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PubMed1999

Probiotics, prebiotics, and synbiotics: approaches for modulating the microbial ecology of the gut.

The microbiota of the human large intestine influences health and well-being. Whereas it has long been accepted that gut bacteria play a role in host pathogenesis, current opinion is that certain microflora components can have beneficial effects on gastroenteritis resistance, blood lipids, antitumor properties, lactose tolerance, and gastrointestinal immunity. It is postulated that in the infant gut an elevated bifidobacterial count may be associated with health advantages that breast-fed infants may have over formula-fed infants. Whereas beneficial aspects of the human gut flora still need definitive confirmation and mechanistic explanations, there is now interest in modulating the composition of gut flora such that a potentially more remedial community exists. This may be achieved through the targeted use of dietary supplementation. This article provides an overview of how probiotics, prebiotics, and synbiotics may contribute toward nutritional modulation of the gut microecology, with emphasis on the neonatal intestine where appropriate. The use of modern molecular methods, as an essential step forward for assessing the validity and accuracy of the modulatory approach, is also discussed.

Dietary Supplements↗

PubMed1988

Enumeration and isolation of cellulolytic and hemicellulolytic bacteria from human feces.

The fibrolytic microbiota of the human large intestine was examined to determine the numbers and types of cellulolytic and hemicellulolytic bacteria present. Fecal samples from each of five individuals contained bacteria capable of degrading the hydrated cellulose in spinach and in wheat straw pretreated with alkaline hydrogen peroxide (AHP-WS), whereas degradation of the relatively crystalline cellulose in Whatman no. 1 filter paper (PMC) was detected for only one of the five samples. The mean concentration of cellulolytic bacteria, estimated with AHP-WS as a substrate, was 1.2 X 10(8)/ml of feces. Pure cultures of bacteria isolated on AHP-WS were able to degrade PMC, indicating that interactions with other microbes were primarily responsible for previous low success rates in detecting fecal cellulolytic bacteria with PMC as a substrate. The cellulolytic bacteria included Ruminococcus spp., Clostridium sp., and two unidentified strains. The mean concentration of hemicellulolytic bacteria, estimated with larchwood xylan as a substrate, was 1.8 X 10(10)/ml of feces. The hemicellulose-degrading bacteria included Butyrivibrio sp., Clostridium sp., Bacteroides sp., and two unidentified strains, as well as four of the five cellulolytic strains. This work demonstrates that many humans harbor intestinal cellulolytic bacteria and that a hydrated cellulose source such as AHP-WS is necessary for their consistent detection and isolation.

Adult↗

PubMed1987

Cecectomy causes long-term reduction of colonization resistance in the mouse gastrointestinal tract.

Removal of the cecum from normal mice caused a major perturbation of the microbial ecology of the gastrointestinal tract. There was a permanent reduction in colonization resistance resulting in a 1,000-fold increase in the concentration of facultatively anaerobic coliform bacteria. The animals were significantly more susceptible to peroral challenge by the intestinal pathogen Salmonella enteritidis. Coincident with this increase in coliform counts and susceptibility to salmonellae was a decrease in the numbers of strictly anaerobic fusiform bacteria that dominate the rodent intestinal tract, resulting in reduced levels of acetic, propionic, and butyric acids. Cecectomized mice are likely to be a useful model for study of the interaction between intestinal pathogens and the normal microbiota and for studies of translocation of bacteria into host tissues after loss of colonization resistance.

Animals↗

PubMed2006

Comparative genomic hybridization analysis of Enterococcus faecalis: identification of genes absent from food strains.

Enterococcus faecalis, a member of the natural microbiota of animal and human intestinal tracts, is also present as a natural contaminant in a variety of fermented foods. Over the last decade, E. faecalis has emerged as a major cause of nosocomial infections. We investigated the genetic diversity in 30 clinical and food isolates, including strains V583 and MMH594, in order to determine whether clinical and food isolates could be distinguished. Data were obtained using comparative genomic hybridization and specific PCR with a total of 202 probes of E. faecalis, selected using the available V583 genome sequence and part of the MMH594 pathogenicity island. The cognate genes encoded mainly exported proteins. Hybridization data were analyzed by a two-component mixture model that estimates the probability of any given gene to be either present or absent in the strains. A total of 78 genes were found to be variable, as they were absent in at least one isolate. Most of the variable genes were clustered in regions that, in the published V583 sequence, related to prophages or mobile genetic elements. The variable genes were distributed in three main groups: (i) genes equally distributed between clinical and dairy food isolates, (ii) genes absent from dairy food-related isolates, and (iii) genes present in MMH594 and V583 strains only. Further analysis of the distribution of the last gene group in 70 other isolates confirmed that six of the probed genes were always absent in dairy food-related isolates, whereas they were detected in clinical and/or commensal isolates. Two of them corresponded to prophages that were not detected in the cognate isolates, thus possibly extending the number of genes absent from dairy food isolates. Genes specifically detected in clinical isolates may prove valuable for the development of new risk assessment markers for food safety studies and for identification of new factors that may contribute to host colonization or infection.

DNA, Bacterial↗

PubMed2001

[Functional constipation syndrome: experience in the use of sour milk products and biologically active food supplements in the complex treatment of patients].

Sour milk product "Bifeedock" and biologically-active food additives of "Litovite" and "Pektsecom" type are used in the overall treatment of functional constipation and accompanying colon disbacteriosis of I and II degree. They help to improve the clinical symptomatics and the functional state of the gastrointestinal tract. According to the data analysis, the elimination of the colon stasis results in the improved microbiocenosis expressed in the suppression of growth of conditionally pathogenic microflora. It also stimulates the growth of the symbiotic elements of microbiota (bifidobacteria, lactobacteria and the intestinal E. coli).

Adult↗

PubMed2023

Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum.

The beneficial effects attributed to Bifidobacterium are largely attributed to their immunomodulatory capabilities, which are likely to be species- and even strain-specific. However, their strain-specificity in direct and indirect immune modulation remain largely uncharacterized. We have shown that B. pseudolongum UMB-MBP-01, a murine isolate strain, is capable of suppressing inflammation and reducing fibrosis in vivo. To ascertain the mechanism driving this activity and to determine if it is specific to UMB-MBP-01, we compared it to a porcine tropic strain B. pseudolongum ATCC25526 using a combination of cell culture and in vivo experimentation and comparative genomics approaches. Despite many shared features, we demonstrate that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses signatures in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution. Importantly, the administration of each B. pseudolongum strain resulted in major divergence in the structure, composition, and function of gut microbiota. This was accompanied by markedly different changes in intestinal transcriptional activities, suggesting strain-specific modulation of the endogenous gut microbiota as a key to immune modulatory host responses. Our study demonstrated a single probiotic strain can influence local, regional, and systemic immunity through both innate and adaptive pathways in a strain-specific manner. It highlights the importance to investigate both the endogenous gut microbiome and the intestinal responses in response to probiotic supplementation, which underpins the mechanisms through which the probiotic strains drive the strain-specific effect to impact health outcomes.

Mice↗

PubMed1998

The colonization of a simulator of the human intestinal microbial ecosystem by a probiotic strain fed on a fermented oat bran product: effects on the gastrointestinal microbiota.

The effects of Lactobacillus-GG-fermented oat bran product on the microbiota and its metabolic activity in the human gut were investigated, using a simulator of the human intestinal microbial ecosystem (SHIME), by analysing the bacterial population, shortchain fatty acids and gas production. In addition, the effects of fermented oat bran supernatant and supernatant samples from reactors 4, 5 and 6 (large intestine) on the growth of Escherichia coli IHE 13047, Enterococcus faecalis VTT E-93203, Lactobacillus rhamnosus VTT E-94522 (Lactobacillus GG) and Lactococcus lactis subsp. lactis VTT E-90414 were monitored to ascertain possible stimulatory/inhibitory effects by an in vitro turbidometric method. Our experiments showed that Lactobacillus GG colonized the SHIME reactor and this colonization could be maintained for several weeks without extra supplementation. Oat bran feeding also favoured the growth of bifidobacteria and caused an increase in the production of acetic, propionic and butyric acid as well as CH4 and CO2. However, the effects of oat bran, either on bacterial populations or on their metabolic activity, were not directly dose-dependent. In turbidometric measurements, the supernatant of fermented oat bran exerted an inhibitory effect of Lactobacillus GG, but stimulated the growth of enterococci.

Avena↗

PubMed2026

Potential contribution of the microbiota-gut-brain axis to doxorubicin-associated cognitive impairment: Mechanisms, evidence, and therapeutic opportunities.

Chemotherapy-induced cognitive impairment (CICI), often termed chemobrain, is a clinically important complication of cancer treatment that can affect memory, attention, executive function, and processing speed during and after therapy. Doxorubicin is of particular mechanistic interest because brain parenchymal exposure is limited, yet preclinical studies consistently identify neuroinflammatory, oxidative, vascular, and synaptic abnormalities after treatment. This critical narrative review evaluates whether intestinal injury and disruption of the microbiota-gut-brain axis may contribute to these central effects. Preclinical evidence indicates that doxorubicin can alter microbial community structure, injure the intestinal barrier, modify SCFA-associated taxa or predicted functions, alter selected metabolite profiles, and promote systemic inflammatory and metabolic signaling. These peripheral changes could interact with brain endothelial cells, glia, mitochondria, hippocampal neurogenesis, and synaptic-plasticity pathways. However, the proposed doxorubicin-gut-brain pathway remains a predominantly preclinical and incompletely tested framework. No longitudinal human study has yet established, within the same patients, the temporal sequence linking doxorubicin exposure, microbiome or metabolome changes, systemic inflammation, and objective cognitive outcomes. Existing animal studies also vary in dose, regimen, tumor context, sampling time, microbiome methodology, and control of behavioral or microbiological confounders, while causal rescue experiments remain limited. Key priorities are therefore longitudinal human cohorts with pretreatment baselines and repeated multi-omics and cognitive assessments; animal studies that test temporal precedence and causal rescue or pathway blockade in the same model; mediation analyses that determine whether microbial or metabolic changes lie between treatment and cognitive dysfunction; and mechanism-informed clinical trials that demonstrate target engagement, cognitive benefit, oncology safety, and preservation of antitumor efficacy. Microbiome-directed interventions are promising but remain investigational for doxorubicin-associated CICI.

blood–brain barrier↗

PubMed2005

Microbial regulation of intestinal radiosensitivity.

We describe a method for treating germ-free (GF) mice with gamma-irradiation and transplanting them with normal or genetically manipulated bone marrow while maintaining their GF status. This approach revealed that GF mice are markedly resistant to lethal radiation enteritis. Furthermore, administering lethal doses of total body irradiation to GF mice produces markedly fewer apoptotic endothelial cells and lymphocytes in the mesenchymal cores of their small intestinal villi, compared with conventionally raised animals that have acquired a microbiota from birth. Analysis of GF and conventionally raised Rag1-/- mice disclosed that mature lymphocytes are not required for the development of lethal radiation enteritis or the microbiota-associated enhancement of endothelial radiosensitivity. Studies of gnotobiotic knockout mice that lack fasting-induced adipose factor (Fiaf), a fibrinogen/angiopoietin-like protein normally secreted from the small intestinal villus epithelium and suppressed by the microbiota, showed that Fiaf deficiency results in loss of resistance of villus endothelial and lymphocyte populations to radiation-induced apoptosis. Together, these findings provide insights about the cellular and molecular targets involved in microbial regulation of intestinal radiosensitivity.

Angiopoietin-Like Protein 4↗

PubMed2006

Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation.

All animals exist in intimate associations with microorganisms that play important roles in the hosts' normal development and tissue physiology. In vertebrates, the most populous and complex community of microbes resides in the digestive tract. Here, we describe the establishment of the gut microbiota and its role in digestive tract differentiation in the zebrafish model vertebrate, Danio rerio. We find that in the absence of the microbiota, the gut epithelium is arrested in aspects of its differentiation, as revealed by the lack of brush border intestinal alkaline phosphatase activity, the maintenance of immature patterns of glycan expression and a paucity of goblet and enteroendocrine cells. In addition, germ-free intestines fail to take up protein macromolecules in the distal intestine and exhibit faster motility. Reintroduction of a complex microbiota at later stages of development or mono-association of germ-free larvae with individual constituents of the microbiota reverses all of these germ-free phenotypes. Exposure of germ-free zebrafish to heat-killed preparations of the microbiota or bacterial lipopolysaccharide is sufficient to restore alkaline phosphatase activity but not mature patterns of Gal alpha1,3Gal containing glycans, indicating that the host perceives and responds to its associated microbiota by at least two distinct pathways.

Alkaline Phosphatase↗

PubMed2024

Dissecting the anti-obesity components of ginseng: How ginseng polysaccharides and ginsenosides target gut microbiota to suppress high-fat diet-induced obesity.

INTRODUCTION: Ginseng demonstrates therapeutic potential in treating obesity, with both experimental and clinical studies suggesting its anti-obesity effects are mediated by gut microbiota. Nonetheless, the specific chemical components responsible for this effect remain largely unidentified. OBJECTIVES: This study aims to investigate the anti-obesity effects and mechanisms of ginseng polysaccharides (GP) and ginsenosides (GS), the primary chemical components of ginseng, with a focus on their impact on gut microbiota. METHODS: The impact of GP and GS on high-fat diet (HFD)-induced obesity was assessed using a mouse model. Molecular mechanisms were explored through a combination of chemical analysis, metagenomics, RT-qPCR, ELISA, and biochemical assays. RESULTS: GP or GS administration effectively prevented adiposity in HFD-fed mice, and both effects were mediated by gut microbiota. Chemical analysis revealed diverse glycosyl groups in GP and GS. Metagenomics data suggested that GP-enriched species, e.g., Bacteroides stercorirosoris and Clostridiales bacterium encoded carbohydrate-active enzymes GH35, GH43 and PL9_1, while GS-enriched Sulfurospirillum halorespirans encoded GH16_5. These enzymes facilitated the utilization of glycosyl groups in GP and GS, selectively stimulating bacterial growth and reshaping the gut microbiota. Furthermore, bacterial species enriched by GP or GS encoded specific functional genes involved in short-chain fatty acid (SCFA) synthesis (K00625 and K00925 for GP; K18118, K00100, and K18122 for GS) and intestinal gluconeogenesis (IGN) (K01678, K00024, and K01596 for GP; K18118 and K00278 for GS). Consequently, the SCFA-GLP-1/PYY signaling and IGN were activated by both GP and GS to ameliorate obesity phenotypes. CONCLUSION: GP and GS, containing diverse glycosyl groups, selectively stimulate specific gut bacteria, triggering mechanisms involved in SCFA-GLP-1/PYY signaling and IGN activation to reduce adiposity in HFD-fed mice. The study enhances understanding of the chemical components crucial for the gut microbiota-mediated anti-obesity effect of ginseng. The mechanistic understanding provides valuable insights for developing ginseng-based drugs or health products to combat obesity.

Gastrointestinal Microbiome↗

PubMed2003

Development and validation of a nested-PCR-denaturing gradient gel electrophoresis method for taxonomic characterization of bifidobacterial communities.

The taxonomic characterization of a bacterial community is difficult to combine with the monitoring of its temporal changes. None of the currently available identification techniques are able to visualize a "complete" community, whereas techniques designed for analyzing bacterial ecosystems generally display limited or labor-intensive identification potential. This paper describes the optimization and validation of a nested-PCR-denaturing gradient gel electrophoresis (DGGE) approach for the species-specific analysis of bifidobacterial communities from any ecosystem. The method comprises a Bifidobacterium-specific PCR step, followed by purification of the amplicons that serve as template DNA in a second PCR step that amplifies the V3 and V6-V8 regions of the 16S rRNA gene. A mix of both amplicons is analyzed on a DGGE gel, after which the band positions are compared with a previously constructed database of reference strains. The method was validated through the analysis of four artificial mixtures, mimicking the possible bifidobacterial microbiota of the human and chicken intestine, a rumen, and the environment, and of two fecal samples. Except for the species Bifidobacterium coryneforme and B. indicum, all currently known bifidobacteria originating from various ecosystems can be identified in a highly reproducible manner. Because no further cloning and sequencing of the DGGE bands is necessary, this nested-PCR-DGGE technique can be completed within a 24-h span, allowing the species-specific monitoring of temporal changes in the bifidobacterial community.

Animals↗

PubMed2005

Reproducing the bifidogenic effect of human milk in formula-fed infants: why and how?

Awareness of the key role of the intestinal microflora in the generation of the immunophysiological regulation and in the defence against pathogenic agents has attracted our interest in ways of manipulating the microbiota to improve health. Dietary modulation of the intestinal microflora is today one of the main topics of interest in the nutritional sciences. Performing this modulation in the neonatal or early infancy period, when immunological programming takes place, is a relatively new concept. Fructo-oligosaccharides (FOS) and galacto-oligosaccharides (GOS) are prebiotics whose bifidogenic activity has been proven in adults. However, only recently have they been combined in infant formulas to reproduce the prebiotic effect of human milk oligosaccharides. In two consecutive trials, it has been demonstrated that supplementation of infant formulas with a mixture of GOS and FOS modified the fecal flora of term and preterm infants, stimulating the growth of Bifidobacteria. In the trial with term infants, the bifidogenic effect of the prebiotic mixture was dose dependent and there was also a significant increase in the number of Lactobacilli in the supplemented group. These findings offer a promising horizon for the early prevention of allergy and infections in infants.

Bifidobacterium↗

PubMed2024

Deficiency of IL-22-binding protein enhances the ability of the gut microbiota to protect against enteric pathogens.

Interleukin 22 (IL-22) promotes intestinal barrier integrity, stimulating epithelial cells to enact defense mechanisms against enteric infections, including the production of antimicrobial peptides. IL-22 binding protein (IL-22BP) is a soluble decoy encoded by the Il22ra2 gene that decreases IL-22 bioavailability, attenuating IL-22 signaling. The impact of IL-22BP on gut microbiota composition and functioning is poorly understood. We found that Il22ra2-/- mice are better protected against Clostridioides difficile and Citrobacter rodentium infections. This protection relied on IL-22-induced antimicrobial mechanisms before the infection occurred, rather than during the infection itself. Indeed, the gut microbiota of Il22ra2-/- mice mitigated infection of wild-type (WT) mice when transferred via cohousing or by cecal microbiota transplantation. Indicator species analysis of WT and Il22ra2-/- mice with and without cohousing disclosed that IL22BP deficiency yields a gut bacterial composition distinct from that of WT mice. Manipulation of dietary fiber content, measurements of intestinal short-chain fatty acids and oral treatment with acetate disclosed that resistance to C. difficile infection is related to increased production of acetate by Il22ra2-/--associated microbiota. Together, these findings suggest that IL-22BP represents a potential therapeutic target for those at risk for or with already manifest infection with this and perhaps other enteropathogens.

Animals↗

PubMed2006

Analysis of treatment effects on the microbial ecology of the human intestine.

A large number of studies have investigated gastrointestinal microbiota and changes in the gastrointestinal community. However, a concern in these studies is how best to assess changes in gastrointestinal community structure. This paper presents two different human trials where the fecal terminal restriction fragment length polymorphism data sets were analyzed to search for treatment effects. Principle components analysis and cluster analysis based on grouped data are compared with analysis of data by subject using distance coefficients. Comparison with baseline within an individual before grouping by treatment provided a clearer indication of treatment effects than did an evaluation of data grouped before analysis. In addition, a large within-subject sample size and multiple baseline samples are necessary to accurately analyze treatment effects.

Adult↗

PubMed1986

Mucus colonization as a determinant of pathogenicity in intestinal infection by Campylobacter jejuni: a mouse cecal model.

Human isolates of the intestinal pathogen Campylobacter jejuni have been shown to colonize mucus on the outer surface and deep within the intestinal crypts of gnotobiotic or germfree mice. The cecal crypts are preferentially colonized. A model of mucus colonization by C. jejuni in the mouse cecum has been developed, using antibiotic- and magnesium sulfate-treated specific-pathogen-free animals. These spiral-shaped bacteria colonize the mucus in a similar manner to the normal spiral-shaped microbiota. No evidence of adhesion to the intestinal surface was found with a wide variety of microscopic techniques. The campylobacters were seen to be highly motile in living preparations of gut tissue and rapidly tracked along intestinal mucus. Just as many of the normal spiral-shaped bacteria of intestinal surfaces can achieve close association with the epithelium through mucus association and do not adhere to the surface, C. jejuni colonizes the intestinal mucosa via mucus colonization. Thus, a major determinant of pathogenicity in intestinal infection with C. jejuni is proposed to be an ability to colonize intestinal mucus. The possession of specific adhesins is unlikely to be a significant determinant of pathogenicity. Better understanding of the mechanism of mucus association and the properties of the bacterium that are responsible will provide a basis for the rational selection of preventative measures. The model of mucus association in adult antibiotic-treated mice provides an opportunity for colonization studies with variant organisms and immunization studies.

Adhesiveness↗

PubMed1988

Stability of enterocytes and certain enzymatic activities in suspensions of cells from the villous tip to the crypt of Lieberkühn of the mouse small intestine.

A series of studies in this laboratory have focused on how an indigenous microbiota influences the activities of alkaline phosphatase, phosphodiesterase I, and thymidine kinase in the enterocytes of the upper small intestine of mice. To draw conclusions about the role of the microflora in determining levels of enzymatic activity, we found it necessary to develop a procedure by which cell suspensions could be obtained containing enterocytes isolated sequentially from the villous tip to the crypt of Lieberkühn. The procedure was modified from the one developed for rats by Weiser (J. Biol. Chem. 248:2536-2541, 1973), involved a minimum number of interfering factors (e.g., proteolytic enzymes and mechanical agitation), and worked reproducibly for mice. During development of the procedure, some variables affecting the assays of the enzymes known to be present in enterocytes were also explored. Rods to which were tied everted segments of gut were incubated in a series of tubes containing a solution of EDTA the concentration of which was changed from 1.5 to 5.0 mM, thus giving a greater yield of enterocytes at every step. The cells incubating in the chelating solution were most stable when 0.23 M sucrose was included in the EDTA solutions. Success in assaying enzymatic activities in the cell suspensions depended on (i) how the cells were isolated, (ii) the assay procedure for thymidine kinase, and (iii) whether cellular suspensions or extracts were assayed.

Alkaline Phosphatase↗

PubMed2004

Message from a human gut symbiont: sensitivity is a prerequisite for sharing.

Microbial genome sequencing projects are beginning to provide insights about the molecular foundations of human-bacterial symbioses. The intestine contains our largest collection of symbionts, where members of Bacteroides comprise approximately 25% of the microbiota in adults. The recently defined proteome of a prominent human intestinal symbiont, Bacteroides thetaiotaomicron, contains an elaborate environmental-sensing apparatus. This apparatus includes an unprecedented number of extracytoplasmic function (ECF) sigma-factors, and a large collection of novel hybrid two-component systems composed of membrane-spanning periplasmic proteins with histidine kinase, phosphoacceptor, response regulator receiver and DNA-binding domains. These sensors are linked to the organism's large repertoire of genes involved in acquiring and processing dietary polysaccharides ('the glycobiome'). This arrangement illustrates how a successful symbiont has evolved strategies for detecting and responding to conditions in its niche so that it can sustain beneficial relationships with its microbial and human partners.

Amino Acid Sequence↗