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PubMed2006

Identification of dominant bacteria in feces and colonic mucosa from healthy Spanish adults by culturing and by 16S rDNA sequence analysis.

The aim of this work was to examine by culturing the changes in the total and indicator populations of the feces of two individuals over 1 year and to identify the dominant microbial components of a single sample of feces from each donor. Populations and dominant bacteria from a sample of colonic mucosa from a further individual were also assessed. The culture results were then compared to those obtained with the same samples by 16S rDNA cloning and sequencing. High interindividual variation in representative microbial populations of the gastrointestinal tract (GIT) was revealed by both the culture and the culture-independent techniques. Species belonging to Clostridium clusters (XIVa, IV, and XVIII) predominated in both the fecal and the mucosal samples (except in the mucose cultured isolates), members of Clostridium coccoides cluster XIVa being the most numerous microorganisms. Species of gamma-proteobacteria (Escherichia coli and Shigella spp.), bifidobacteria, and actinobacteria appeared in lower numbers than those of clostridia. From the mucosal cultured sample, only facultative anaerobes and bifidobacteria were recovered, suggesting destruction of the anaerobe population during processing. In accordance with this, the microbial diversity revealed by 16S rDNA sequence analysis was greater than that revealed by culturing. Despite large interindividual differences, distinct human communities may have group-associated GIT microbiota characteristics, such as the low number of Bacteroides seen in the subjects in this study.

Adult↗

PubMed2005

Probiotic potential of 3 Lactobacilli strains isolated from breast milk.

Breast milk is an important factor in the initiation, development, and composition of the neonatal gut microbiota. In a previous study, the authors isolated lactic acid bacteria from milk of healthy mothers. Since some of the identified isolates belonged to the genus Lactobacillus, the objective of this work was to evaluate the probiotic potential of 2 Lactobacillus gasseri and 1 Lactobacillus fermentum strains. Different assays, including survival to conditions simulating those existing in the gastrointestinal tract, production of antimicrobial compounds, adherence to intestinal cells, production of biogenic amines, degradation of mucin, enzymatic profile, and pattern of antibiotic resistance, were performed. Globally, the results showed that the probiotic potential of lactobacilli isolated from milk of healthy mothers is, at least, similar to that of the strains commonly used in commercial probiotic products. This fact, together with the presence of prebiotic substances, indicates that breast milk is a natural synbiotic food.

Adult↗

PubMed2002

Inventing probiotic functional foods for patients with allergic disease.

OBJECTIVE: The primary objective of this review is to discuss the rationale for and applicability of probiotics as part of the nutritional approach to the prevention and management of allergic disease. DATA SOURCES: This review represents a synthesis of recent literature published in the fields of probiotics, nutrition, and allergic disease. STUDY SELECTION: The expert opinions of the authors were used to select the relevant data for the review. RESULTS: The hygiene hypothesis suggests that allergic disease may arise from a lack of counterbalancing microbial exposure at an early age. Thus, the initial compositional development of gut microbiota is considered a key determinant in the development of both the immune responder phenotype and the normal gut barrier functions. A wide range of data documents the specific actions of selected probiotics. The regulatory role of probiotics in allergic disease has been demonstrated as improving the clinical course or preventing the development of atopic eczema in infants given a probiotic-supplemented diet. In addition, certain types of fatty acids and antioxidants have been proposed for protective effects against the development of allergy and to diminish the inflammatory response in allergic disease. CONCLUSIONS: The increase in the prevalence of allergic disease during the past decades is likely to be explained by changes in the environment, including reduced microbial exposure and altered food consumption. Scientifically composed functional foods containing probiotics and other functional components offer a nutritional strategy for both the prevention and the management of allergic disease. Further research is needed to characterize the gut microbiota and to clarify the mechanisms of action that control specific physiologic processes not only in the evolution of allergic disease in at-risk populations but also in the management of allergic diseases.

Complementary Therapies↗

PubMed2005

Toll-like receptors-2, -3 and -4 expression patterns on human colon and their regulation by mucosal-associated bacteria.

The colonic epithelium provides an interface between the host and micro-organisms colonising the gastrointestinal tract. Molecular recognition of bacteria is facilitated through Toll-like receptors (TLR). The colonic epithelium expresses relatively high levels of mRNA for TLR3 and less for TLR2 and -4. Little is known of the expression patterns and mode of induction of expression for these pattern recognition receptors in human colon. The aim of this study was to investigate their localization in the gut and induction of expression in epithelial cell lines by mucosal bacteria. TLR2 and -4 were expressed only in crypt epithelial cells, expression was lost as the cells matured and moved towards the gut lumen. In contrast, TLR3 was only produced in mature epithelial cells. HT29 and CACO-2 had different levels of expression for TLR1-4. Co-culture of HT29 cells with different mucosal isolates showed that they were highly responsive to bacterial challenge, with up-regulation of mRNA for TLR1-4. In contrast, CACO-2 cells were refractive to bacterial challenge, showing little difference in mRNA levels. TLR3 was induced in HT29 only by Gram-positive commensals with up-regulation of both mRNA and protein and an enhancement of the antiviral immune response. This pattern of expression allows induction of responsiveness to bacteria only by the crypt epithelium so that tolerance to commensal organisms can be maintained. In contrast, mature columnar epithelium is able to respond to viral pathogens, which are not part of the normal gut commensal microbiota.

Bacteroides fragilis↗

PubMed2006

Specific amino acids increase mucin synthesis and microbiota in dextran sulfate sodium-treated rats.

During the anabolic response associated with inflammation, mucin synthesis and colonic protection may be compromised by the limited availability of specific amino acids. We therefore determined the effect of dietary amino acid supplementation on the microbiota, mucin status, and mucosal damage in dextran sulfate sodium (DSS)-treated rats. From 8 d before to 28 d after colitis induction, male Sprague-Dawley rats (10 mo old, n = 8/group) were fed a control diet supplemented or not with 2 different doses of an amino acid cocktail containing L-threonine, L-serine, L-proline, and L-cysteine. All diets were isonitrogenous (adjusted with L-alanine). The higher dose of amino acids increased the number of Muc2-containing goblet cells in the surface epithelium of the ulcerated area, stimulated mucin production in the colon, and restored the mucin amino acid composition and mucosal content to healthy, control values. The colonic mucin synthesis rate was specifically stimulated by 95%, whereas the protein turnover was unchanged. All bacterial populations, markedly altered by the DSS treatment, were promoted. In conclusion, in inflammatory situations, an increase in threonine, serine, proline, and cysteine dietary supply can promote mucin synthesis, reequilibrate the gut microbiota, and thus favor colonic protection and mucosal healing.

Amino Acids↗

PubMed1988

Influence of indigenous microbiota on activities of alkaline phosphatase, phosphodiesterase I, and thymidine kinase in mouse enterocytes.

An indigenous microflora introduced into the gastrointestinal tracts of animals in a population of germfree mice affected in different ways three enzymes in small bowel enterocytes. Cells were obtained by techniques designed for sequentially removing enterocytes from the tip of the villus to the crypts of Lieberkühn. The specific activity of alkaline phosphatase, a component of the enterocyte microvillous membrane, did not differ in cells isolated from germfree mice and from those associated with a microflora, while that of phosphodiesterase I, also a part of the microvillous membrane, was approximately 1.5-fold greater in the suspensions from all levels of the villi in germfree mice than in those from the associated animals. By contrast, the specific activity of thymidine kinase, a cytosol enzyme, in suspensions in which the cells were isolated from the lower portion of the villi and crypts was about one-half as great in cells from germfree mice as in those from the same regions of animals with a microbiota. These results support the hypothesis that activities of certain enzymes involved in metabolism, uptake, and incorporation by enterocytes of components of dietary nuclei acids are influenced by a microflora.

Alkaline Phosphatase↗

PubMed2006

Comparison of antagonistic ability against enteropathogens by G+ and G- anaerobic dominant components of human fecal microbiota.

To confirm if anaerobic G+-components are those responsible for the function of colonization resistance, obligate anaerobic G+- and G- -bacteria from normal dominant microbiota of human feces were isolated from three successive collections and then used in in vitro assays for antagonism against two enteropathogenic bacteria. The production of inhibitory diffusible compounds was determined on supplemented BHI agar and MRS agar media for G- - and G+-bacteria, respectively. Salmonella enterica subsp. enterica serovar Typhimurium and Shigella sonnei were used as indicators. G+-bacteria presented a higher overall antagonistic frequency against both pathogenic bacteria (57 and 64 % for S. enterica serovar Typhimurium and S. sonnei, respectively) when compared to G+-microorganisms but with a quite elevated variation between volunteers (0-100 %) and collection samples (40-72 and 40-80 % for S. enterica sv. Typhimurium and S. sonnei, respectively). On the other hand, only three among 143 G- -isolates tested showed antagonistic activity. The results showed that, at least in vitro, obligate anaerobic G+-components of the dominant human fecal microbiota present a higher potential for antagonism against the enteropathogenic models tested than do G- -bacteria.

Adult↗

PubMed2026

Multi-omics insights into the physiological mechanisms of bile acid accumulation in the gallbladder in brumation-like snakes.

Hibernation/brumation represents an important physiological adaptation for animals to cope with seasonal environmental changes. Field observations suggested increased gallbladder weight in the Five-pacer viper (Deinagkistrodon acutus) during brumation, and our quantitative measurements confirmed this increase together with bile acid accumulation. By integrating a multi-omic approach, this study elucidates the regulatory mechanisms of bile acid accumulation in the gallbladder during brumation. Results showed that taurocholic acid (TCA) and taurodeoxycholic acid (TDCA) were the major components in the gallbladder of the brumation-like group, with significantly elevated concentrations of bile acids, whereas bile acid concentrations in serum and intestinal contents were markedly reduced, indicating suppression of the enterohepatic circulation and consequent accumulation of bile acids in the gallbladder. Hepatic transcriptomic analysis revealed significant downregulation of bile acid synthesis and regulatory genes in brumation-like snakes. In contrast, the alternative synthesis pathway gene sterol 27-hydroxylase (CYP27A1) and some transporter genes were slightly upregulated. Further, some modification genes and regulatory genes showed no significant differences between active and brumation-like states. Gut microbiota analysis demonstrated Akkermansia muciniphila, Bacteroides fragilis, and Citrobacter freundii were more enriched in the active group, which were common microbes related to bile acid metabolism, and the correlation analysis confirmed this relationship. Taken together, these findings indicate that the "physiological bile acid accumulation" observed in snakes during brumation-like state is jointly driven by suppressed hepatic synthesis, reduced enterohepatic circulation, and remodeled microbial community structure. The study provides novel comparative physiological insights into extreme metabolic homeostasis in animals.

Animals↗

PubMed2006

Monitoring of stool microbiota in subjects with diarrhea indicates distortions in composition.

We utilized denaturing gradient gel electrophoresis profiling to survey stool microbiota in 175 persons with diarrhea and 113 asymptomatic persons in a diarrhea surveillance study. Compared with healthy controls, the microbiota profiles in diarrhea cases more frequently exhibited decreased diversity and strong bands indicating the overgrowth of selected bacteria or bacterial groups.

Bacteria↗

PubMed2005

Analysis of the large bowel microbiota of colitic mice using PCR/DGGE.

AIM: To test combined polymerase chain reaction amplification of 16S rRNA gene sequences and denaturing gradient gel electrophoresis (PCR/DGGE) as an analytical method to investigate the composition of the large bowel microbiota of mice during the development of colitis. METHODS AND RESULTS: The colonic microbiota of formerly germfree interleukin 10 (IL-10)-deficient mice that had been exposed to the faecal microbiota of specific pathogen-free animals was screened using PCR/DGGE. The composition of the large bowel microbiota of IL-10-deficient mice changed as colitis progressed. DNA fragments originating from four bacterial populations ('Bacteroides sp.', Bifidobacterium animalis, Clostridium cocleatum, enterococci) were more apparent in PCR/DGGE profiles of colitic mice relative to non-colitic animals, whereas two populations were less apparent (Eubacterium ventriosum, Acidophilus group lactobacilli). Specific DNA:RNA dot blot analysis showed that bifidobacterial ribosomal RNA (rRNA) abundance increased as colitis developed. CONCLUSIONS: PCR/DGGE was shown to be an effective method to demonstrate changes in the composition of the large bowel microbiota of mice in relation to progression of inflammatory disease. The intensity of staining of DNA fragments in DGGE profiles reflected increased abundance of bifidobacterial rRNA in the microbiota of colitic animals. As bifidobacterial fragments in PCR/DGGE profiles generated from microbiota DNA showed increased intensity of fragment staining, an increase in bifidobacterial numbers in colitic mice was indicated. SIGNIFICANCE AND IMPACT OF THE STUDY: PCR/DGGE analysis demonstrated an altered composition of the large bowel microbiota of colitic mice. This work will allow specific groups of bacteria to be targeted in future research concerning the pathogenesis of colitis.

Animals↗

PubMed2026

From dysbiosis to resilience: Microbiome engineering for sustainable shrimp aquaculture.

The intensification of shrimp aquaculture has increased exposure to disease, environmental perturbations, and antimicrobial pressure, making microbial stability increasingly relevant to sustainable production. Microbiome stability-encompassing resistance to disturbance and resilience of functional recovery-provides an ecological framework for understanding how shrimp and culture-environment microbial communities respond to intensive farming. This review examines the transition from microbial homeostasis to dysbiosis and evaluates how microbiome engineering could redirect disrupted communities towards resilient states. Evidence is integrated across the intestine, hepatopancreas, rearing water, sediment and biofloc to assess how host genetics, ontogeny, diet, culture conditions, antibiotics and pollutants shape microbiome assembly and destabilization. Disease-associated changes in acute hepatopancreatic necrosis disease, white faeces syndrome, Enterocytozoon hepatopenaei infection, and white spot syndrome virus infection are critically evaluated, with explicit separation of associations, pathogen-induced dysbiosis, and community-level causality. Established and emerging interventions-including probiotics, prebiotics, synbiotics, functional diets, biofloc management, phages, postbiotics, microbiota transplantation and synthetic microbial communities-are assessed according to their capacity to modify microbial function, persistence and recovery rather than taxonomic change alone. We further examine how multi-omics, microbiome-informed breeding, and environmental monitoring could support biomarker development, predictive decision support and context-specific intervention. We argue that progress requires a shift from taxonomic description to function-guided engineering, from endpoint comparisons to direct measurement of resilience, and from laboratory efficacy to reproducible farm-scale validation. Overall, microbiome management may contribute to more disease-resilient and sustainable shrimp production, provided that its effectiveness can be validated under commercial farming conditions.

Dysbiosis↗

PubMed1967

Inhibition of rumen methanogenesis by methane analogues.

Extremely low concentrations of chloroform and carbon tetrachloride and somewhat larger concentrations of methylene chloride inhibited the formation of methane by the rumen microbiota in the presence or absence of added substrate. The accumulation of hydrogen at these low concentrations indicates a selective inhibition of methanogenesis. Presumably, these inhibitors affect one or more of the reactions by which methane is formed from hydrogen and carbon dioxide.

Animals↗

PubMed2003

Composition of microbiota in content and mucus from cecae of broiler chickens as measured by fluorescent in situ hybridization with group-specific, 16S rRNA-targeted oligonucleotide probes.

Six group-specific 16S rRNA-targeted oligonucleotide probes were used to investigate the composition of the microbiota of cecal content and mucus from broiler chickens. Together, the probes hybridized to as many as 94.7% of the bacteria detectable with the universal probe Bact338 in the content of the cecum of 2-d-old chicks. Fewer bacteria gave signals with these probes as the birds aged, and coverage was as low as 76% for the bacteria in cecal content of a 6-wk-old chicken. In the cecal content of 2-d-old chicks, approximately 56, 34, and 3% of the bacteria detectable with the universal probe reacted with the probes Enter1432 (enterics), Lacto722 (Lactobacillus/Streptococcus/Enterococcus), and Bif164 (bifidobacteria), respectively. Probes Clept1240 (Clostridium leptum subgroup), Erec482 (Clostridium coccoides-Eubacterium rectale), and Bacto1080 (Bacteroides groups) did not produce signals. In cecal content from 1-wk-old chicks, all six probes gave signals, and in samples from 6-wk-old birds approximately 3, 9, 6, 32, 22, and 8% of the bacteria detectable with the universal probe hybridized with the probes Enter1432, Lacto722, Bif164, Clept1240, Erec482, and Bacto1080, respectively. At this age, the six probes detected the phylogenetic groups in similar proportions in the microbiota of cecal content and cecal mucus. The exception was the enterics probe because more bacteria from the mucus fraction than from cecal content gave signals with this probe (13.4 vs. 4.4%, P<0.001).

Aging↗

PubMed2006

[Molecular-and-genetic and molecular-and-biological studies of Bifidobacterium and Lactobacillus representatives].

The article contains the results of molecular-and-genetic studies of representatives of the genera Bifidobacterium and Lactobacillus. Presently, the genomes of B. longum and L. plantarum, whose sizes are 2,256,640 and 3,308,274 nucleotide pairs, respectively, have been totally sequenced. Application of various methods of gene identification and genotyping to investigation of the taxonomy of these microbiota representatives, have enriched our knowledge of the variety of these bacteria, allowed classification of the known and revealing of knew species, vegetating in different biotopes of the human organism. Molecular-and-genetic approaches have clarified the taxonomic position of the industrial strains of lactate bacteria, which are used in food industry, helped to determine the kinetics of the passage of probiotic bifidobacterial and lactobacillic strains through the alimentary tract, and to determine the length of their preservation in the intestines after oral administration. The article also contains data on the therapeutic effect of some probiotics and synbiotics, evaluated by double blind placebo-controlled studies, which included determination of the population level of endogenous and peroral exogenous bifidobacteria and lactobacilli.

Adolescent↗

PubMed2006

Specificities of the fecal microbiota in inflammatory bowel disease.

BACKGROUND: Abnormalities have been described in the fecal microbiota of patients with IBD, but it is not known whether they are specific for inflammatory bowel disease (IBD) or to some extent common to other forms of colitis. The aim of this study was to compare the bacterial composition of the dominant fecal microbiota in patients with Crohn's disease (CD), ulcerative colitis (UC), infectious colitis (IC), and in healthy subjects (HS). METHODS: Fluorescent in situ hybridization adapted to flow cytometry was used to analyze the bacterial composition of fecal samples from 13 patients with active CD, 13 patients with active UC, 5 patients with IC, and 13 HS. We used 6 group-specific probes targeting 16S rRNA and spanning the main phylogenetic groups of the fecal microbiota. RESULTS: A significantly higher proportion of the total fecal bacteria were recognized by the 6 probes in HS (86.6%+/-12.7) and in IC (84.0%+/-11.7) than in patients with IBD (70.9%+/-15 in CD and 60.1%+/-25.7 in UC). The Clostridium coccoides group was reduced in UC (20.0%+/-13.3 versus 42.0%+/-12.0 in HS; P<.001), whereas the C leptum group was reduced in CD (13.1%+/-11.9 versus 25.2%+/-14.2 in HS; P=.002). The Bacteroides group was more abundant in IC (36.4%+/-22.9) than in the other 3 groups (13.8%+/-11.8 in CD, 11.7%+/-11.7 in UC, 12.1%+/-7.0 in HS; P<.001 for all 3 comparisons). CONCLUSIONS: In IBD the dominant fecal microbiota comprises unusual bacterial species. Moreover, CD and UC fecal microbiota harbor specific discrepancies and differ from that of IC and healthy subjects.

Adult↗

PubMed1999

The B-cell system of human mucosae and exocrine glands.

The mucosae and exocrine glands harbour the largest activated B-cell system of the body, amounting to some 80-90% of all immunoglobulin (Ig)-producing cells. The major product of these immunocytes is polymeric (p)IgA (mainly dimers) with associated J chain. Both pIgA and pentameric IgM contain a binding site for the polymeric Ig receptor (pIgR), or secretory component (SC), which is a requirement for their active external transport through secretory epithelia. The pIgR/SC binding site depends on covalent incorporation of the J chain into the quaternary structure of the polymers when they are produced by the local immunocytes. This important differentiation characteristic appears to be sufficient functional justification for the J chain to be expressed also by most B cells terminating at secretory effector sites with IgD or IgG production; they probably represent a "spin-off" from sequential downstream CH switching on its way to pIgA expression, thus apparently reflecting a maturational stage of effector B-cell clones compatible with homing to these sites. Observations in IgA-deficient individuals suggest that the magnitude of this homing is fairly well maintained even when the differentiation pathway to IgA is blocked. Certain microenvironmental elements such as specific cytokines and dendritic cells appear to be required for induction of IgA synthesis, but it remains virtually unknown why this isotype normally is such a dominating product of local immunocytes and why they have such a high level of J chain expression. Also, despite the recent identification of some important requirements in terms of adhesion molecules (e.g. integrin alpha 4 beta 7 and MAdCAM-1) that explain the "gut-seeking" properties of enterically induced B cells, the origin of regionalized homing of B cells to secretory effector sites outside the gut remains elusive. Moreover, little is known about immune regulation underlying the striking disparity of both the class (IgD, IgM) and subclass (IgA1, IgA2, IgG1, IgG2) production patterns shown by local immunocytes in various regions of the body, although the topical microbiota and other environmental stimuli might be important. Rational design of local vaccines will depend on better knowledge of both inductive and migratory properties of human mucosal B cells.

Animals↗

PubMed2004

Microbial-gut interactions in health and disease. Probiotics.

The definition of probiotics has evolved from a live active culture which improves the balance of the gut microbiota composition to specific effects, in particular, the immunomodulatory potential of clearly defined strains. The strains with beneficial properties, potential sources of probiotics, most frequently belong to the genera Bifidobacterium and Lactobacillus, and some of these strains exhibit powerful anti-inflammatory properties. Indeed, probiotic therapy has attracted research interest in human infectious, inflammatory and allergic disease. The most fully documented disease altering the gut microbiota is acute infectious diarrhoea in childhood. Current probiotic research aims to provide safe but sufficient bacterial stimulus in order to avert deviant immune responsiveness related to allergic and inflammatory diseases. However, further rigorous scientific efforts are required to characterize the immunomodulatory potential of specific probiotic strains for these targets.

Bifidobacterium↗

PubMed2004

Impact of commensal microbiota on murine gastrointestinal tract gene ontologies.

The gastrointestinal tract (GIT) of eukaryotes is colonized by a vast number of bacteria, where the commensal microbiota play an important role in defining the healthy gut. To investigate the influence of commensal bacteria on multiple regions of the host GIT transcriptome, the gene expression profiles of the corpus, jejunum, descending colon, and rectum of conventional (n = 3) and germ-free mice (n = 3) were examined using the Affymetrix Mu74Av2 GeneChip. Differentially regulated genes were identified using the global error assessment model, and a novel method of Gene Ontology (GO) clustering was used to identify significantly modulated biological functions. The microbiota modify the greatest number of genes in the jejunum (267 genes with an alpha < 0.001) and the fewest in the rectum (137 genes with an alpha < 0.001). Clustering genes by GO biological process and molecular function annotations revealed that, despite the large number of differentially regulated genes, the residential microbiota most significantly modified genes involved in such biological processes as immune function and water transport all along the length of the mouse GIT. Additionally, region-specific communication between the host and microbiota were identified in the corpus and jejunum, where tissue kallikrein and apoptosis regulator activities were modulated, respectively. These findings identify important interactions between the microbiota and the mouse gut tissue transcriptome and, furthermore, suggest that interactions between the microbial population and host GIT are implicated in the coordination of region-specific functions.

Animals↗