Human gut microbiota and its relationship to health and disease

Isolation and gut microbiota modulation of antibiotic-resistant probiotics from human feces

Antibiotic-resistant probiotics may be advantageous for antibiotic-induced gut microbiota imbalance. In this article, we aimed to isolate antibiotic-resistant bacteria as potential probiotics. Feces from 3 healthy adults and 2 infants were used to isolate the antibiotic-resistant bacteria. Then we established gut microbiota imbalance mice model by antibiotics treatment and used it to assess the effect of the probiotics. Finally, we identified 8 isolates, and 6 of them were used as probiotics cocktail. Number of anaerobe, lactobacilli, and Bifidobacterium in feces were higher in the probiotic group (9.47±0.35 log10CFU/g, 8.74±0.18 log10CFU/g, 7.24±0.38 log10CFU/g, respectively) compared with model group (P<0.05). Richness and diversity index of probiotic group (19.79±0.29 and 2.95±0.06, respectively) were larger than model group (P<0.05). Diarrhea and mucosal edema had been alleviated during probiotic treatment. Our results validated that bacteriotherapy was available to treat gut microbiota imbalance.

CODEX-aligned dietary fiber definitions help to bridge the 'fiber gap'

A comprehensive dietary fiber (DF) definition was adopted by the CODEX Alimentarius Commission (CAC) (1) to reflect the current state of knowledge about DF, (2) to recognize that all substances that behave like fiber regardless of how they are produced can be named as DF if they show physiological benefits, and (3) to promote international harmonization for food labeling and food composition tables. This review gives the history and evolution of the state of DF knowledge as looked at by refinements in DF methods and definitions subsequent to the launch of the DF hypothesis. The refinements parallel both interventional and epidemiological research leading to better understanding of the role of DF in contributing to the numerous physiological benefits imparted by all the various digestion resistant carbohydrates. A comparison of the CODEX definition (including its footnote that authorizes the inclusion of polymers with DP 3-9) and approved CODEX Type 1 methods with other existing definitions and methods will point out differences and emphasize the importance of adoption of CODEX-aligned definitions by all jurisdictions. Such harmonization enables comparison of nutrition research, recommendations, food composition tables and nutrition labels the world over. A case will be made that fibers are analogous to vitamins, in that they vary in structure, function and amount needed, but each when present in the right amount contributes to optimal health. Since the intake of DF is significantly below recommended levels throughout the world, the recognition that 'all fibers fit' is an important strategy in bridging the 'fiber gap' by enfranchising and encouraging greater intake of foods with inherent and added DF. Fortifying foods with added DF makes it easier to increase intakes while maintaining calories at recommended levels.

Characterization of a new bacteriocin from Lactobacillus plantarum LE5 and LE27 isolated from ensiled corn

Bacteriocins are low molecular peptides with antimicrobial activity, which are of great interest as food bio-preservatives and for treating diseases caused by pathogenic bacteria. In this study, we present the characterization of bacteriocins produced by Lactobacillus plantarum LE5 and LE27 isolated from ensiled corn. Bacteriocins were purified through ammonium sulfate precipitation and double dialysis by using 12- and 1-kDa membranes. Bacteriocins showed activity against Listeria innocua, Listeria monocytogenes, and Enteroccocus faecalis. Molecular weight was estimated through Tricine-SDS-PAGE and overloading the gel onto Mueller-Hinton agar seeded with L. monocytogenes, showing an inhibition zone between 5 and 10 kDa. NanoLC-MS/MS analysis allowed the identification of UPF0291 protein (UniProtKB/Swiss-Prot Q88VI7), which is also presented in other lactic acid bacteria without assigned function. Ab initio modeling showed it has an α-helix-rich structure and a large positive-charged region. Bacteriocins were stable between 4 and 121 °C and pH 2 and 12, and the activity was inhibited by SDS and proteases. Mode of action assay suggests that the bacteriocin causes of target microorganism. Taken together, these results describe a possible new class IIa bacteriocin produced by L. plantarum, which has a wide stability to physicochemical conditions, and that could be used as an alternative for the control of foodborne diseases.

Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction

Background

There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE).

Findings

In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I’Etoile, France) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals.

DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA was very successful.

Conclusion

QIAamp DNA Stool Mini Kit DNA extracts are optimal for DGGE runs and this extraction method yields a higher amount of DNA compared to easyMag®.

Management of reproduction and pregnancy complications in maternal obesity: which role for dietary polyphenols?

Obesity is a global and dramatic public health problem; maternal obesity represents one of the main risk factors of infertility and pregnancy complications as it is associated with adverse maternal and offspring outcomes. In the last few years, adipose tissue dysfunction associated with altered adipocytokine secretion has been suggested to play a critical role in all the phases of reproductive process. Obesity is a nutrition-related disorder. In this regard, dietary intervention strategies, such as high intake of fruit and vegetables, have shown significant effects in both preserving health and counteracting obesity-associated diseases. Evidence has been provided that polyphenols, important constituents of plant-derived food, can influence developmental program of oocyte and embryo, as well as pregnancy progression by modulating several cellular pathways. This review will examine the controversial results so far obtained on adipocytokine involvement in fertility impairment and pregnancy complications. Furthermore, the different effects exerted by polyphenols on oocyte, embryo, and pregnancy development will be also taken in account.

Resembling breast milk: influence of polyamine-supplemented formula on neonatal BALB/cOlaHsd mouse microbiota

Infant microbiota is influenced by numerous factors, such as delivery mode, environment, prematurity and diet (breast milk or formula). In addition to its nutritional value, breast milk contains bioactive substances that drive microbial colonisation and support immune system development, which are usually not present in infant formulas. Among these substances, polyamines have been described to be essential for intestinal and immune functions in newborns. However, their effect on the establishment of microbiota remains unclear. Therefore, the aim of the present study was to ascertain whether an infant formula supplemented with polyamines has an impact on microbial colonisation by modifying it to resemble that in breast-fed neonatal BALB/c mice. In a 4 d intervention, a total of sixty pups (14 d old) were randomly assigned to the following groups: (1) breast-fed group; (2) non-enriched infant formula-fed group; (3) three different groups fed an infant formula enriched with increasing concentrations of polyamines (mixture of putrescine, spermidine and spermine), following the proportions found in human milk. Microbial composition in the contents of the oral cavity, stomach and small and large intestines was analysed by quantitative PCR targeted at fourteen bacterial genera and species. Significantly different (P< 0·05) microbial colonisation patterns were observed in the entire gastrointestinal tract of the breast-fed and formula-fed mice. In addition, our findings demonstrate that supplementation of polyamines regulates the amounts of total bacteria,Akkermansia muciniphila,Lactobacillus,Bifidobacterium,Bacteroides–PrevotellaandClostridiumgroups to levels found in the breast-fed group. Such an effect requires further investigation in human infants, as supplementation of an infant formula with polyamines might contribute to healthy gastrointestinal tract development.

Structural basis for arabinoxylo-oligosaccharide capture by the probiotic Bifidobacterium animalis subsp. lactis Bl-04

Glycan utilization plays a key role in modulating the composition of the gut microbiota, but molecular insight into oligosaccharide uptake by this microbial community is lacking. Arabinoxylo-oligosaccharides (AXOS) are abundant in the diet, and are selectively fermented by probiotic bifidobacteria in the colon. Here we show how selectivity for AXOS uptake is established by the probiotic strain Bifidobacterium animalis subsp. lactis Bl-04. The binding protein BlAXBP, which is associated with an ATP-binding cassette (ABC) transporter that mediates the uptake of AXOS, displays an exceptionally broad specificity for arabinosyl-decorated and undecorated xylo-oligosaccharides, with preference for tri- and tetra-saccharides. Crystal structures of BlAXBP in complex with four different ligands revealed the basis for this versatility. Uniquely, the protein was able to recognize oligosaccharides in two opposite orientations, which facilitates the optimization of interactions with the various ligands. Broad substrate specificity was further enhanced by a spacious binding pocket accommodating decorations at different mainchain positions and conformational flexibility of a lid-like loop. Phylogenetic and genetic analyses show that BlAXBP is highly conserved within Bifidobacterium, but is lacking in other gut microbiota members. These data indicate niche adaptation within Bifidobacterium and highlight the metabolic syntrophy (cross-feeding) among the gut microbiota.

Recent progress on the role of gut microbiota in the pathogenesis of inflammatory bowel disease

In recent years investigations of inflammatory bowel disease (IBD) have advanced rapidly with regard to the relationship between the host immune response and gut microbiota. Patients with IBD have been shown to have an abnormal composition of gut microbiota and host immune dysregulation. Abnormal components of gut microbiota, to which the host mounts aberrant immune responses in genetically vulnerable individuals, appear to play a critical role in the pathogenesis of IBD. Therefore, inappropriate innate and adaptive host immune responses to abnormal components of gut microbiota and their products form the basis of IBD pathogenesis. Modern molecular genetic methods should be utilized to help to illuminate the pathogenetic mechanism of IBD and to develop personalized therapeutic strategies for this disease.

Monitoring immune modulation by nutrition in the general population: identifying and substantiating effects on human health

Optimal functioning of the immune system is crucial to human health, and nutrition is one of the major exogenous factors modulating different aspects of immune function. Currently, no single marker is available to predict the effect of a dietary intervention on different aspects of immune function. To provide further guidance on the assessment and interpretation of the modulation of immune functions due to nutrition in the general population, International Life Sciences Institute Europe commissioned a group of experts from academia, government and the food industry to prepare a guidance document. A draft of this paper was refined at a workshop involving additional experts. First, the expert group defined criteria to evaluate the usefulness of immune function markers. Over seventy-five markers were scored within the context of three distinct immune system functions: defence against pathogens; avoidance or mitigation of allergy; control of low-grade (metabolic) inflammation. The most useful markers were subsequently classified depending on whether they by themselves signify clinical relevance and/or involvement of immune function. Next, five theoretical scenarios were drafted describing potential changes in the values of markers compared with a relevant reference range. Finally, all elements were combined, providing a framework to aid the design and interpretation of studies assessing the effects of nutrition on immune function. This stepwise approach offers a clear rationale for selecting markers for future trials and provides a framework for the interpretation of outcomes. A similar stepwise approach may also be useful to rationalise the selection and interpretation of markers for other physiological processes critical to the maintenance of health and well-being.

Preliminary studies demonstrating acetoclastic methanogenesis in a rat colonic ring model

Washed rat colonic rings were incubated in closed flasks under N2 at physiologic pH and temperature levels. In the absence of an exogenous substrate, negligible H2 but some CH4 concentrations were detected in vitro after one hour of incubation, but high concentrations (H2 > 100 ppm, CH4 > 10 ppm) of both gases were found after 24 hours of culture. Production of H2 and CH4 by the washed colonic rings was stimulated by lactose addition. Maximum H2 production occurred at about pH 7.0, while maximum CH4 production occurred between pH 4.0 and 6.0. The increased production of both gases at 24 hours was associated with dramatic increases (10(4)-fold) in anaerobic bacteria colony counts on the colonic rings and in the incubation media, as well as dramatic increases (100-fold) in acetate concentrations in the media, while lactate concentrations first rose and then fell significantly. These results suggest that gas production in colonic ring preparations is subject to quantitative changes in microbiota, pH, and metabolite formation analogous to in vivo conditions. In addition, microbiota firmly attached to colonic tissue appears to utilize colonic tissue to support its growth in the absence of an exogenous substrate.

The interaction between gut microbiota and age-related changes in immune function and inflammation

Intestinal microbiota and gut immune systems interact each other, maintaining a condition of homeostasis in the context of the intestinal habitat. However, both systems undergo modifications in elderly, thus accounting for a low grade inflammatory status which, in turn, may evolve toward more severe pathological conditions such as inflammatory bowel disease and colon rectal cancer. In addition, in western societies dietary habits may negatively influence the microbiota composition, also altering gut immune response which is per se impaired in elderly. In order to prevent the outcome of aged-related disease, supplementation of nutraceuticals able to correct abnormalities of both immune system and microbiota has become more frequent than in the past. In this respect, a better identification of components of the aged microbiota as well as a deeper analysis of gut mucosal immunity function should be pursued.

Identification of Lactobacillus strains with probiotic features from the bottlenose dolphin (Tursiops truncatus)

Aims

In order to develop complementary health management strategies for marine mammals, we used culture-based and culture-independent approaches to identify gastrointestinal lactobacilli of the common bottlenose dolphin, Tursiops truncatus.

Methods and Results

We screened 307 bacterial isolates from oral and rectal swabs, milk and gastric fluid, collected from 38 dolphins in the U.S. Navy Marine Mammal Program, for potentially beneficial features. We focused our search on lactobacilli and evaluated their ability to modulate TNF secretion by host cells and inhibit growth of pathogens. We recovered Lactobacillus salivarius strains which secreted factors that stimulated TNF production by human monocytoid cells. These Lact. salivarius isolates inhibited growth of selected marine mammal and human bacterial pathogens. In addition, we identified a novel Lactobacillus species by culture and direct sequencing with 96·3% 16S rDNA sequence similarity to Lactobacillus ceti.

Conclusions

Dolphin-derived Lact. salivarius isolates possess features making them candidate probiotics for clinical studies in marine mammals.

Significance and Impact of the Study

This is the first study to isolate lactobacilli from dolphins, including a novel Lactobacillus species and a new strain of Lact. salivarius, with potential for veterinary probiotic applications. The isolation and identification of novel Lactobacillus spp. and other indigenous microbes from bottlenose dolphins will enable the study of the biology of symbiotic members of the dolphin microbiota and facilitate the understanding of the microbiomes of these unique animals.

Gut microbiota, probiotics, and human health

The review is devoted to the problems of microbiota and the ways of it correction employing beneficial life bacteria- probiotics. It covers the issues related to the functioning of human microbiota and its importance for the health, individual variability of microbial content, functioning of the probiotics in the human organism and the history of probiotic studies with particular focus on the microbiological investigations in the USSR. The article discusses the safety issues related to probiotics and the problems with probiotic therapy, trying to explain the reasons for the side effects caused by probiotics. The necessity of personified selection of the probiotic strain or individual microbial therapy autoprobiotics is also discussed.

Use of whey permeate containing in situ synthesised galacto-oligosaccharides for the growth and preservation of Lactobacillus plantarum

Galacto-oligosaccharides (GOS) are prebiotics that have a beneficial effect on human health by promoting the growth of probiotic bacteria in the gut. GOS are commonly produced from lactose in an enzymatic reaction catalysed by β-galactosidase, named transglycosylation. Lactose is the main constituent of whey permeate (WP), normally wasted output from the cheese industry. Therefore, the main goal of this work was to optimise the synthesis of GOS in WP using β-galatosidase from Aspergillus oryzaea. WP and whey permeate enzymatically treated (WP-GOS) were used as culture media of Lactobacillus plantarum 299v. Lb. plantarum 299v attained the stationary phase in approximately 16 h, reaching 3·6 and 4·1×108 CFU/ml in WP and WP-GOS, respectively. The in situ synthesised GOS were not consumed during growth. No significant differences were observed in the growth kinetics of microorganisms in both media. After fermentation, microorganisms were dehydrated by freeze-drying and spray-drying and stored. The recovery of microorganisms after fermentation, dehydration and storage at 4 °C for at least 120 d was above 108 CFU/g. These studies demonstrated that WP is an appropriate substrate for the synthesis of GOS and the obtained product is also adequate as culture medium of Lb. plantarum 299v. The coexistence of GOS and dehydrated viable probiotic microorganisms, prepared using an effluent as raw material, represents the main achievement of this work, with potential impact in the development of functional foods.

Importance of prebiotic and probiotic: the role of galactooligosacharides as prebiotic additives: a review

In today's well-resistant pathogens and excessive use of antibiotics which weake and undermine the immune system the importance of pre- and probiotics is more desired. Probiotics - lactic acid bacteria - our intestinal symbiotes, has significant affect on our intestinal tract and brings us to number of positive physiological effects – inhibit the development of pathogenic microflora and serious stimulate the immune system, which subsequently leads to secondary health benefits - efficient use of energy from food, better resorption of minerals and vitamins by intestinal epithelium, suppression of diseases and inflammatory processes in the human intestine and many others. This article discusses the impact of prebiotics (essential substrate for probiotic bacteria), but also natural occurrence and important of prebiotics. Galactooligosaccharides (GOS) as prebiotic are the most suitable and therefore their commercial application is discussed.

Development of the gut microbiota in southern Indian infants from birth to 6 months: a molecular analysis

Acquisition of the gastrointestinal microbiota at birth may have long-term health impacts. We longitudinally characterised major microbial communities in the faeces of a cohort of infants using molecular methods. Faecal samples were prospectively obtained at several time points after birth from eighty-three infants. Real-time PCR using SYBR green and primers targeted at 16S rRNA gene sequences were used to quantify Bifidobacterium, Lactobacillus acidophilus group, Bacteroides–Prevotella group, Enterobacteriaceae, Enterococcus, Clostridium coccoides–Eubacterium rectale group, Clostridium leptum group and Staphylococcus. Microbial community abundance was expressed relative to amplification of sequences conserved universally for domain bacteria. Faecal copy number of 16S rRNA genes increased non-significantly from a mean of 4·1 × 10⁹/g on day 1 to 1·1 × 10¹⁰/g on day 4. All microbial communities were detected from day 1 after birth. Enterobacteriaceae and lactobacilli predominated on day 1, while bifidobacteria and staphylocci increased on day 4. Bacteroides–Prevotella and C. coccoides–E. rectale increased by day 180. C. leptum was detected in half of the cohort at birth and in a slightly larger percentage by 6 months. Caesarean section was associated with delayed colonisation by several bacterial communities. Higher socio-economic status was associated with more abundant lactobacilli and Bacteroides–Prevotella at 90 and 180 d. Supplemental feeding was associated with a reduction in Enterobacteriaceae. Microbial colonisation of the gut was well established on the first day of birth, and relative abundance of microbial communities was influenced by mode of delivery, socio-economic status and supplemental feeding. These findings may have relevance to infant nutrition and growth.

Lactobacillus acidophilus CRL 1014 improved "gut health" in the SHIME reactor

BACKGROUND

How to maintain "gut health" is a goal for scientists throughout the world. Therefore, microbiota management models for testing probiotics, prebiotics, and synbiotics have been developed.

METHODS

The SHIME model was used to study the effect of Lactobacillus acidophilus 1014 on the fermentation pattern of the colon microbiota. Initially, an inoculum prepared from human feces was introduced into the reactor vessels and stabilized over 2-wk using a culture medium. This stabilization period was followed by a 2-wk control period during which the microbiota was monitored. The microbiota was then subjected to a 4-wk treatment period by adding 5 mL of sterile peptone water with L. acidophilus CRL1014 at the concentration of 10⁸ CFU/mL to vessel one (the stomach compartment). Plate counts, Denaturing Gradient Gel Electrophoresis (DGGE), short-chain fatty acid (SCFA) and ammonium analyses were carried out for monitoring of the microbial community from the colon compartments.

RESULTS

A significant increase (p < 0.01) in the Lactobacillus spp. and Bifidobacterium spp. populations was observed during the treatment period. The DGGE obtained showed changes in the lactobacilli community from the colon compartments of the SHIME reactor. The (SCFA) concentration increased (p < 0.01) during the treatment period, due mainly to significant increased levels of acetic, butyric, and propionic acids. However, ammonium concentrations decreased during the same period (p < 0.01).

CONCLUSIONS

This study showed the beneficial influence of L. acidophilus CRL 1014 on microbial metabolism and lactobacilli community composition for improving human health.

Novel probiotic dissolvable carboxymethyl cellulose films as oral health biotherapeutics: in vitro preparation and characterization

OBJECTIVES

Oral health is influenced by the mouth's resident microorganisms. Dental caries and periodontitis are oral disorders caused by imbalances in the oral microbiota. Probiotics have potential for the prevention and treatment of oral disorders. Current formulations, including supplements and foods, have limitations for oral delivery including short storage time, low residence time in the mouth, effects on food consistency, and low patient compliance. Oral thin films (OTFs) may be efficient in delivering probiotics to the mouth. This research aims to develop a novel carboxymethyl cellulose (CMC)-probiotic-OTF to deliver probiotics for the treatment/prevention of oral disorders.

METHODS

CMC-OTFs were developed with varying CMC concentration (1.25 - 10 mg/mL), weight (5 - 40 g), thickness (16 - 262 μm), hygroscopicity (30.8 - 78.9 mg/cm(2) film), and dissolving time (135 - 600 s). The 10 g 5 mg/mL CMC-OTF was selected and used to incorporate Lactobacillus fermentum NCIMB 5221 (6.75 × 10(8) cells/film), a probiotic with anti-inflammatory potential for periodontitis treatment and capable of inhibiting microorganisms responsible for dental caries and oral candidiasis.

RESULTS

The CMC-OTF maintained probiotic viability and antioxidant activity following 150 days of storage with a production of 549.52 ± 26.08 μM Trolox equivalents.

CONCLUSION

This research shows the successful development and characterization of a novel probiotic-CMC-OTF with potential as an oral health biotherapeutic.

Oral administration of Lactobacillus reuteri GMNL-263 improves insulin resistance and ameliorates hepatic steatosis in high fructose-fed rats

BACKGROUND

Type 2 diabetes mellitus (DM), characterized by peripheral insulin resistance, is the most common form of diabetes. Probiotics are live micro-organisms that, when administered in adequate amounts, confer delaying effect on DM development. In this study, the effects Lactobacillus reuteri GMNL-263 (Lr263), a new probiotic strain developed by our laboratory, on insulin resistance and the development of hepatic steatosis in high-fructose fed rats were explored. Furthermore, the relevant regulatory pathways involved were also investigated.

METHOD

Male Sprague-Dawley rats were fed a high-fructose diet with or without Lr263 administration for 14 weeks. The composition of fecal microbiota, oral glucose tolerance, glycated haemoglobin, insulin, leptin, C-peptide, and incretins were measured. The markers of liver injury, serum and hepatic lipids profile, activity of hepatic antioxidant enzyme, and proinflammatory cytokines in adipose tissue were investigated. Additionally, the expression of hepatic lipogenic genes and insulin signaling related genes in adipose tissue were also studied. Liver sections were examined for hepatic steatosis using hematoxylin-eosin staining.

RESULTS

The levels of serum glucose, insulin, leptin, C-peptide, glycated hemoglobin, GLP-1, liver injury markers, lipid profile in serum and liver were significantly increased in high-fructose-fed rats. However, after Lr263 administration, the elevation of these parameters was significantly suppressed. Feeding of Lr263 reversed the decreased number of bifidobacterium species and lactobacillus species and increased number of clostridium species induced by high fructose treatment. The decreased activities of hepatic antioxidant enzymes in HFD rats were dramatically reversed by Lr263 treatment. Concentrations of IL-6 and TNF-α in adipose tissue which were elevated in high fructose treatment were markedly decreased after Lr263 feeding. Decreased levels of PPAR-γ and GLUT4 mRNA after high fructose treatment were significantly enhanced by Lr263 administration. Lr263 consumption normalized the increased lipogenic gene (Srebp-1c, FAS, and Elvol6) expressions stimulated by high fructose. Administration of Lr263 significantly ameliorated hepatic steatosis observed in high fructose treated rats.

CONCLUSION

Our study provided evidences clarifying the effectiveness of Lr263 on reducing insulin resistance as well as hepatic steatosis formation in high-fructose-fed rats and suggested that Lr263 may be a promising therapeutic agent in treating type 2 diabetes.

Effect of dietary monosaccharides on Pseudomonas aeruginosa virulence

BACKGROUND

Pseudomonas aeruginosa is an opportunistic, gram-negative pathogen associated with many hospital-acquired infections and disease states. In particular, P. aeruginosa has been identified as a crucial factor in the pathogenesis of neonatal necrotizing enterocolitis (NEC). This condition presents more frequently in infants fed a formula-based diet, which may be a result of the specific monosaccharide content of this diet. We hypothesized that P. aeruginosa would express virulence genes differentially when exposed to monosaccharides present in formula versus those in human milk.

METHODS

Using the results of a metabolomics study on infant diets and their resulting fecal samples, we identified several monosaccharides that distinguished milk from formula diets. Of these compounds, four were found to be metabolized by P. aeruginosa. We subsequently grew P. aeruginosa in tryptic soy broth (TSB) supplemented with these four monosaccharides and used quantitative reverse transcriptase-polymerase chain reaction to measure the expression of 59 major P. aeruginosa virulence genes. The results were standardized to an external control of P. aeruginosa grown in TSB alone.

RESULTS

P. aeruginosa did not respond differentially to the monosaccharides after 6 h of growth. However, after 24 h, the organism grown in arabinose (present in formula), xylose (present in human milk), and galactose (present in both formula and feces from milk-fed infants) displayed a significant increase in the expression of virulence genes in all categories. In contrast, P. aeruginosa grown in mannose (present in the feces of milk-fed infants) displayed a significant decrease in virulence gene expression.

CONCLUSION

These results demonstrate the importance of nutrient content on the relative expression of virulence genes in pathogens that colonize commonly the gut of infants. Understanding the effect of current dietary formulas on virulence gene expression in various gut-colonizing pathogens may present a new approach to elucidating the differences between human milk and formula in the development of NEC.

IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation

IBS is a prevalent functional gastrointestinal disorder, in which the microbiota has been demonstrated to play a role. An increasing number of studies have suggested how probiotics may alleviate IBS symptoms and several mechanisms of action have been proposed.   In the present study we characterized the intestinal microbiota of 19 subjects suffering from diagnosed IBS using a fully validated High Taxonomic Fingerprint Microbiota Array (HTF-Microbi.Array). We demonstrated that the IBS microbiota is different from that of healthy individuals due to an unbalance in a number of commensal species, with an increase in relative abundance of lactobacilli, B. cereus and B. clausii, bifidobacteria, Clostridium cluster IX and E. rectale, and a decrease in abundance of Bacteroides/Prevotella group and Veillonella genus. Additionally, we demonstrated that some bacterial groups of the human intestinal microbiota, recently defined as pathobionts, are increased in concentration in the IBS microbiota. Furthermore, we aimed at investigating if the daily administration of a novel probiotic yogurt containing B. animalis subsp lactis Bb12 and K. marxianus B0399, recently demonstrated to have beneficial effects in the management of IBS symptoms, could impact on the biostructure of IBS microbiota, modulating its composition to counteract putative dysbiosis found in IBS subjects. Notably, we demonstrated that the beneficial effects associated to the probiotic preparation are not related to significant modifications in the composition of the human intestinal microbiota.

Fermented milk supplemented with probiotics and prebiotics can effectively alter the intestinal microbiota and immunity of host animals

Fermented milk supplemented with 2 probiotic strains, Bifidobacterium lactis Bi-07 and Lactobacillus acidophilus NCFM, and a prebiotic, isomaltooligosaccharide, was orally administered to 100 healthy adults at 480 g/d for 2 wk in a randomized controlled trial. The fecal bacterial compositions of these subjects were examined by culture before and after the intervention. The same fermented milk was also orally fed to BALB/c mice, and immune as well as fecal bacteria analyses were conducted using the same culturing methods. After the intervention, increases in fecal bifidobacteria and lactobacilli were observed among the subjects compared with the subjects in the control group. In contrast, after the intervention, fecal enterobacilli were significantly decreased in the test group compared with the control group. The same effects on the composition of the intestinal microbiota were observed in mice. Furthermore, the tested mice were found to have significantly increased delayed-type hypersensitivity, plaque-forming cells, and half-hemolysis values after the intervention with the fermented milk. In summary, the synbiotic fermented milk containing probiotics and a prebiotic may contribute to improve intestinal health and may have a positive effect on the humoral and cell-mediated immunity of host animals.

Cholesterol lowering with bile salt hydrolase-active probiotic bacteria, mechanism of action, clinical evidence, and future direction for heart health applications

INTRODUCTION

Cardiovascular diseases (CVD) are the leading cause of global mortality and morbidity. Current CVD treatment methods include dietary intervention, statins, fibrates, niacin, cholesterol absorption inhibitors, and bile acid sequestrants. These formulations have limitations and, thus, additional treatment modalities are needed. Probiotic bacteria, especially bile salt hydrolase (BSH)-active probiotic bacteria, have demonstrated cholesterol-lowering efficacy in randomized controlled trials.

AREAS COVERED

This review describes the current treatments for CVD and the need for additional therapeutics. Gut microbiota etiology of CVD, cholesterol metabolism, and the role of probiotic formulations as therapeutics for the treatment and prevention of CVD are described. Specifically, we review studies using BSH-active bacteria as cholesterol-lowering agents with emphasis on their cholesterol-lowering mechanisms of action. Potential limitations and future directions are also highlighted.

EXPERT OPINION

Numerous clinical studies have concluded that BSH-active probiotic bacteria, or products containing them, are efficient in lowering total and low-density lipoprotein cholesterol. However, the mechanisms of action of BSH-active probiotic bacteria need to be further supported. There is also the need for a meta-analysis to provide better information regarding the therapeutic use of BSH-active probiotic bacteria. The future of BSH-active probiotic bacteria most likely lies as a combination therapy with already existing treatment options.

'Someone should oversee it': patient perspectives on the ethical issues arising with the regulation of probiotics

BACKGROUND

Although many probiotic products are currently available in yogurt or pill form in the United States (US), there is uncertainty surrounding the structure of regulation of these products. As more therapeutic probiotics are developed, changes to existing regulatory process in the United States may be required to meet the needs of patients and users in the population.

OBJECTIVE

This study examined how patients with chronic gastrointestinal (GI) diseases view the regulation of probiotics.

DESIGN

We conducted a multi-site qualitative study consisting of focus groups of patients with chronic gastrointestinal diseases at three tertiary hospitals: at [institutions removed for blinded review].

RESULTS

We conducted 22 focus groups with 136 patients with major gastrointestinal (GI) diseases between March and August 2009. Participants were not familiar with the existing regulation of probiotic products but wanted assurances of accurate labelling of strain as well as safety. Participants raised concerns that regulation of probiotics might be accompanied by greater costs, reduced access and increased involvement of pharmaceutical companies. Although participants voiced significant doubt of government regulators, they felt that products containing genetically modified probiotic strains should have oversight comparable to that of pharmaceutical drugs.

DISCUSSION AND CONCLUSION

If GI patient perspectives are indicative of public perceptions of therapeutic probiotics in the United States, consumers may expect more rigorous regulation in the future while simultaneously wanting low costs, easy access and low involvement of pharmaceutical companies. Manufacturers, translational scientists, clinicians and regulators should be sensitive to consumer attitudes when designing, testing and regulating new therapeutic probiotics.

Genotoxicity of Escherichia coli Nissle 1917 strain cannot be dissociated from its probiotic activity

Oral administration of the probiotic bacterium Escherichia coli Nissle 1917 improves chronic inflammatory bowel diseases, but the molecular basis for this therapeutic efficacy is unknown. E. coli Nissle 1917 harbors a cluster of genes coding for the biosynthesis of hybrid nonribosomal peptide-polyketide(s). This biosynthetic pathway confers the ability for bacteria to induce DNA double strand breaks in eukaryotic cells. Here we reveal that inactivation of the clbA gene within this genomic island abrogated the ability for the strain to induce DNA damage and chromosomal abnormalities in non-transformed cultured rat intestinal epithelial cells but is required for the probiotic activity of E. coli Nissle 1917. Thus, evaluation of colitis severity induced in rodent fed with E. coli Nissle 1917 or an isogenic non-genotoxic mutant demonstrated the need for a functional biosynthetic pathway both in the amelioration of the disease and in the modulation of cytokine expression. Feeding rodents with a complemented strain for which genotoxicity was restored confirmed that this biosynthetic pathway contributes to the health benefits of the probiotic by modulating its immunomodulatory properties. Our data provide additional evidence for the benefit of this currently used probiotic in colitis but remind us that an efficient probiotic may also have side effects as any other medication.

Nutritional genomics for the characterization of the effect of bioactive molecules in lipid metabolism and related pathways

Cardiovascular disease and cancer are the main causes of morbidity and mortality worldwide. Thus, investigators have focused their efforts on gaining insight into understanding the mechanisms involved in the development and evolution of these diseases. In the past decade, and with the contribution of the -omics technologies, strong evidence has supported an essential role of gene-nutrient interactions in these processes, pointing at natural bioactive molecules as promising complementary agents that are useful in preventing or mitigating these diseases. In addition, alterations in lipid metabolism have recently gained strong interest since they have been described as a common event required for the progression of both diseases. In the present review, we give an overview of lipid metabolism, mainly focusing on lipoprotein metabolism and the mechanisms controlling lipid homeostasis. In addition, we review the modulation of lipid metabolism by bioactive molecules, highlighting their potential use as therapeutic agents in preventing, and treating chronic diseases such as cardiovascular disease and cancer. Finally, we report the usefulness of the -omics technologies in nutritional research, focusing on recent findings, within nutritional genomics, in the interaction of bioactive components from foods with several genes that are involved in the development and progression of these diseases.

Probiotics for infectious diseases: more drugs, less dietary supplementation

According to current definitions, probiotics are live microorganisms that, when ingested in adequate quantities, exert a health benefit to the host. The action of probiotics in the host is exerted by three mechanisms: modulation of the content of gut microbiota; maintenance of the integrity of the gut barrier and prevention of bacterial translocation; and modulation of the local immune response by the gut-associated immune system. Regarding their role for the prevention and treatment of infectious diseases, adequate evidence coming from randomised clinical trials (RCTs) is available for antibiotic-associated diarrhoea (AAD), Clostridium difficile infection (CDI), acute gastroenteritis and infectious complications following admission to the Intensive Care Unit (ICU). Existing evidence supports their role for decreasing the incidence of AAD and CDI when administered in parallel with antimicrobials. They also shorten the duration of symptoms when administered in paediatric populations with acute gastroenteritis, particularly of rotavirus aetiology. Available evidence is not sufficient to support administration for the management of CDI. Regarding populations of critically ill patients, data from many RCTs suggest a decrease of infectious complications by starting feeding with probiotics following ICU admission, with the exception of patients suffering from severe pancreatitis. However, it should be underscored that all analysed RCTs are characterised by marked heterogeneity regarding the type of administered probiotic species, precluding robust recommendations.

Probiotics and Immune Response to Exercise

Probiotics are live microorganisms present in several foods and nutritional supplements that may prevent or limit the effects of various illnesses and infections and elicit a range of health benefits in physically active individuals. The primary clinical areas of interest with probiotics include metabolism; gastrointestinal, inflammatory, and functional disorders; the respiratory system; and a range of infections and allergies. The gastrointestinal tract is a key element controlling and regulating adaptation to exercise and physical activity. Gut symptomatology such as nausea, bloating, cramping, pain, diarrhea, and bleeding occurs in some highly active individuals such as athletes, particularly in prolonged exhaustive events. A small number of studies examining probiotic supplementation in highly active individuals indicate modest clinical benefits in terms of reduced frequency, severity, and/or duration of respiratory and gastrointestinal illness. The purported mechanisms of action for probiotics include direct interaction with the gut microbiota, interaction with the gut epithelium and mucosal immune system, and via immune signaling to organs and systems including the liver, brain, and respiratory tract. Future research will identify additional biologically and clinically beneficial strains, validate multicomponent formulations, clarify dose–response issues, and inform the development of guidelines for clinicians, health care practitioners, and the general community.

Enzymology and structure of the GH13_31 glucan 1,6-α-glucosidase that confers isomaltooligosaccharide utilization in the probiotic Lactobacillus acidophilus NCFM

Isomaltooligosaccharides (IMO) have been suggested as promising prebiotics that stimulate the growth of probiotic bacteria. Genomes of probiotic lactobacilli from the acidophilus group, as represented by Lactobacillus acidophilus NCFM, encode α-1,6 glucosidases of the family GH13_31 (glycoside hydrolase family 13 subfamily 31) that confer degradation of IMO. These genes reside frequently within maltooligosaccharide utilization operons, which include an ATP-binding cassette transporter and α-glucan active enzymes, e.g., maltogenic amylases and maltose phosphorylases, and they also occur separated from any carbohydrate transport or catabolism genes on the genomes of some acidophilus complex members, as in L. acidophilus NCFM. Besides the isolated locus encoding a GH13_31 enzyme, the ABC transporter and another GH13 in the maltooligosaccharide operon were induced in response to IMO or maltotetraose, as determined by reverse transcription-PCR (RT-PCR) transcriptional analysis, suggesting coregulation of α-1,6- and α-1,4-glucooligosaccharide utilization loci in L. acidophilus NCFM. The L. acidophilus NCFM GH13_31 (LaGH13_31) was produced recombinantly and shown to be a glucan 1,6-α-glucosidase active on IMO and dextran and product-inhibited by glucose. The catalytic efficiency of LaGH13_31 on dextran and the dextran/panose (trisaccharide) efficiency ratio were the highest reported for this class of enzymes, suggesting higher affinity at distal substrate binding sites. The crystal structure of LaGH13_31 was determined to a resolution of 2.05 Å and revealed additional substrate contacts at the +2 subsite in LaGH13_31 compared to the GH13_31 from Streptococcus mutans (SmGH13_31), providing a possible structural rationale to the relatively high affinity for dextran. A comprehensive phylogenetic and activity motif analysis mapped IMO utilization enzymes from gut microbiota to rationalize preferential utilization of IMO by gut residents.

Properties of probiotic bacteria explored by proteomic approaches

The study of health-beneficial effects that probiotic bacteria can exert on humans and animals is at its beginning. Pending scientific questions include the identification of molecular markers of the health-promoting activity of specific strains, which may be used to select novel probiotic strains and to gain understanding of the mechanisms underlying their effects. In that perspective, the role of bacterial proteins must be evaluated, placing proteomics-based approaches at the core of the field. Until now, most proteomic analyses focused on the dynamics of abundant cytoplasmic proteins during adaptation of bacteria to conditions mimicking the gastro-intestinal tract environment. The development of in silico and experimental procedures allowing identification and quantification of surface-exposed and secreted proteins should boost our understanding of bacteria-host crosstalk.

Composition of the early intestinal microbiota: knowledge, knowledge gaps and the use of high-throughput sequencing to address these gaps

The colonization, development and maturation of the newborn gastrointestinal tract that begins immediately at birth and continues for two years, is modulated by numerous factors including mode of delivery, feeding regime, maternal diet/weight, probiotic and prebiotic use and antibiotic exposure pre-, peri- and post-natally. While in the past, culture-based approaches were used to assess the impact of these factors on the gut microbiota, these have now largely been replaced by culture-independent DNA-based approaches and most recently, high-throughput sequencing-based forms thereof. The aim of this review is to summarize recent research into the modulatory factors that impact on the acquisition and development of the infant gut microbiota, to outline the knowledge recently gained through the use of culture-independent techniques and, in particular, highlight advances in high-throughput sequencing and how these technologies have, and will continue to, fill gaps in our knowledge with respect to the human intestinal microbiota.

Nicotinamide, NAD(P)(H), and Methyl-Group Homeostasis Evolved and Became a Determinant of Ageing Diseases: Hypotheses and Lessons from Pellagra

Compartmentalized redox faults are common to ageing diseases. Dietary constituents are catabolized to NAD(H) donating electrons producing proton-based bioenergy in coevolved, cross-species and cross-organ networks. Nicotinamide and NAD deficiency from poor diet or high expenditure causes pellagra, an ageing and dementing disorder with lost robustness to infection and stress. Nicotinamide and stress induce Nicotinamide-N-methyltransferase (NNMT) improving choline retention but consume methyl groups. High NNMT activity is linked to Parkinson's, cancers, and diseases of affluence. Optimising nicotinamide and choline/methyl group availability is important for brain development and increased during our evolution raising metabolic and methylome ceilings through dietary/metabolic symbiotic means but strict energy constraints remain and life-history tradeoffs are the rule. An optimal energy, NAD and methyl group supply, avoiding hypo and hyper-vitaminoses nicotinamide and choline, is important to healthy ageing and avoids utilising double-edged symbionts or uncontrolled autophagy or reversions to fermentation reactions in inflammatory and cancerous tissue that all redistribute NAD(P)(H), but incur high allostatic costs.

Prebiotic fiber modulation of the gut microbiota improves risk factors for obesity and the metabolic syndrome

Prebiotic fibers are non-digestible carbohydrates that promote the growth of beneficial bacteria in the gut. Prebiotic consumption may benefit obesity and associated co-morbidities by improving or normalizing the dysbiosis of the gut microbiota. We evaluated the dose response to a prebiotic diet on the gut microbiota, body composition and obesity associated risk factors in lean and genetically obese rats. Prebiotic fibers increased Firmicutes and decreased Bacteroidetes, a profile often associated with a leaner phenotype. Bifidobacteria and Lactobacillus numbers also increased. Changes in the gut microbiota correlated with energy intake, glucose, insulin, satiety hormones, and hepatic cholesterol and triglyceride accumulation. Here we provide a comprehensive analysis evaluating the results through the lens of the gut microbiota. Salient, new developments impacting the interpretation and significance of our data are discussed. We propose that prebiotic fibers have promise as a safe and cost-effective means of modulating the gut microbiota to promote improved host:bacterial interactions in obesity and insulin resistance. Human clinical trials should be undertaken to confirm these effects.