Studies suggesting that the development of atopy is linked to gut microbiota composition are inconclusive on whether dysbiosis precedes or arises from allergic symptoms. Using a mouse model of cow's milk allergy, we aimed at investigating the link between the intestinal microbiota, allergic sensitization, and the severity of symptoms. Germ‐free and conventional mice were orally sensitized with whey proteins and cholera toxin, and then orally challenged with β‐lactoglobulin (BLG). Allergic responses were monitored with clinical symptoms, plasma markers of sensitization, and the T‐helper Th1/Th2/regulatory‐T‐cell balance. Microbiota compositions were analysed using denaturing gradient gel electrophoresis and culture methods. Germ‐free mice were found to be more responsive than conventional mice to sensitization, displaying a greater reduction of rectal temperature upon challenge, higher levels of blood mouse mast cell protease‐1 (mMCP‐1) and BLG‐specific immunoglobulin G1 (IgG1), and a systemic Th2‐skewed response. This may be explained by a high susceptibility to release mMCP‐1 even in the presence of low levels of IgE. Sensitization did not alter the microbiota composition. However, the absence of or low Staphylococcus colonization in the caecum was associated with high allergic manifestations. This work demonstrates that intestinal colonization protects against oral sensitization and allergic response. This is the first study to show a relationship between alterations within the subdominant microbiota and severity of food allergy.

Faecal microbiota of healthy infant displays a large abundance of Bifidobacterium spp. and Bacteroides spp. Although some studies have reported an association between these two genera and allergy, these findings remain a subject of debate. Using a gnotobiotic mouse model of cow's milk allergy, we investigated the impact of an infant gut microbiota – mainly composed of Bifidobacterium and Bacteroides spp. – on immune activation and allergic manifestations. The transplanted microbiota failed to restore an ileal T-cell response similar to the one observed in conventional mice. This may be due to the low bacterial translocation into Peyer's patches in gnotobiotic mice. The allergic response was then monitored in germ-free, gnotobiotic, and conventional mice after repeated oral sensitization with whey proteins and cholera toxin. Colonized mice displayed a lower drop of rectal temperature upon oral challenge with b-lactoglobulin, lower plasma mMCP-1, and lower anti-BLG IgG1 than germ-free mice. The foxp3 gene was highly expressed in the ileum of both colonized mice that were protected against allergy. This study is the first demonstration that a transplanted healthy infant microbiota mainly composed of Bifidobacterium and Bacteroides had a protective impact on sensitization and food allergy in mice despite altered T-cell response in the ileum.

The beneficial effects of Bifidobacterium are partly due to its immunostimulatory properties. These immunostimulatory properties may be linked to the presence of unmethylated CpG motifs specific to bacterial DNA, which may induce a TH1 response by activating Toll-like receptors (TLR). Using in silico analyses, PCR amplification, and dot blotting, we characterized the CpG content of various bifidobacterial strains and evaluated the immunostimulatory properties and genomic heterogeneity of these motifs in the genus. Our in silico study, based on entire genome sequences from five bifidobacterial strains, showed that Bifidobacterium genomes contain numerous CpG motifs, including 5-purine-purine-CG-pyrimidine-pyrimidine-3 and 5-purine-TCG-pyrimidine-pyrimidine-3 motifs, and biologically active sequences previously identified in lactic acid bacteria. We identified four CpG-rich sequences with Bifidobacterium longum NCC2705. Two sequences with a percent G؉C of about 68% included 14 and 16 CpG motifs. Two sequences with a percent G؉C of about 60% included 16 and 6 CpG motifs. These sequences induce the production of monocyte chemoattractant protein 1 (MCP-1) and tumor necrosis factor alpha (TNF-␣) through a pattern of TLR9 stimulation on RAW 264.7 macrophages. No link could be established between their immunostimulatory properties, the number of CpG motifs, and percent G؉C. We investigated inter-and intraspecies heterogeneity in 71 strains of various origins. These sequences were highly conserved in the genus. No link was found between the presence of the CpG-rich sequence and the origin of the strains (healthy, allergic, or preterm infants). The high frequency of CpG motifs in the DNA of Bifidobacterium may play an important role in the immunostimulatory properties of commensal or probiotic bifidobacterial strains.

Preventive actions of probiotics as antidiarrheal agents are well documented, but their mechanisms are poorly understood. Two selected probiotics, Bacillus subtilis CU1 and Lactobacillus plantarum CNCM I-4547, were tested in mouse experimental models of diarrhea and the possible mechanisms of action were investigated. Diarrhea was induced in mice by oral castor oil administration or by i.v. injection of lipopolysaccharide (LPS) of Salmonella enteritis. The antidiarrheal drug loperamide was used as control. Fecal water excretion was quantified for 2 h and paracellular permeability and electrical parameters of the colon were assessed in Ussing chambers. The expression of colonic exchangers or channels and of Toll-like receptor 4 (TLR4) was assessed by immunohistochemistry. Prophylactic treatment with B. subtilis CU1 or with L. plantarum CNCM I-4547 reduced LPS-induced diarrhea. The reduction of water excretion was in the same range as those induced by loperamide. In the castor oil model, this effect was only observed with B. subtilis CU1. The two probiotic treatments abolished the increase in paracellular permeability induced by LPS, but not by castor oil. However, only L. plantarum CNCM I-4547 treatment decreased the colonic expression of TLR-4. After B. subtilis CU1, colonic expression of cystic fibrosis transmembrane conductance regulator (CFTR) was reduced and that of Na+/H+ exchanger 3 (NHE3) increased. B. subtilis CU1 may increase the capacity of the colon to absorb excess of water in diarrheic conditions by acting on CFTR and NHE3 expression. The two probiotics strains showed an impact on diarrhea through limitation of water excretion that may involve paracellular permeability or electrolyte transport for L. plantarum CNCM I-4547 and B. subtilis CU1 respectively.

Bacterial vaginosis and vulvovaginal candidiasis are common causes of impaired health and quality of life for women. Although antimicrobial agents remain the main strategy for the treatment of vaginal infections, their repeated use involves high rates of resistance and recurrence. Alternative approaches such as probiotics are studied. Saccharomyces cerevisiae CNCM I-3856 already demonstrated beneficial effects in experimental models of vaginal infections. This randomized, double-blind, placebo-controlled clinical study was performed to evaluate the recovery of S. cerevisiae CNCM I-3856 in vaginal samples in healthy women after oral consumption. Sixty healthy women were randomized to receive a daily dose of S. cerevisiae CNCM I-3856 or a placebo for 4 weeks. Subcultures and quantitative polymerase chain reaction (qPCR) were used to detect the strain in vaginal and stool samples. A safety assessment was carried out throughout the study. Fifty-seven women completed the study. Over the 4-week supplementation phase, S. cerevisiae CNCM I-3856 has been detected in the vaginal samples of 21% of women (n = 4/19) in the 500 mg Probiotic group and 16% of women (n = 3/19) in the 1000 mg Probiotic group. The strain was detected in the faeces of 90% of women consuming the probiotic. This is the first clinical study demonstrating the migration of yeast from intestine to vagina where it may exert its benefits.

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How to define and promote a healthy state of the vaginal microbiome is not well understood. Knowledge of which underlying factors shape the microbial community composition of the vagina and how to modulate them will contribute to vaginal disease prevention and improve fertility.

Microbiomes are an essential contributor to the metabolic activity in the human gastrointestinal tract. The fermentation of otherwise indigestible nutritional components like dietary fibers relies on a complex interplay of metabolic pathways that are distributed across the individual bacteria. Yet, which of the bacteria are responsible for which parts of the distributed metabolism and how they should be grouped together is insufficiently understood. Here, we present the NicheMap(TM), an approach to map the different bacterial taxa that make up the gut microbiome onto the different functional niches of microbial carbohydrate fermentation. Our approach uses in vitro measurements of bacterial growth and metabolic activity to identify which bacterial taxa are responsible for which metabolic function in the relevant complex context of whole human fecal microbiomes. We identified 'characteristic taxa' selected for by a panel growth substrates representative of dietary components that are resistant to digestion by host enzymes. These characteristic taxa offer predictions of which bacteria are stimulated by the various components of human diet. We validated these predictions using microbiome data from a human nutritional supplementation study. We suggest a template of how bacterial taxonomic diversity is organized along the trophic cascade of intestinal carbohydrate fermentation. We anticipate that our results and our approach will provide a key contribution towards building a structure-function map for gut microbiomes. Having such a map on hand is an important step in moving the microbiome from a descriptive science to an interventional one.