A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner

Glowacki, Robert W. P.; Pudlo, Nicholas A.; Tunçil, Yunus E.; Luís, Ana S.; Sajjakulnukit, Peter; Terekhov, Anton I.; Lyssiotis, Costas A.; Hamaker, Bruce R.; Martens, Eric C.

doi:10.1016/j.chom.2019.11.009

Cited by 38 publications

(43 citation statements)

References 45 publications

(61 reference statements)

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“…Bacteroidetes has a powerful polysaccharide degradation system that can absorb undigested polysaccharides and then metabolize them into short-chain fatty acids, thereby improving intestinal epithelial barrier function and downregulating the level of inflammatory cytokines (Glowacki et al, 2020). Hence, to a certain extent, Bacteroides can limit the intestinal invasion of pathogens and toxins related to KD.…”

Section: Discussionmentioning

confidence: 99%

Effects of changes on gut microbiota in children with acute Kawasaki disease

Shen¹,

Ding²,

Yang³

et al. 2020

PeerJ

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Background Kawasaki disease (KD) is an acute febrile illness of early childhood. The exact etiology of the disease remains unknown. At present, research on KD is mostly limited to susceptibility genes, infections, and immunity. However, research on the correlation between gut microbiota and KD is rare. Methods Children with a diagnosis of acute KD and children undergoing physical examination during the same period were included. At the time of admission, the subjects’ peripheral venous blood and feces were collected. Faecal samples were analyzed for bacterial taxonomic content via high-throughput sequencing. The abundance, diversity, composition, and characteristic differences of the gut microbiota in KD and healthy children were compared by alpha diversity, beta diversity, linear discriminant analysis and LDA effect size analysis. Blood samples were used for routine blood examination, biochemical analysis, and immunoglobulin quantitative detection. Results Compared with the control group, the community richness and structure of gut microbiota in the KD group was significantly reduced (Chao1 richness estimator, mean 215.85 in KD vs. mean 725.76 in control, p < 0.01; Shannon diversity index, mean 3.32 in KD vs. mean 5.69 in control, p < 0.05). LEfSe analysis identified two strains of bacteria significantly associated with KD: Bacteroidetes and Dorea. Bacteroidetes were enriched in healthy children (mean 0.16 in KD vs. mean 0.34 in control, p < 0.05). Dorea was also enriched in healthy children but rarely existed in children with KD (mean 0.002 in KD vs. mean 0.016 in control, p < 0.05). Compared with the control, IgA and IgG in the KD group decreased (IgA, median 0.68 g/L in KD vs. median 1.06 g/L in control, p < 0.001; IgG, median 6.67 g/L in KD vs. median 9.71 g/L in control, p < 0.001), and IgE and IgM levels were not significantly changed. Conclusions Dysbiosis of gut microbiota occurs in children with acute KD and may be related to the etiology or pathogenesis of KD. It is worth noting that for the first time, we found that Dorea, a hydrogen-producing bacterium, was significantly reduced in children with acute KD. Overall, our results provide a theoretical basis for the prevention or diagnosis of KD based on intestinal microecology.

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Section: Discussionmentioning

confidence: 99%

Effects of changes on gut microbiota in children with acute Kawasaki disease

Shen¹,

Ding²,

Yang³

et al. 2020

PeerJ

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“…These changes were reflected by the increased propensity toward utilization of five monosaccharides including neuraminic acid (NANa), N-acetylglucosamine (GlcNAc), mannose (Man), and glucose (Glc) that constitute O- and N-linked glycans, as well as ribose (Rib). The latter monosaccharide is utilized by many gut bacteria such as Bacteroides spp., while ribose and ribose-containing molecules such as nucleic acids may serve as nutrients for these gut symbionts (Glowacki et al, 2020 ). The increased potential of mannose metabolism was reported in patients with ileal CD (Morgan et al, 2012 ).…”

Section: Discussionmentioning

confidence: 99%

Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases

Iablokov

Klimenko

Efimova³

et al. 2021

Front. Mol. Biosci.

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The gut microbiome is of utmost importance to human health. While a healthy microbiome can be represented by a variety of structures, its functional capacity appears to be more important. Gene content of the community can be assessed by “shotgun” metagenomics, but this approach is still too expensive. High-throughput amplicon-based surveys are a method of choice for large-scale surveys of links between microbiome, diseases, and diet, but the algorithms for predicting functional composition need to be improved to achieve good precision. Here we show how feature engineering based on microbial phenotypes, an advanced method for functional prediction from 16S rRNA sequencing data, improves identification of alterations of the gut microbiome linked to the disease. We processed a large collection of published gut microbial datasets of inflammatory bowel disease (IBD) patients to derive their community phenotype indices (CPI)—high-precision semiquantitative profiles aggregating metabolic potential of the community members based on genome-wide metabolic reconstructions. The list of selected metabolic functions included metabolism of short-chain fatty acids, vitamins, and carbohydrates. The machine-learning approach based on microbial phenotypes allows us to distinguish the microbiome profiles of healthy controls from patients with Crohn's disease and from ones with ulcerative colitis. The classifiers were comparable in quality to conventional taxonomy-based classifiers but provided new findings giving insights into possible mechanisms of pathogenesis. Feature-wise partial dependence plot (PDP) analysis of contribution to the classification result revealed a diversity of patterns. These observations suggest a constructive basis for defining functional homeostasis of the healthy human gut microbiome. The developed features are promising interpretable candidate biomarkers for assessing microbiome contribution to disease risk for the purposes of personalized medicine and clinical trials.

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“…Glowacki and coworkers show how a high-fiber diet can foster competitive colonization of Bacteroides thetaiotaomicron (Bt) in mice through ribose utilization. 4 Furthermore, they demonstrate that exogenous ribose can affect gut microbial architecture.…”

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confidence: 99%

“…In a recent issue of Cell Host & Microbe, Glowacki and colleagues tackle this issue and demonstrate how a high-fiber diet can foster competitive colonization of specific microbes through a novel nutrient utilization pathway. 4 Microbiota depends heavily on microbiotaaccessible-carbohydrates (MACs) for energy, which are primarily found in fiber rich foods. As early as the 1960s, a large intake of dietary fiber has been correlated with the lack of diabetes and heart disease; 5 more recent studies reveal the ability of short-chain fatty acids (SCFAs), the end-products resulting from microbial fermentation of fibercontaining diets, to interface with host physiology and protect against inflammatory conditions like colitis.…”

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confidence: 99%

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Gut Bacteria have a novel sweet tooth: ribose sensing and scavenging from fiber

Karri

Hirschi

2020

Gut Microbes

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Dietary fiber is known to influence symbiotic gut microbiota community structure and physiology; however, how and if dietary fiber can induce further exogenous nutrient uptake within gut microbes is ill-defined. Recent findings highlight how during periods of high-fiber consumption, a prevalent gut bacteria senses and scavenges the ubiquitous sugar ribose. This molecular adaptation exemplifies how particular gut microbes have developed a sophisticated system to scavenge nutrients in a diet-dependent manner.

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A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner

Cited by 38 publications

References 45 publications

Effects of changes on gut microbiota in children with acute Kawasaki disease

Effects of changes on gut microbiota in children with acute Kawasaki disease

Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases

Gut Bacteria have a novel sweet tooth: ribose sensing and scavenging from fiber

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