Gut Microbiome Metagenomics in Lean and Obese Individuals with Prediabetes and After Dietary Supplementation with Red Raspberry Fruit and Fermentable Fibers
Xuhuiqun ZhangJayanthi GangiredlaCarmen TarteraMark K. MammelTammy J. BarnabaIndika EdirisingheBritt Burton‐Freeman
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Abstract:
Metagenomic analysis of the human gut microbiome is a rich dataset for discovery of possible biomarker discovery linking molecular and genomic data of resident microbial communities to host factors such as diet and clinical indices of disease risk. The objectives of this research are to: 1) characterize the structural and functional capacity of the gut microbiome of individuals with prediabetes and insulin resistance (PreDM), including relationship to body adiposity; 2) assess the influence of fruit supplementation, specifically red raspberries (RRB), a source of dietary fiber and tannins, on metagenomic biomarkers, 3) assess whether adding fructo-oligosaccharide (FOS), a known prebiotic fiber, would augment the dietary fruit effect. In a randomized, 4-week treatment crossover clinical trial, subjects (n = 36: PreDM, n = 26; metabolically-healthy Reference group, n = 10) consumed RRB (1 cup fresh equivalence) daily or RRB with 8g FOS daily for 4 weeks separated by 4-week washout. DNA extracted from stool samples were assessed using whole-metagenome shotgun sequencing at week 0 for the PreDM and Reference groups and then after RRB vs. RRB + FOS supplementation. Blautia obeum (P = 0.02) and Blautia wexlerae (P < 0.001) were overly abundant characterizing the PreDM gut. Among PreDM, the obese subgroup (n = 15) were characterized by overabundant Bacteroides vulgatus and underabundant Bifidobacterium longum compared with PreDM lean group (n = 11) (P < 0.05). RRB supplementation increased Clostridium orbiscindensin all participants (P = 0.04), whereas adding FOS significantly increased Bifidobacterium spp.in all participants (P < 0.05), and reduced B. obeum (P = 0.04) and B. wexlerae (P = 0.03) in PreDM group. Distinguishing compositional characteristics of gut microbiome were evident among metabolically at risk individuals, and dietary strategies incorporating fruit/RRB with prebiotics/FOS revealed possible microbial biomarkers for clinical indices related to adiposity. Funds were provided by the National Processed Raspberry Council.Keywords:
Prediabetes
Prebiotic
Bifidobacterium longum
ABSTRACT Human milk is known to carry its own microbiota, of which the precise origin remains obscure. Breastfeeding allows mother-to-baby transmission of microorganisms as well as the transfer of many other milk components, such as human milk oligosaccharides (HMOs), which act as metabolizable substrates for particular bacteria, such as bifidobacteria, residing in infant intestinal tract. In the current study, we report the HMO composition of 249 human milk samples, in 163 of which we quantified the abundance of members of the Bifidobacterium genus using a combination of metagenomic and flow cytometric approaches. Metagenomic data allowed us to identify four clusters dominated by Bifidobacterium adolescentis and Bifidobacterium pseudolongum, Bifidobacterium crudilactis or Bifidobacterium dentium, as well as a cluster represented by a heterogeneous mix of bifidobacterial species such as Bifidobacterium breve and Bifidobacterium longum. Furthermore, in vitro growth assays on HMOs coupled with in silico glycobiome analyses allowed us to elucidate that members of the Bifidobacterium bifidum and B. breve species exhibit the greatest ability to degrade and grow on HMOs. Altogether, these findings indicate that the bifidobacterial component of the human milk microbiota is not strictly correlated with their ability to metabolize HMOs.
Bifidobacterium longum
Bifidobacterium breve
Bifidobacterium bifidum
Actinomycetaceae
Human gastrointestinal tract
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ABSTRACT tet (W) was found responsible for tetracycline resistance (MICs, 4 to ≥32 μg ml −1 ) in dominant bifidobacterial species from the gastrointestinal tracts of healthy humans. The gene from Bifidobacterium longum H66 proved to be identical over a 2.6-kbp region to the recently described tet (W) determinant of Butyrivibrio fibrisolvens .
Bifidobacterium longum
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Bifidobacterium longum
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Prebiotic
Bifidobacterium longum
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Faecal and serum samples were collected over a period of 6 months from 55 institutionalized elderly subjects, who were enrolled in a double-blind placebo-controlled study. Participants were randomized in one of the three treatment groups: intervention (two probiotic Bifidobacterium longum strains: 2C and 46), placebo and commercial control (Bifidobacterium lactis Bb-12). The faecal Bifidobacterium microbiota was characterized by genus and species-specific PCR. Serum levels of the cytokines IL-10, tumor necrosis factor (TNF)-alpha and transforming growth factor (TGF)-beta1 were determined by enzyme-linked immunosorbent assay. Each participant harboured on average approximately three different bifidobacterial species. The most frequently detected species were B. longum, Bifidobacterium adolescentis and Bifidobacterium bifidum. Depending on the treatment, the intervention resulted in specific changes in the levels of certain Bifidobacterium species, and positive correlations were found between the different species. Negative correlations were observed between the levels of Bifidobacterium species and the pro-inflammatory cytokine TNF-alpha and the regulatory cytokine IL-10. The presence of faecal B. longum and Bifidobacterium animalis correlated with reduced serum IL-10. The anti-inflammatory TGF-beta1 levels were increased over time in all three groups, and the presence of Bifidobacterium breve correlated with higher serum TGF-beta1 levels. This indicates that modulation of the faecal Bifidobacterium microbiota may provide a means of influencing inflammatory responses.
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For the first time in Iran 40 strains of Bifidobacterium were isolated from feces of Iranian subjects. By using phenotypic tests, 18 isolates were identified as Bifidobacterium longum, 10 as Bifidobacterium bifidum and one as Bifidobacterium catenolatum. In order to validate these results and also to identify other isolates that had not been identified by phenotypic tests, two methods of PCR with genus-specific primers of Bif164f and Bif601r and 16SrRNA gene sequence analysis were applied. Results of PCR confirmed the obtained phenotypic identifications. Moreover by this method the 8 remaining strains were identified as Bifidobacterium species. Using sequencing 16SrRNA gene, 5 B. longum strains were identified that had different fermentation pattern from B. longum. Some new ribose negative Bifidobacterium longum strains were also identified. The obtained results present new strains of Bifidobacterium longum.
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Different in vitro models have been developed to assess how food compounds affect the human gut microbiota. Using two such models (SHIME(R) and TIM-2), we compared how long-chain arabinoxylan (LC-AX), a wheat-derived potentially prebiotic fiber, and inulin (IN), a well-established prebiotic compound, modulate SCFA production and bifidobacteria composition. While both the SHIME and TIM-2 differ in experimental design, they both demonstrated that LC-AX and IN specifically increased the health-promoting metabolites propionate and butyrate, respectively. Furthermore, LC-AX stimulated Bifidobacterium longum, while IN stimulated other bifidobacteria including Bifidobacterium adolescentis. The SHIME experiment also revealed that effects of LC-AX were more persistent during the 2-week wash-out period. These results confirm a recent in vivo study, during which humanized rats were treated with the same LC-AX/IN. In conclusion, results from different human gut models suggest that, besides IN, LC-AX are promising prebiotic candidates with high specificity toward Bifidobacterium longum and a selective propionate increase.
Arabinoxylan
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ABSTRACT A healthy intestinal microbiota is considered to be important for priming of the infants' mucosal and systemic immunity. Breast-fed infants typically have an intestinal microbiota dominated by different Bifidobacterium species. It has been described that allergic infants have different levels of specific Bifidobacterium species than healthy infants. For the accurate quantification of Bifidobacterium adolescentis , Bifidobacterium angulatum , Bifidobacterium bifidum , Bifidobacterium breve , Bifidobacterium catenulatum , Bifidobacterium dentium , Bifidobacterium infantis , and Bifidobacterium longum in fecal samples, duplex 5′ nuclease assays were developed. The assays, targeting rRNA gene intergenic spacer regions, were validated and compared with conventional PCR and fluorescent in situ hybridization methods. The 5′ nuclease assays were subsequently used to determine the relative amounts of different Bifidobacterium species in fecal samples from infants receiving a standard formula or a standard formula supplemented with galacto- and fructo-oligosaccharides (OSF). A breast-fed group was studied in parallel as a reference. The results showed a significant increase in the total amount of fecal bifidobacteria (54.8% ± 9.8% to 73.4% ± 4.0%) in infants receiving the prebiotic formula (OSF), with a diversity of Bifidobacterium species similar to breast-fed infants. The intestinal microbiota of infants who received a standard formula seems to resemble a more adult-like distribution of bifidobacteria and contains relatively more B. catenulatum and B. adolescentis (2.71% ± 1.92% and 8.11% ± 4.12%, respectively, versus 0.15% ± 0.11% and 1.38% ± 0.98% for the OSF group). In conclusion, the specific prebiotic infant formula used induces a fecal microbiota that closely resembles the microbiota of breast-fed infants also at the level of the different Bifidobacterium species.
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Bifidobacterium bifidum
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ABSTRACT A highly sensitive quantitative PCR detection method has been developed and applied to the distribution analysis of human intestinal bifidobacteria by combining real-time PCR with Bifidobacterium genus- and species-specific primers. Real-time PCR detection of serially diluted DNA extracted from cultured bifidobacteria was linear for cell counts ranging from 10 6 to 10 cells per PCR assay. It was also found that the method was applicable to the detection of Bifidobacterium in feces when it was present at concentrations of >10 6 cells per g of feces. Concerning the distribution of Bifidobacterium species in intestinal flora, the Bifidobacterium adolescentis group, the Bifidobacterium catenulatum group, and Bifidobacterium longum were found to be the three predominant species by examination of DNA extracted from the feces of 46 healthy adults. We also examined changes in the population and composition of Bifidobacterium species in human intestinal flora of six healthy adults over an 8-month period. The results showed that the composition of bifidobacterial flora was basically stable throughout the test period.
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Actinomycetaceae
Human feces
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