Gut Microbiota Of Healthy Individuals Research Articles

Isoflavone Rich Diet Ameliorates Experimental Autoimmune Encephalomyelitis (EAE) through Modulation of Gut Bacteria Depleted in Multiple Sclerosis Patients

Abstract Multiple sclerosis (MS), an autoimmune disease of the central nervous system, has been shown to be influenced by gut bacteria. We and others have shown that MS patients have depletion of isoflavone-metabolizing bacteria compared to healthy individuals. We hypothesize that gut bacteria-mediated isoflavone metabolism induces an anti-inflammatory state and reduction/depletion of these gut bacteria might predispose to MS development and/or severity. To test this, we placed mice on a diet with or without isoflavones and induced EAE, an animal model of MS. Mice on an isoflavone diet developed milder disease compared to those on an isoflavone-free diet. This phenomenon was dependent on the presence of isoflavone-metabolizing gut bacteria as confirmed by antibiotic depletion and bacterial reconstitution. Mice on an isoflavone diet exhibited altered peripheral immune responses, CNS cellular infiltration, and CNS pathology post EAE induction compared to mice on an isoflavone-free diet. Additionally, the gut microbiome of mice on an isoflavone diet and an isoflavone-free diet closely resembles the gut microbiota of healthy individuals and MS patients, respectively. Thus our results suggest that dietary isoflavone metabolites produced with the help of gut bacteria can influence the disease through modulation of the immune system.

Time-restricted feeding is associated with changes in human gut microbiota related to nutrient intake.

Time-restricted feeding (TRF) is a dietary therapeutic remedy for the prevention and treatment of metabolic diseases. Gut microbiota may influence the host metabolism and nutritional status of individuals. Given the significance of TRF and gut microbiota in metabolic diseases, the aim of this study was to explore the association between TRF and gut microbiota in healthy individuals, which is not clearly elucidated. Thirty healthy men (18-30 y of age) were divided in to two groups (TRF: n = 15 and non-TRF: n = 15). The TRF group was instructed to not consume any food for 16 h/d. Two-day food diary was used for dietary data collection. Stool samples were collected from both groups after 25 d of TRF or non-TRF. Gut microbiota profile was analyzed and quantified by using 16S rRNA gene sequencing. Cluster analysis revealed that Prevotlla_9, Faecalibacterium, and Dialister were the most abundant species in TRF, whereas Prevotell_7, Alloprevotella, and Prevotella_2 were less abundant in the non-TRF group. At the genus level, gut microbiota of the TRF group was significantly changed compared with that of the non-TRF group. Moreover, bar plot analysis revealed that Bacteroidetes was the most abundant phylum in TRF group, followed by Firmicutes. Heat map correlation showed that polyunsaturated fatty acids and vitamin D were positively correlated with Firmicutes, whereas iodine, vitamin E, magnesium, and carbohydrate intake were negative correlated with microbial richness. The present study demonstrated that TRF is associated with microbial composition and relative abundance. TRF intervention might increase microbial abundance, thereby influencing the host metabolism and nutritional status.

Urolithin Metabotypes Can Determine the Modulation of Gut Microbiota in Healthy Individuals by Tracking Walnuts Consumption over Three Days.

Walnuts are rich in polyphenols ellagitannins, modulate gut microbiota (GM), and exert health benefits after long-term consumption. The metabolism of ellagitannins to urolithins via GM depends on urolithin metabotypes (UM-A, -B, or -0), which have been reported to predict host responsiveness to a polyphenol-rich intervention. This study aims to assess whether UMs were associated with differential GM modulation after short-term walnut consumption. In this study, 27 healthy individuals consumed 33 g of peeled raw walnuts over three days. GM profiling was determined using 16S rRNA illumina sequencing and specific real-time quantitative polymerase chain reactions (qPCRs), as well as microbial activity using short-chain fatty acids analysis in stool samples. UMs stratification of volunteers was assessed using ultra performance liquid chromatography–electro spray ionization–quadrupole time of flight–mass spectrometry (UPLC-ESI-QTOF-MS) analysis of urolithins in urine samples. The gut microbiota associated with UM-B was more sensitive to the walnut intervention. Blautia, Bifidobacterium, and members of the Coriobacteriaceae family, including Gordonibacter, increased exclusively in UM-B subjects, while some members of the Lachnospiraceae family decreased in UM-A individuals. Coprococcus and Collinsella increased in both UMs and higher acetate and propionate production resulted after walnuts intake. Our results show that walnuts consumption after only three days modulates GM in a urolithin metabotype-depending manner and increases the production of short-chain fatty acids (SCFA).

Linking diet, gut microbiota and autoimmunity: A phytoestrogen diet alters the gut microbiota and influences Experimental Autoimmune Encephalomyelitis (EAE)

Abstract The etiology of multiple sclerosis (MS) involves genetic predisposition and an unknown environmental trigger. The gut microbiome may be an environmental contributing factor. Previously, we have shown that certain gut bacteria especially those with ability to metabolize phytoestrogen are less abundant in MS patients compared to healthy individuals. We hypothesize that phytoestrogen metabolism via microbial flora induces an anti-inflammatory state in the intestine. Therefore their reduced levels might predispose to disease development and/or severity. To test this, we placed C57Bl/6 mice on a diet with or without phytoestrogens and induced Experimental Autoimmune Encephalomyelitis (EAE), an experimental model of MS. We observed that mice on a phytoestrogen diet developed milder disease compared to those on a phytoestrogen free diet; a phenomenon dependent on the presence of phytoestrogen-metabolizing bacteria in the gut. We also found that a phytoestrogen diet alters the gut microbiota compared to a phytoestrogen-free diet with the gut microbiota of phytoestrogen group closely resembling the gut microbiota of healthy individuals. The gut microbiota of mice on a phytoestrogen-free diet closely resembles the gut microbiota of MS patients. Furthermore, mice on a phytoestrogen-diet exhibit an altered immune profile in the colonic lamina propria and mesenteric lymph nodes. Finally, we found that phytoestrogen-metabolites altered the cytokine-producing function of human colonic epithelial cells in vitro. Our results suggest that dietary phytoestrogen metabolites produced by commensal bacteria can alter the phenotype and function of the intestinal immune system, which may influence central nervous system autoimmunity.

A Diverse Range of Human Gut Bacteria Have the Potential To Metabolize the Dietary Component Gallic Acid.

The human gut microbiota contains a broad variety of bacteria that possess functional genes, with resultant metabolites that affect human physiology and therefore health. Dietary gallates are phenolic components that are present in many foods and beverages and are regarded as having health-promoting attributes. However, the potential for metabolism of these phenolic compounds by the human microbiota remains largely unknown. The emergence of high-throughput sequencing (HTS) technologies allows this issue to be addressed. In this study, HTS was used to assess the incidence of gallate-decarboxylating bacteria within the gut microbiota of healthy individuals for whom bacterial diversity was previously determined to be high. This process was facilitated by the design and application of degenerate PCR primers to amplify a region encoding the catalytic C subunit of gallate decarboxylase (LpdC) from total metagenomic DNA extracted from human fecal samples. HTS resulted in the generation of a total of 3,261,967 sequence reads and revealed that the primary gallate-decarboxylating microbial phyla in the intestinal microbiota were Firmicutes (74.6%), Proteobacteria (17.6%), and Actinobacteria (7.8%). These reads corresponded to 53 genera, i.e., 47% of the bacterial genera detected previously in these samples. Among these genera, Anaerostipes and Klebsiella accounted for the majority of reads (40%). The usefulness of the HTS-lpdC method was demonstrated by the production of pyrogallol from gallic acid, as expected for functional gallate decarboxylases, among representative strains belonging to species identified in the human gut microbiota by this method.IMPORTANCE Despite the increasing wealth of sequencing data, the health contributions of many bacteria found in the human gut microbiota have yet to be elucidated. This study applies a novel experimental approach to predict the ability of gut microbes to carry out a specific metabolic activity, i.e., gallate metabolism. The study showed that, while gallate-decarboxylating bacteria represented 47% of the bacterial genera detected previously in the same human fecal samples, no gallate decarboxylase homologs were identified from representatives of Bacteroidetes The presence of functional gallate decarboxylases was demonstrated in representative Proteobacteria and Firmicutes strains from the human microbiota, an observation that could be of considerable relevance to the in vivo production of pyrogallol, a physiologically important bioactive compound.

Structural Characterization of the Lactobacillus Plantarum FlmC Protein Involved in Biofilm Formation

Lactobacillus plantarum is one of the most predominant species in the human gut microbiota of healthy individuals. We have previously characterized some probiotic features of L. plantarum LM3, as the high resistance to different stress, the binding ability toward some extracellular matrix proteins and plasminogen and the immunomodulatory role of the surface expressed adhesin EnoA1. We have also identified the flmA, flmB and flmC genes, coding for putative proteins named FlmA, FlmB and FlmC, whose null mutations partially impaired biofilm development; the L. plantarum LM3–6 strain, carrying a deletion in flmC, showed a high rate of autolysis, supporting the hypothesis that FlmC might be involved in cell wall integrity. Here, we report the in-silico characterization of ΔTM-FlmC, a portion of the FlmC protein. The protein has been also expressed, purified and characterized by means of CD spectroscopy, ICP-mass and UHPLC-HRMS. The obtained experimental data validated the predicted model unveiling also the presence of a bound lipid molecule and of a Mg(II) ion. Overall, we provide strong evidences that ΔTM-FlmC belongs to the LytR-CpsA-Psr (LCP) family of domains and is involved in cell envelope biogenesis.

'Collinsella provencensis' sp. nov., 'Parabacteroides bouchesdurhonensis' sp. nov. and 'Sutterella seckii,' sp. nov., three new bacterial species identified from human gut microbiota.

We report here the main characteristics of ‘Collinsella provencensis’ strain Marseille-P3740 (CSUR P3740), ‘Parabacteroides bouchesdurhonensis’ strain Marseille-P3763 (CSUR P3763) and ‘Sutterella seckii’ strain Marseille-P3660 (CSUR P3660), which were isolated using culturomics from the human gut microbiota of healthy individuals living in Marseille.

Draft Genome Sequences of Two Enterobacter cloacae subsp. cloacae Strains Isolated from Australian Hematology Patients with Bacteremia.

ABSTRACTEnterobacter cloacae is a common member of the gut microbiota in healthy individuals. However, it is also an opportunistic pathogen, capable of causing bacteremia. We report the draft genomes of two Enterobacter cloacae subspecies cloacae strains isolated from hematology patients with bacteremia. Both isolates carry genes encoding extended-spectrum β-lactamases.

Human α-Defensin 6 Self-Assembly Prevents Adhesion and Suppresses Virulence Traits of Candida albicans.

Human α-defensin 6 (HD6) is a host-defense peptide that contributes to intestinal innate immunity and mediates homeostasis at mucosal surfaces by forming noncovalent oligomers that capture bacteria and prevent bacterial invasion of the epithelium. This work illustrates a new role of HD6 in defending the host epithelium against pathogenic microorganisms. We report that HD6 blocks adhesion of Candida albicans to human intestinal epithelial cells and suppresses two C. albicans virulence traits, namely, invasion of human epithelial cells and biofilm formation. Moreover, a comparison of HD6 and a single-point variant F2A that does not form higher-order oligomers demonstrates that the self-assembly properties of HD6 are essential for functional activity against C. albicans. This opportunistic fungal pathogen, which resides in the intestine as a member of the gut microbiota in healthy individuals, can turn virulent and cause a variety of diseases ranging from superficial infections to life-threatening systemic infections. Our results indicate that HD6 may allow C. albicans to persist as a harmless commensal in the gastrointestinal tract. Moreover, HD6 and HD6-inspired molecules may provide a foundation for exploring new antimicrobial strategies that attenuate the virulence traits of C. albicans and other microbial pathogens.

The human intestinal microbiota of constipated-predominant irritable bowel syndrome patients exhibits anti-inflammatory properties.

The intestinal microbiota of patients with constipated-predominant irritable bowel syndrome (C-IBS) displays chronic dysbiosis. Our aim was to determine whether this microbial imbalance instigates perturbation of the host intestinal mucosal immune response, using a model of human microbiota-associated rats (HMAR) and dextran sulfate sodium (DSS)-induced experimental colitis. The analysis of the microbiota composition revealed a decrease of the relative abundance of Bacteroides, Roseburia-Eubacterium rectale and Bifidobacterium and an increase of Enterobacteriaceae, Desulfovibrio sp., and mainly Akkermansia muciniphila in C-IBS patients compared to healthy individuals. The bacterial diversity of the gut microbiota of healthy individuals or C-IBS patients was maintained in corresponding HMAR. Animals harboring a C-IBS microbiota had reduced DSS colitis with a decreased expression of pro-inflammatory cytokines from innate, Th1, and Th17 responses. The pre-treatment of conventional C57BL/6 mice or HMAR with A. muciniphila, but not with Escherichia coli, prior exposure to DSS also resulted in a reduction of colitis severity, highlighting that the anti-inflammatory effect of the gut microbiota of C-IBS patients is mediated, in part, by A. muciniphila. This work highlights a novel aspect of the crosstalk between the gut microbiota of C-IBS patients and host intestinal homeostasis.

Pyruvate dehydrogenase subunit β of Lactobacillus plantarum is a collagen adhesin involved in biofilm formation.

Multi-functional surface proteins have been observed in a variety of pathogenic bacteria, where they mediate host cell adhesion and invasion, as well as in commensal bacterial species, were they mediate positive interaction with the host. Among these proteins, some glycolytic enzymes, expressed on the bacterial cell surface, can bind human extracellular matrix components (ECM). A major target for them is collagen, an abundant glycoprotein of connective tissues. We have previously shown that the enolase EnoA1 of Lactobacillus plantarum, one of the most predominant species in the gut microbiota of healthy individuals, is involved in binding with collagen type I (CnI). In this study, we found that PDHB, a component of the pyruvate dehydrogenase complex, contributes to the L. plantarum LM3 adhesion to CnI. By a cellular adhesion assay to immobilized CnI, we show that LM3-B1 cells, carrying a null mutation in the pdhB gene, bind to CnI - coated surfaces less efficiently than wild-type cells. Moreover, we show that the PDHB-CnI interaction requires a native state for PDHB. We also analyzed the ability to develop biofilm in wild-type and mutant strains and we found that the lack of the PDHB on cell surface generates cells partially impaired in biofilm development.

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease

ObjectivePatients with IBD display substantial heterogeneity in clinical characteristics. We hypothesise that individual differences in the complex interaction of the host genome and the gut microbiota can explain the onset...

Ability of cranberry proanthocyanidins in combination with a probiotic formulation to inhibit in vitro invasion of gut epithelial cells by extra-intestinal pathogenic E. coli

Cranberries and probiotics are individually considered as functional foods. This study evaluated the potential synergy between bioactive proanthocyanidins (c-PAC) derived from cranberries and probiotics on reducing the invasiveness of extra-intestinal pathogenic Escherichia coli (ExPEC) in a cell culture model. ExPEC can be a component of the gut microbiota in healthy individuals, and reducing the invasiveness of ExPEC is a potential means to lessen the risk of subsequent urinary tract infections (UTI), the most common bacterial infections in women. c-PAC (>92 % A-type) concentrations greater than 36 µg c-PAC/mL significantly (p < 0.05) reduced ExPEC invasion, and was not inhibited by the presence of probiotics. Scanning electron microscopy suggests that the mechanism by which c-PAC prevent ExPEC invasion is by cross-linking surface virulence factors. A probiotic blend also significantly reduced invasion, albeit via a different mechanism. This study demonstrated the potential benefit of combining functional A-type c-PAC components in cranberry foods with probiotics.

The Lactobacillus plantarum Eno A1 Enolase Is Involved in Immunostimulation of Caco-2 Cells and in Biofilm Development.

The role of probiotics in prevention and treatment of a variety of diseases is now well assessed. The presence of adhesive molecules on the cell surface of probiotics has been related to the ability to confer health benefit to the host. We have previously shown that the enolase EnoA1 of Lactobacillus plantarum, one of the most predominant species in the gut microbiota of healthy individuals, is cell surface-expressed and is involved in binding with human fibronectin and plasminogen. By means of comparative analysis between L. plantarum LM3 (wild type) and its isogenic LM3-CC1 (ΔenoA1) mutant strain, here we show that EnoA1 affects the ability of this bacterium to modulate immune response as determined by analysis of expression of immune system molecules in Caco-2 cells. Indeed, we observed induction of TLR2 expression in cells exposed to L. plantarum LM3, while no induction was detectable in cells exposed to LM3-CC1. This difference was much less consistent when expression of TLR4 was determined in cells exposed to the two strains. Pro-inflammatory (IL-6) and anti-inflammatory cytokines (IL-10, TGF-β), and the antimicrobial peptide HBD-2 were induced in Caco-2 cells exposed to L. plantarum LM3, while lower levels of induction were detected in cells exposed to LM3-CC1. We also analyzed the ability to develop biofilm of the two strains, and observed a decrease of about 65 % in the development of mature biofilm in LM3-CC1 compared to the wild type.

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

The human gut is the natural habitat for a large and dynamic bacterial community that has a great relevance for health. Metagenomics is increasing our knowledge of gene content as well as of functional and genetic variability in this microbiome. However, little is known about the active bacteria and their function(s) in the gastrointestinal tract. We performed a metatranscriptomic study on ten healthy volunteers to elucidate the active members of the gut microbiome and their functionality under conditions of health. First, the microbial cDNAs obtained from each sample were sequenced using 454 technology. The analysis of 16S transcripts showed the phylogenetic structure of the active microbial community. Lachnospiraceae, Ruminococcaceae, Bacteroidaceae, Prevotellaceae, and Rickenellaceae were the predominant families detected in the active microbiota. The characterization of mRNAs revealed a uniform functional pattern in healthy individuals. The main functional roles of the gut microbiota were carbohydrate metabolism, energy production and synthesis of cellular components. In contrast, housekeeping activities such as amino acid and lipid metabolism were underrepresented in the metatranscriptome. Our results provide new insights into the functionality of the complex gut microbiota in healthy individuals. In this RNA-based survey, we also detected small RNAs, which are important regulatory elements in prokaryotic physiology and pathogenicity.