteria, known as adhesins, play critical roles in the binding to host cells or the extracellular matrix (ECM). To elucidate the mechanisms associated with the adhesion of Bifidobacterium longum BBMN68, a centenarian originated potential probiotic, PSORTdb was employed to identify putative extracellular localized proteins in the B. longum BBMN68. Of the 560 predicted extracellular proteins, 21 were further identified as putative adhesion proteins using the conserved domain database of NCBI, and four were successfully overexpressed in the heterologous host, Lactococcus lactis NZ9000. Notably, a recombinant strain expressing FimM showed a significantly increased adhesive affinity for both HT-29 and mucus-secreting LS174T goblet cells (2.2- and 5.4-fold higher than that of the control strain, respectively). Amino acid sequence alignment showed that FimM is a major pilin subunit protein containing a Cna-B type domain and a C-terminal LPKTG sequence. However, in silico analysis of the fimM-coding cluster revealed that BBMN68_RS10200, encoding a pilus-specific class C sortase, was a pseudogene, indicating that FimM may function as a surface adhesin that cannot polymerize into a pili-like structure. Immunogold electron microscopy results further confirmed that FimM localized to the surface of L. lactis NZfimM and B. longum BBMN68 but did not assemble into pilus filaments. Moreover, the adhesive affinity of L. lactis NZfimM to fibronectin, fibrinogen, and mucin were 3.8-, 2.1-, and 3.1-fold higher than that of the control. The affinity of FimM for its attachment receptors was further verified through an inhibition assay using anti-FimM antibodies. In addition, homologs of FimM were found in Bifidobacterium bifidum 85B, Bifidobacterium gallinarum CACC 514, and 23 other B. longum strains by sequence similarity analysis using BLASTP. Our results suggested that FimM is a novel surface adhesin that is mainly present in B. longum strains.

Extracellular Vesicles Produced by Bifidobacterium longum Export Mucin-Binding Proteins

Extracellular proteins are important factors in host-microbe interactions; however, the specific factors that enable bifidobacterial adhesion and survival in the gastrointestinal (GI) tract are not fully characterized. Here, we discovered that Bifidobacterium longum NCC2705 cultured in bacterium-free supernatants of human fecal fermentation broth released a myriad of particles into the extracellular environment. The aim of this study was to characterize the physiological properties of these extracellular particles. The particles, approximately 50 to 80 nm in diameter, had high protein and double-stranded DNA contents, suggesting that they were extracellular vesicles (EVs). A proteomic analysis showed that the EVs primarily consisted of cytoplasmic proteins with crucial functions in essential cellular processes. We identified several mucin-binding proteins by performing a biomolecular interaction analysis of phosphoketolase, GroEL, elongation factor Tu (EF-Tu), phosphoglycerate kinase, transaldolase (Tal), and heat shock protein 20 (Hsp20). The recombinant GroEL and Tal proteins showed high binding affinities to mucin. Furthermore, the immobilization of these proteins on microbeads affected the permanence of the microbeads in the murine GI tract. These results suggest that bifidobacterial exposure conditions that mimic the intestine stimulate B. longum EV production. The resulting EVs exported several cytoplasmic proteins that may have promoted B. longum adhesion. This study improved our understanding of the Bifidobacterium colonization strategy in the intestinal microbiome.IMPORTANCE Bifidobacterium is a natural inhabitant of the human gastrointestinal (GI) tract. Morphological observations revealed that extracellular appendages of bifidobacteria in complex microbial communities are important for understanding its adaptations to the GI tract environment. We identified dynamic extracellular vesicle (EV) production by Bifidobacterium longum in bacterium-free fecal fermentation broth that was strongly suggestive of differing bifidobacterial extracellular appendages in the GI tract. In addition, export of the adhesive moonlighting proteins mediated by EVs may promote bifidobacterial colonization. This study provides new insight into the roles of EVs in bifidobacterial colonization processes as these bacteria adapt to the GI environment.

2'-Fucosyllactose promotes Bifidobacterium bifidum DNG6 adhesion to Caco-2 cells

Adhesion to the intestinal mucosa is the prerequisite for bifidobacteria to colonize and exert biological functions, whereas the choice of carbon source affects the ability of bifidobacteria to adhere to and interact with intestinal epithelial cells. However, knowledge about the relationship between human milk oligosaccharide consumption by bifidobacteria and its adhesion is still limited. In this study, we aim to investigate the effect of 2'-fucosyllactose (2'-FL) as the carbon source on the growth and adhesion properties of Bifidobacterium bifidum DNG6, and make comparisons with galactooligosaccharides and glucose. We found that the growth and adhesion properties of B. bifidum DNG6 grown in different carbon sources were varied. The 2'-FL as a carbon source improves the adhesion ability of B. bifidum DNG6. The expression of adhesion-associated genes was significantly higher in B. bifidum DNG6 grown in 2'-FL after incubation with Caco-2 cells compared with that in galactooligosaccharides and glucose. Our results indicated that 2'-FL may promote B. bifidum DNG6 adhesion to Caco-2 cells through high expression of genes encoding adhesion proteins. The findings of this study contribute to a better understanding of the involvement of human milk oligosaccharides in the adhesion of bifidobacteria and further support the potential application of 2'-FL as a prebiotic in infant nutritional supplements.

Potential Immunomodulatory Activity of a Selected Strain Bifidobacterium bifidum H3-R2 as Evidenced in vitro and in Immunosuppressed Mice

The microbiota is directly involved in the development and modulation of the intestinal immune system. In particular, members of the genus Bifidobacterium play a primary role in immune regulation. In the present study, Bifidobacterium bifidum H3-R2 was screened from 15 bifidobacterium strains by in vitro experiment, showing a positive tolerance to digestive tract conditions, adhesion ability to intestinal epithelial cells and a regulatory effect on immune cell activity. Immunostimulatory activity of B. bifidum H3-R2 was also elucidated in vivo in cytoxan (CTX)-treated mice. The results showed that the administration of B. bifidum H3-R2 ameliorated the CTX-induced bodyweight loss and imbalanced expression of inflammatory cytokines, enhanced the production of secretory immunoglobulin A (SIgA), and promoted splenic lymphocyte proliferation, natural killer (NK) cell activity and phagocytosis of macrophages in immunosuppressed mice. In addition, B. bifidum H3-R2 restored injured intestinal mucosal, and increased the villus length and crypt depth in CTX-treated mice. The results could be helpful for understanding the functions of B. bifidum H3-R2, supporting its potential as a novel probiotic for immunoregulation.

Comparative Proteomics and Secretomics Revealed Virulence and Antibiotic Resistance-Associated Factors in Vibrio parahaemolyticus Recovered From Commonly Consumed Aquatic Products

Vibrio parahaemolyticus is a seafoodborne pathogen that can cause severe gastroenteritis and septicemia diseases in humans and even death. The emergence of multidrug-resistant V. parahaemolyticus leads to difficulties and rising costs of medical treatment. The bacterium of environmental origins containing no major virulence genes (tdh and trh) has been reported to be associated with infectious diarrhea disease as well. Identification of risk factors in V. parahaemolyticus is imperative for assuming food safety. In this study, we obtained secretomic and proteomic profiles of V. parahaemolyticus isolated from 12 species of commonly consumed aquatic products and identified candidate protein spots by using two-dimensional gel electrophoresis and liquid chromatography tandem mass spectrometry techniques. A total of 11 common and 28 differential extracellular proteins were found from distinct secretomic profiles, including eight virulence-associated proteins: outer membrane channel TolC, maltoporin, elongation factor Tu, enolase, transaldolase, flagellin C, polar flagellin B/D, and superoxide dismutase, as well as five antimicrobial and/or heavy metal resistance-associated ABC transporter proteins. Comparison of proteomic profiles derived from the 12 V. parahaemolyticus isolates also revealed five intracellular virulence-related proteins, including aldehyde-alcohol dehydrogenase, outer membrane protein A, alkyl hydroperoxide reductase C, phosphoenolpyruvate-protein phosphotransferase, and phosphoglycerate kinase. Additionally, our data indicated that aquatic product matrices significantly altered proteomic profiles of the V. parahaemolyticus isolates with a number of differentially expressed proteins identified. The results in this study meet the increasing need for novel diagnosis candidates of the leading seafoodborne pathogen worldwide.

Prolonged Heat Stress of Lactobacillus paracasei GCRL163 Improves Binding to Human Colorectal Adenocarcinoma HT-29 Cells and Modulates the Relative Abundance of Secreted and Cell Surface-Located Proteins

Lactobacillus casei group bacteria improve cheese ripening and may interact with host intestinal cells as probiotics, where surface proteins play a key role. Three complementary methods [trypsin shaving (TS), LiCl-sucrose (LS) extraction, and extracellular culture fluid precipitation] were used to analyze cell surface proteins of Lactobacillus paracasei GCRL163 by label-free quantitative proteomics after culture to the mid-exponential phase in bioreactors at pH 6.5 and temperatures of 30-45 °C. A total of 416 proteins, including 300 with transmembrane, cell wall anchoring, and secretory motifs and 116 cytoplasmic proteins, were quantified as surface proteins. Although LS caused significantly greater cell lysis as growth temperature increased, higher numbers of extracytoplasmic proteins were exclusively obtained by LS treatment. Together with the increased positive surface charge of cells cultured at supra-optimal temperatures, proteins including cell wall hydrolases Msp1/p75 and Msp2/p40, α-fucosidase AlfB, SecA, and a PspC-domain putative adhesin were upregulated in surface or secreted protein fractions, suggesting that cell adhesion may be altered. Prolonged heat stress (PHS) increased binding of L. paracasei GCRL163 to human colorectal adenocarcinoma HT-29 cells, relative to acid-stressed cells. This study demonstrates that PHS influences cell adhesion and relative abundance of proteins located on the surface, which may impact probiotic functionality, and the detected novel surface proteins likely linked to the cell cycle and envelope stress.

Bifidobacterium dentium Fortifies the Intestinal Mucus Layer via Autophagy and Calcium Signaling Pathways

Much remains unknown about how the intestinal microbiome interfaces with the protective intestinal mucus layer. Bifidobacterium species colonize the intestinal mucus layer and can modulate mucus production by goblet cells. However, select Bifidobacterium strains can also degrade protective glycans on mucin proteins. We hypothesized that the human-derived species Bifidobacterium dentium would increase intestinal mucus synthesis and expulsion, without extensive degradation of mucin glycans. In silico data revealed that B. dentium lacked the enzymes necessary to extensively degrade mucin glycans. This finding was confirmed by demonstrating that B. dentium could not use naive mucin glycans as primary carbon sources in vitro To examine B. dentium mucus modulation in vivo, Swiss Webster germfree mice were monoassociated with live or heat-killed B. dentium Live B. dentium-monoassociated mice exhibited increased colonic expression of goblet cell markers Krüppel-like factor 4 (Klf4), Trefoil factor 3 (Tff3), Relm-β, Muc2, and several glycosyltransferases compared to both heat-killed B. dentium and germfree counterparts. Likewise, live B. dentium-monoassociated colon had increased acidic mucin-filled goblet cells, as denoted by Periodic Acid-Schiff-Alcian Blue (PAS-AB) staining and MUC2 immunostaining. In vitro, B. dentium-secreted products, including acetate, were able to increase MUC2 levels in T84 cells. We also identified that B. dentium-secreted products, such as γ-aminobutyric acid (GABA), stimulated autophagy-mediated calcium signaling and MUC2 release. This work illustrates that B. dentium is capable of enhancing the intestinal mucus layer and goblet cell function via upregulation of gene expression and autophagy signaling pathways, with a net increase in mucin production.IMPORTANCE Microbe-host interactions in the intestine occur along the mucus-covered epithelium. In the gastrointestinal tract, mucus is composed of glycan-covered proteins, or mucins, which are secreted by goblet cells to form a protective gel-like structure above the epithelium. Low levels of mucin or alterations in mucin glycans are associated with inflammation and colitis in mice and humans. Although current literature links microbes to the modulation of goblet cells and mucins, the molecular pathways involved are not yet fully understood. Using a combination of gnotobiotic mice and mucus-secreting cell lines, we have identified a human-derived microbe, Bifidobacterium dentium, which adheres to intestinal mucus and secretes metabolites that upregulate the major mucin MUC2 and modulate goblet cell function. Unlike other Bifidobacterium species, B. dentium does not extensively degrade mucin glycans and cannot grow on mucin alone. This work points to the potential of using B. dentium and similar mucin-friendly microbes as therapeutic agents for intestinal disorders with disruptions in the mucus barrier.

Experimental models to study intestinal microbes–mucus interactions in health and disease

A close symbiotic relationship exists between the intestinal microbiota and its host. A critical component of gut homeostasis is the presence of a mucus layer covering the gastrointestinal tract. Mucus is a viscoelastic gel at the interface between the luminal content and the host tissue that provides a habitat to the gut microbiota and protects the intestinal epithelium. The review starts by setting up the biological context underpinning the need for experimental models to study gut bacteria-mucus interactions in the digestive environment. We provide an overview of the structure and function of intestinal mucus and mucins, their interactions with intestinal bacteria (including commensal, probiotics and pathogenic microorganisms) and their role in modulating health and disease states. We then describe the characteristics and potentials of experimental models currently available to study the mechanisms underpinning the interaction of mucus with gut microbes, including in vitro, ex vivo and in vivo models. We then discuss the limitations and challenges facing this field of research.

Proteomics for the Investigation of Surface-Exposed Proteins in Probiotics

Probiotics are commensal microorganisms that are present in the intestinal tract and in many fermented foods and positively affect human health, promoting digestion and uptake of dietary nutrients, strengthening intestinal barrier function, modulating immune response, and enhancing antagonism toward pathogens. The proteosurfaceome, i.e., the complex set of proteins present on the bacterial surface, is directly involved as leading actor in the dynamic communication between bacteria and host. In the last decade, the biological relevance of surface-exposed proteins prompted research activities exploiting the potentiality of proteomics to define the complex network of proteins that are involved in the molecular mechanisms at the basis of the adaptation to gastrointestinal environment and the probiotic effects. These studies also took advantages of the recent technological improvements in proteomics, mass spectrometry and bioinformatics that triggered the development of ad hoc designed innovative strategies to characterize the bacterial proteosurfaceome. This mini-review is aimed at describing the key role of proteomics in depicting the cell wall protein architecture and the involvement of surface-exposed proteins in the intimate and dynamic molecular dialogue between probiotics and intestinal epithelial and immune cells.

An insight into gut microbiota and its functionalities

Gut microbiota has evolved along with their hosts and is an integral part of the human body. Microbiota acquired at birth develops in parallel as the host develops and maintains its temporal stability and diversity through adulthood until death. Recent developments in genome sequencing technologies, bioinformatics and culturomics have enabled researchers to explore the microbiota and in particular their functions at more detailed level than before. The accumulated evidences suggest that though a part of the microbiota is conserved, the dynamic members vary along the gastrointestinal tract, from infants to elderly, primitive tribes to modern societies and in different health conditions. Though the gut microbiota is dynamic, it performs some basic functions in the immunological, metabolic, structural and neurological landscapes of the human body. Gut microbiota also exerts significant influence on both physical and mental health of an individual. An in-depth understanding of the functioning of gut microbiota has led to some very exciting developments in therapeutics, such as prebiotics, probiotics, drugs and faecal transplantation leading to improved health.

Bovine colostrum-driven modulation of intestinal epithelial cells for increased commensal colonisation

Nutritional intake may influence the intestinal epithelial glycome and in turn the available attachment sites for bacteria. In this study, we tested the hypothesis that bovine colostrum may influence the intestinal cell surface and in turn the attachment of commensal organisms. Human HT-29 intestinal cells were exposed to a bovine colostrum fraction (BCF) rich in free oligosaccharides. The adherence of several commensal bacteria, comprising mainly bifidobacteria, to the intestinal cells was significantly enhanced (up to 52-fold) for all strains tested which spanned species that are found across the human lifespan. Importantly, the changes to the HT-29 cell surface did not support enhanced adhesion of the enteric pathogens tested. The gene expression profile of the HT-29 cells following treatment with the BCF was evaluated by microarray analysis. Many so called "glyco-genes" (glycosyltransferases and genes involved in the complex biosynthetic pathways of glycans) were found to be differentially regulated suggesting modulation of the enzymatic addition of sugars to glycoconjugate proteins. The microarray data was further validated by means of real-time PCR. The current findings provide an insight into how commensal microorganisms colonise the human gut and highlight the potential of colostrum and milk components as functional ingredients that can potentially increase commensal numbers in individuals with lower counts of health-promoting bacteria.

Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant

BACKGROUND

Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricularia ecophysiology-the interactions with and within the complex communities of microorganisms colonizing their traps and external surfaces.

RESULTS

Bacteria, fungi, algae, and protozoa inhabit the miniature ecosystem of the Utricularia trap lumen and are involved in the regeneration of nutrients from complex organic matter. By combining molecular methods, microscopy, and other approaches to assess the trap-associated microbial community structure, diversity, function, as well as the nutrient turn-over potential of bacterivory, we gained insight into the nutrient acquisition strategies of the Utricularia hosts.

CONCLUSIONS

We conclude that Utricularia traps can, in terms of their ecophysiological function, be compared to microbial cultivators or farms, which center around complex microbial consortia acting synergistically to convert complex organic matter, often of algal origin, into a source of utilizable nutrients for the plants.

Influence of Probiotics Administration on Gut Microbiota Core: A Review on the Effects on Appetite Control, Glucose, and Lipid Metabolism

An increasing number of studies has shown that dietary probiotics exert beneficial health effects in both humans and animals. It is well established that gut microbiota play a pivotal role in regulating host metabolism, and a growing number of studies has elucidated that probiotics positively interfere with gut microbiota. Accumulating evidence shows that probiotics, through their metabolic activity, produce metabolites that in turn contribute to positively affect host physiology. For these reasons, probiotics have shown significant potential as a therapeutic tool for a diversity of diseases, but the mechanisms through which probiotics act has not been fully elucidated yet. The goal of this review was to provide evidence on the effects of probiotics on gut microbiota changes associated with host metabolic variations, specifically focusing on feed intake and lipid and glucose metabolism. In addition, we review probiotic interaction with the gut microbiota. The information collected here will give further insight into the effects of probiotics on the gut microbiota and their action on metabolite release, energy metabolism, and appetite. This information will help to improve knowledge to find better probiotic therapeutic strategies for obesity and eating disorders.

[Identification of Heparin-binding Proteins on the Cell Surface of Cryptococcus neoformans]

Interactions between virulence factors of pathogens and host responses play an important role in the establishment of infection by microbes. We focused on interactions between Cryptococcus neoformans proteins and heparin, which is abundant on host epithelial cells. Surface proteins were extracted and analyzed. Fractions from anion-exchange column chromatography interacted with heparin in surface plasmon resonance analyses. Heparin-binding proteins were purified and then separated by gel electrophoresis; and were identified as transaldolase, glutathione-disulfide reductase, and glyoxal oxidase. These results imply that multifunctional molecules on C. neoformans cells, such as those involved in heparin binding, may play roles in adhesion that trigger responses in the host.

Bifidobacterium bifidum Extracellular Sialidase Enhances Adhesion to the Mucosal Surface and Supports Carbohydrate Assimilation

Bifidobacterium is a natural inhabitant of the human gastrointestinal (GI) tract. We studied the role of the extracellular sialidase (SiaBb2, 835 amino acids [aa]) from Bifidobacterium bifidum ATCC 15696 in mucosal surface adhesion and carbohydrate catabolism. Human milk oligosaccharides (HMOs) or porcine mucin oligosaccharides as the sole carbon source enhanced B. bifidum growth. This was impaired in a B. bifidum ATCC 15696 strain harboring a mutation in the siabb2 gene. Mutant cells in early to late exponential growth phase also showed decreased adhesion to human epithelial cells and porcine mucin relative to the wild-type strain. These results indicate that SiaBb2 removes sialic acid from HMOs and mucin for metabolic purposes and may promote bifidobacterial adhesion to the mucosal surface. To further characterize SiaBb2-mediated bacterial adhesion, we examined the binding of His-tagged recombinant SiaBb2 peptide to colonic mucins and found that His-SiaBb2 as well as a conserved sialidase domain peptide (aa 187 to 553, His-Sia) bound to porcine mucin and murine colonic sections. A glycoarray assay revealed that His-Sia bound to the α2,6-linked but not to the α2,3-linked sialic acid on sialyloligosaccharide and blood type A antigen [GalNAcα1-3(Fucα1-2)Galβ] at the nonreducing termini of sugar chains. These results suggest that the sialidase domain of SiaBb2 is responsible for this interaction and that the protein recognizes two distinct carbohydrate structures. Thus, SiaBb2 may be involved in Bifidobacterium-mucosal surface interactions as well as in the assimilation of a variety of sialylated carbohydrates.

Adhesion to the host mucosal surface and carbohydrate assimilation are important for bifidobacterium colonization and survival in the host gastrointestinal tract. In this study, we investigated the mechanistic basis for B. bifidum extracellular sialidase (SiaBb2)-mediated adhesion. SiaBb2 cleaved sialyl-human milk oligosaccharides and mucin glycans to produce oligosaccharides that supported B. bifidum growth. Moreover, SiaBb2 enhanced B. bifidum adhesion to mucosal surfaces via specific interactions with the α2,6 linkage of sialyloligosaccharide and blood type A antigen on mucin carbohydrates. These findings provide insight into the bifunctional role of SiaBb2 and the adhesion properties of B. bifidum strains.

Simulated gastrointestinal conditions increase adhesion ability of Lactobacillus paracasei strains isolated from kefir to Caco-2 cells and mucin

Gastrointestinal conditions along the digestive tract are the main stress to which probiotics administrated orally are exposed because they must survive these adverse conditions and arrive alive to the intestine. Adhesion to epithelium has been considered one of the key criteria for the characterization of probiotics because it extends their residence time in the intestine and as a consequence, can influence the health of the host by modifying the local microbiota or modulating the immune response. Nevertheless, there are very few reports on the adhesion properties to epithelium and mucus of microorganisms after passing through the gastrointestinal tract. In the present work, we evaluate the adhesion ability in vitro of L. paracasei strains isolated from kefir grains after acid and bile stress and we observed that they survive simulated gastrointestinal passage in different levels depending on the strain. L. paracasei CIDCA 8339, 83120 and 83123 were more resistant than L. paracasei CIDCA 83121 and 83124, with a higher susceptibility to simulated gastric conditions. Proteomic analysis of L. paracasei subjected to acid and bile stress revealed that most of the proteins that were positively regulated correspond to the glycolytic pathway enzymes, with an overall effect of stress on the activation of the energy source. Moreover, it is worth to remark that after gastrointestinal passage, L. paracasei strains have increased their ability to adhere to mucin and epithelial cells in vitro being this factor of relevance for maintenance of the strain in the gut environment to exert its probiotic action.