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An oral tyrosine challenge test for functional phenotyping of microbiota-derived phenyl sulfate production.

Phenyl sulfate (PS), a gut microbiota-derived metabolite implicated in the pathogenesis of diabetic kidney disease, is generated through microbial conversion of dietary tyrosine to phenol, followed by hepatic sulfation via SULT1A1. We developed an oral tyrosine challenge test (OTyCT) to phenotype individual PS-producing capacity. Forty-eight healthy adults underwent a standardized tyrosine load with serial plasma PS levels measured over 48 h using LC-MS. OTyCT revealed substantial interindividual variability of PS production independent of baseline PS levels, highlighting marked heterogeneity in host-microbiome metabolic interactions. Sixteen participants in the highest tertile of the incremental area under the curve of PS were defined as high-PS producers. High PS producers exhibited distinct gut microbial signatures despite comparable abundances of known phenol-biosynthetic genes and host SULT1A1 genotypes. These findings suggest that susceptibility to PS-related complications may vary according to gut microbial profiles, supporting OTyCT as a practical tool for metabolic phenotyping and microbiome-informed precision nutrition. Clinical Trial registry name and registration number: Identification of P-Cresyl Sulfate Producer Phenotype by Oral Tyrosine Challenge Test: Interactions Among Diet, Gut Microbiota, and Host Genome, NCT04204174.

Journal Article↗

The gastrointestinal ecosystem: a precarious alliance among epithelium, immunity and microbiota.

The gastrointestinal (GI) tract is a complex ecosystem generated by the alliance of GI epithelium, immune cells and resident microbiota. The three components of the GI ecosystem have co-evolved such that each relies on the presence of the other two components to achieve its normal function and activity. Experimental systems such as cell culture, germ-free animal models and intestinal isografts have demonstrated that each member of the GI ecosystem can follow a predetermined developmental pathway, even if isolated from the other components of the ecosystem. However, the presence of all three components is required for full physiological function. Genetic or functional alterations of any one component of this ecosystem can result in a broken alliance and subsequent GI pathology. A more detailed understanding of the interactions among microbiota, GI epithelium and the immune system should provide insight into multiple human disease states.

Animals↗

Microbiological characteristics of subgingival microbiota in adult periodontitis, localized juvenile periodontitis and rapidly progressive periodontitis subjects.

OBJECTIVE: To describe the prevalence of the cultivable subgingival microbiota in periodontal diseases and to draw attention to the polymicrobial nature of periodontic infections. METHODS: The study population consisted of 95 patients, 51 females and 44 males, aged 14-62 years. Twenty-nine patients exhibited adult periodontitis (AP), six localized juvenile periodontitis (LJP), and 60 rapidly progressive periodontitis (RPP). Two to four pooled bacterial samples were obtained from each patient. Samples were collected with sterile paper points from the deepest periodontal pockets. The samples were cultured under anaerobic and microaerophilic conditions using selective and non-selective media. Isolates were characterized to species level by conventional biochemical tests and by a commercial rapid test system. RESULTS: Prevotella intermedia and Capnocytophaga spp. were the most frequently detected microorganisms in all diagnostic groups. Porphyromonas gingivalis and Peptostreptococcus micros were found more frequently in AP and RPP patients, while Actinobacillus actinomycetemcomitans and Eikenella corrodens were associated with AP, LJP and RPP patients. The other bacterial species, including Actinomyces spp., Streptococcus spp. and Eubacterium spp., were detected at different levels in the three disease groups. CONCLUSIONS: The data show the complexity of the subgingival microbiota associated with different periodontal disease groups, indicating that the detection frequency and levels of recovery of some periodontal pathogens are different in teeth affected by different forms of periodontal disease.

Adolescent↗

Degradation of scrapie associated prion protein (PrPSc) by the gastrointestinal microbiota of cattle.

A food-borne origin of the transmission of bovine spongiform encephalopathy (BSE) to cattle is commonly assumed. However, the fate of infectious prion protein during polygastric digestion remains unclear. It is unknown at present, whether infectious prion proteins, considered to be very stable, are degraded or inactivated by microbial processes in the gastrointestinal tract of cattle. In this study, rumen and colon contents from healthy cattle, taken immediately after slaughter, were used to assess the ability of these microbial consortia to degrade PrP(Sc). Therefore, the consortia were incubated with brain homogenates of scrapie (strain 263K) infected hamsters under physiological anaerobic conditions at 37 degrees C. Within 20 h, PrP(Sc) was digested both with ruminal and colonic microbiota up to immunochemically undetectable levels. Especially polymyxin resistant (mainly gram-positive) bacteria expressed PrP(Sc) degrading activity. These data demonstrate the ability of bovine gastrointestinal microbiota to degrade PrP(Sc) during digestion.

Animals↗

Molecular analysis of the bacterial microbiota in the human stomach.

The microbiota of the human stomach and the influence of Helicobacter pylori colonization on its composition remain largely unknown. We characterized bacterial diversity within the human gastric mucosa by using a small subunit 16S rDNA clone library approach and analyzed 1,833 sequences generated by broad-range bacterial PCR from 23 gastric endoscopic biopsy samples. A diverse community of 128 phylotypes was identified, featuring diversity at this site greater than previously described. The majority of sequences were assigned to the Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria phyla. Ten percent of the phylotypes were previously uncharacterized, including a Deinococcus-related organism, relatives of which have been found in extreme environments but not reported before in humans. The gastric clone libraries from 19 subjects contained H. pylori rDNA; however, only 12 of these subjects tested positive for H. pylori by conventional laboratory methods. Statistical analysis revealed a large degree of intersubject variability of the gastric ecosystem. The presence of H. pylori did not affect the composition of the gastric community. This gastric bacterial rDNA data set was significantly different from sequence collections of the human mouth and esophagus described in other studies, indicating that the human stomach may be home to a distinct microbial eco-system. The gastric microbiota may play important, as-yet-undiscovered roles in human health and disease.

Adult↗

Specificities of chemosensory receptors in the human gut microbiota.

The human gut is rich in metabolites and harbors a complex microbial community, yet surprisingly little is known about the spectrum of chemical signals detected by the large variety of sensory receptors present in the gut microbiome. Here, we systematically mapped the ligand specificities of selected extracytoplasmic sensory domains from twenty members of the human gut microbiota, with a primary focus on the abundant and physiologically important class of Clostridia. Twenty-five metabolites from different chemical classes-including amino acids, nucleobase derivatives, amines, indole, and carboxylates-were identified as specific ligands for fifteen sensory domains from nine bacterial species, which represent all three major functional classes of transmembrane receptors: chemotaxis receptors, histidine kinases, and enzymatic sensors. We have further characterized the specificity and evolution of ligand binding to Cache superfamily sensors specific for lactate, dicarboxylic acids, and for uracil and short-chain fatty acids (SCFAs). Structural and biochemical analysis of the dCache sensor of uracil and SCFAs revealed that its two different ligand types bind at distinct sensory modules. Overall, combining experimental identification with computational analyses, we were able to assign ligands to approximately half of the Cache-type chemotaxis receptors found in the eleven gut commensal genomes from our set, with carboxylic acids representing the largest ligand class. Among these, the most commonly found ligand specificities were for lactate and formate, indicating a particular importance of these metabolites in the human gut microbiota and consistent with their observed growth-promoting effects on selected bacterial commensals.

Humans↗

Effects of dietary fibre-rich juice colloids from apple pomace extraction juices on intestinal fermentation products and microbiota in rats.

Effects of colloids isolated from apple pomace extraction juices (so-called B-juices) produced by enzymic liquefaction on food intake, body and faecal weights, short-chain fatty acid (SCFA) profile and selected intestinal microbiota were investigated in rats. Ten male Wistar rats per group were fed diets without any apple dietary fibre (DF) (control) or supplement with 5 % B-juice colloids or an alcohol-insoluble substance (AIS) from apples for 6 weeks. Rats fed with apple DF (5 % B-juice colloids or AIS) gained less weight than control rats (P<0.05). B-juice colloids did not affect food intake, whereas feeding AIS resulted in a 10 % higher food consumption than in control rats. Both juice colloids and AIS increased the weight of caecal contents in rats and lowered luminal pH values (P<0.05). In addition, SCFA concentrations and total yields were also raised (P<0.05) in caecum of these rats indicating good fermentability of apple substrates by gut microflora. Distinctly higher concentrations of acetate and propionate were found in intestinal contents of juice colloid-fed rats (P<0.05), whereas AIS also increased butyrate yield. Changes in microbiota due to apple DF in diets were restricted in the caecum to the Eubacterium rectale cluster (AIS; P<0.05) and in faeces to the Bacteroidaceae (juice colloids and AIS; P<0.05). The present study shows the physiological effects of apple DF isolated from pomace extraction juices produced by enzymic liquefaction on intestinal fermentation. Results may be helpful for the development of such innovative juice products that are rich in DF of fruit origin.

Animals↗

Human colonic microbiota: ecology, physiology and metabolic potential of intestinal bacteria.

In both health and disease, the colonic microbiota plays an important role in several areas of human physiology. This complex assemblage of microorganisms endows great metabolic potential on the large intestine, primarily through its degradative abilities. Many hundreds of different types of bacteria, varying widely in physiology and biochemistry, exist in a multitude of different microhabitats in the lumen of the large gut, the mucin layer and on mucosal surfaces. Both microbiota and host obtain clear benefits from association. For example, growth substrates from diet and body tissues, together with a relatively stable environment for bacteria to proliferate are provided by the host, which in turn has evolved to use butyrate, a bacterial fermentation product, as its principal source of energy for epithelial cells in the distal bowel. The main sources of carbon and energy for intestinal bacteria are complex carbohydrates (starches, non-starch polysaccharides). Carbohydrate metabolism is of great importance in the large intestine, since generically, and in terms of absolute numbers, the vast majority of culturable microorganisms are saccharolytic. The amounts and types of fermentation products formed by colonic bacteria depend on the relative amounts of each substrate available, their chemical structures and compositions, as well as the fermentation strategies (biochemical characteristics and catabolite regulatory mechanisms) of bacteria participating in depolymerization and fermentation of the substrates. Protein breakdown and dissimilatory amino acid metabolism result in the formation of a number of putatively toxic metabolites, including phenols, indoles and amines. Production of these substances is inhibited or repressed in many intestinal microorganisms by a fermentable source of carbohydrate. Owing to the anatomy and physiology of the colon, putrefactive processes become quantitatively more important in the distal bowel, where carbohydrate is more limiting.

Adult↗

Different effects of difructose anhydride III and inulin-type fructans on caecal microbiota in rats.

The effects of different kinds of inulin-type fructans on caecal microbiota were evaluated in rats. Four groups of male Wistar rats were fed either a control diet, or diets containing 5% inulin, 5% fructooligosaccharides (FOS), or 5% difructose anhydride III (DFAIII) for two weeks. In the DFAIII group, caecal propionate, butyrate, counts of bifidobacteria, and total anaerobes were lower than in the inulin group, while caecal propionate, succinate, counts of bifidobacteria, and total anaerobes were lower than in the FOS group. Compared to controls, in the DFAIII group the counts of clostridia in caecum were increased by 3 log units. However, this change was statistically not significant. There were no differences between inulin and FOS groups for the pool of short chain fatty acids in caecum and bacterial counts. Results indicate that DFAIII has different effects on caecal microbiota compared to inulin and FOS and that these differences are most likely due to the alpha(3-->2) bonds in DFAIII.

Animals↗

Mechanisms by which anaerobic microbiota inhibit the establishment in mice of intestinal colonization by vancomycin-resistant Enterococcus.

We used a mouse model to test the hypothesis that anaerobic microbiota in the colon inhibit the establishment of vancomycin-resistant enterococci (VRE) colonization by depleting nutrients within cecal contents and limiting the association of VRE with the mucus layer. Anaerobic growth of VRE was assessed in cecal contents and cecal mucus of mice that had received treatment with subcutaneous clindamycin or saline. VRE grew to high concentrations in cecal contents of clindamycin-treated mice and in cecal mucus of both groups but not in cecal contents of saline-treated mice, unless the cecal contents were autoclaved or converted into sterile filtrates. After orogastric inoculation of VRE, clindamycin-treated mice acquired high concentrations of VRE within the mucus layer, whereas saline-treated mice did not. These results suggest that colonic microbiota inhibit VRE by producing inhibitory substances or conditions rather than by depleting nutrients. The colonic mucus layer provides a potential niche for growth of VRE.

Animals↗

Vancomycin-resistant Enterococci may obtain nutritional support by scavenging carbohydrate fragments generated during mucin degradation by the anaerobic microbiota of the colon.

Vancomycin-resistant Enterococcus (VRE) is an important nosocomial pathogen that colonizes the intestinal tract. The substrates that provide nutritional support for VRE in the colon are not known. We tested the hypothesis that enzymatic breakdown of complex polysaccharides and glycoconjugates by other members of the indigenous microbiota could provide a source of nutrients for VRE. Nine vancomycin-resistant E. faecium strains were unable to ferment complex plant polysaccharides or hog gastric or bovine submaxillary mucin; however, each of the strains was able to ferment monosaccharides that are components of mucins and plant polysaccharides. Preincubation of hog gastric mucin with partially purified enzyme mixtures obtained from supernatants of Ruminococcus torques or a human stool specimen resulted in release of monosaccharides that supported growth of VRE. These results suggest that enzymatic breakdown of complex polysaccharides such as mucin by members of the indigenous microbiota may provide a source of nutritional support for VRE.

Bacteroides↗

In vitro fermentation pattern of D-tagatose is affected by adaptation of the microbiota from the gastrointestinal tract of pigs.

Knowledge of the fermentation pattern of D-tagatose is important for the assessment of energy value and compliance of D-tagatose. In vitro fermentation experiments with pig intestinal contents and bacteria harvested from the gastrointestinal tract of pigs were used to investigate the degradation of D-tagatose and the formation of fermentation products. Two groups of eight pigs were fed either a control diet containing 150 g/kg sucrose or a diet which had 100 g/kg of the sucrose replaced by D-tagatose. After 18 d the pigs were killed and the gastrointestinal contents collected for in vitro studies. No microbial fermentation of D-tagatose occurred in the stomach or in the small intestine, whereas the sugar was fermented in the cecum and colon. Formate, acetate, propionate, butyrate, valerate, caproate and some heptanoate were produced by the microbial fermentation of D-tagatose by gut microbiota. Hydrogen and methane were also produced. The population of D-tagatose-degrading bacteria in fecal samples and the capacity of bacteria from the hindgut to degrade D-tagatose were higher in the pigs adapted to D-tagatose compared with unadapted pigs. In unadapted pigs, the major fermentation product from D-tagatose was acetic acid. Much more butyric and valeric acids were produced from D-tagatose by bacterial slurries of tagatose-adapted pigs compared with unadapted pigs; this was especially the case for samples from the colon. We conclude that D-tagatose is not fermented in the upper gastrointestinal tract, and the ability of the large intestinal microbiota to ferment D-tagatose is dependent on adaptation.

Acetic Acid↗

Inulin alters the intestinal microbiota and short-chain fatty acid concentrations in growing pigs regardless of their basal diet.

Inulin stimulates intestinal bifidobacteria in humans and rodents but its effect in pigs is inconsistent. We assessed the effect of inulin on the intestinal microbiota by fluorescent in situ hybridization in growing pigs (age 9-12 wk). Pigs (n = 64) were assigned to 2 types of basal diets [wheat and barley (WB) or corn and wheat gluten (CG)] with or without 3% inulin (WBI or CGI) for 3 and 6 wk (n = 8/group) to test whether naturally occurring dietary fibers influence the inulin effect. Intestinal organic acids, pH values, and residual inulin were determined. The composition of the microbiota was highly individual. The duration of feeding did not affect any of the variables tested; therefore, data for the 2 periods were pooled. Bifidobacteria were detected in less than half of the pigs. Inulin did not stimulate lactobacilli and bifidobacteria numbers irrespective of the basal diet, although 20-50% of inulin was degraded in the jejunum. The number of pigs with colonic bifidobacteria was higher in those fed diets containing inulin (40 vs. 13%; P < 0.05). Total colonic short-chain fatty acid (SCFA) concentrations were lower in both inulin-fed groups due to reduced acetate (P < 0.05). Proportions of colonic butyrate were higher in pigs fed inulin-supplemented diets (P < 0.05). Colonic pH tended to be lower in the WB groups (WB; 6.6 +/- 0.6), and was higher due to inulin (CGI, 7.1 +/- 0.1; P < 0.05). In conclusion, inulin affected intestinal SCFA and the number of pigs harboring bifidobacteria; this effect was independent of the basal diet.

Acetates↗

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↗

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↗

Molecular-phylogenetic analyses of human gastrointestinal microbiota.

Molecular-phylogenetic methods have revolutionized the analysis of complex microbial communities. Polymerase chain reaction amplification and phylogenetic analysis of small-subunit ribosomal RNA gene sequences allow microbes to be identified objectively, even in the absence of cultivation. Furthermore, the sequence information obtained by these means can be used to design sequence-based tools for identifying, tracking, and diagnosing the presence of microbes in complex samples. In this article, we summarize this approach and review its application to the study of the human gastrointestinal microbiota. Although just beginning, molecular-phylogenetic surveys of human gut microbes have revealed that most microbes identified in the gastrointestinal tract represent novel, previously undescribed species. A full description of the microbial constituents of the human gut will set the groundwork for interpreting how the gastrointestinal microbiota influence the health of the host.

Journal Article↗

Exploiting molecular methods to explore endodontic infections: Part 2--Redefining the endodontic microbiota.

The second part of this review discusses the application of molecular methods in endodontic microbiology research for a comprehensive characterization of the microbiota associated with different types of endodontic infections. Despite their recent introduction in endodontic research, molecular methods have already given a significant contribution to the understanding of endodontic infections and the future holds the perspective of a still better refinement of the knowledge about these infections. Molecular methods have revealed a higher complexity of the endodontic microbiota than previously reported by cultivation approaches. In addition to detecting some cultivable species in increased prevalence, molecular methods have also expanded the list of putative endodontic pathogens by inclusion of some fastidious bacterial species or even uncultivated bacteria that have never been previously found in endodontic infections.

DNA Probes↗

Influence of normal microbiota on some aspects of the immune response during experimental infection with Trypanosoma cruzi in mice.

To study the influence of normal associated microbiota on systemic immunological responses during experimental Chagas' disease, germ-free and conventional NIH Swiss mice were infected with Y strain of Trypanosoma cruzi. Although no statistical differences in mortality and parasitaemia were found, conventional mice showed IFN-gamma, TNF-alpha and NO production (P < 0.05) by spleen cell cultures and higher blood levels of immunoglobulins of the IgG2a isotype (P < 0.05) when compared to their germ-free counterparts. Moreover, higher levels of IgG1 were also found in conventional animals. On the other hand, no differences in IL10 production were found between germ-free and conventional mice after infection (P < 0.05). Interestingly, spleen cell cultures from non-infected germ-free mice spontaneously produced higher levels of IL10 than cultures from conventional mice. Moreover, cultures from non-infected germ-free mice responded to T. cruzi antigens with IFN-gamma production, contrary to cultures from conventional animals. In conclusion, the presence of the normal microbiota skews the immune response towards production of inflammatory cytokines during experimental infection with T. cruzi in mice. However, the increase in production of cytokines that is linked to resistance to this parasite did not alter the outcome of infection significantly, probably due to high virulence of the Y strain.

Animals↗