Treatment with a spore-based probiotic containing five strains of Bacillus induced changes in the metabolic activity and community composition of the gut microbiota in a SHIME® model of the human gastrointestinal system

Marzorati, Massimo; Abbeele, Pieter Van den; Bubeck, Sarah S.; Bayne, Thomas; Krishnan, Kiran; Young, Aicacia

doi:10.1016/j.foodres.2021.110676

Cited by 31 publications

(21 citation statements)

References 66 publications

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“…Finally, a critical remark on the limitation of the applied experimental design is that the reference to which treatment effects were compared consisted of a preceding control period. Such longitudinal control is common in a SHIME setup [69][70][71], and the stability of in vitro communities upon applying a 2-week stabilization period has previously been demonstrated [67]. It would have been ideal to follow the stability of the microbial communities during the entire duration of the current study by means of incorporating four additional untreated parallel control arms.…”

Section: Discussionmentioning

confidence: 99%

Consistent Prebiotic Effects of Carrot RG-I on the Gut Microbiota of Four Human Adult Donors in the SHIME® Model despite Baseline Individual Variability

et al. 2021

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The human gut microbiome is currently recognized to play a vital role in human biology and development, with diet as a major modulator. Therefore, novel indigestible polysaccharides that confer a health benefit upon their fermentation by the microbiome are under investigation. Based on the recently demonstrated prebiotic potential of a carrot-derived pectin extract enriched for rhamnogalacturonan I (cRG-I), the current study aimed to assess the impact of cRG-I upon repeated administration using the M-SHIME technology (3 weeks at 3g cRG-I/d). Consistent effects across four simulated adult donors included enhanced levels of acetate (+21.1 mM), propionate (+17.6 mM), and to a lesser extent butyrate (+4.1 mM), coinciding with a marked increase of OTUs related to Bacteroides dorei and Prevotella species with versatile enzymatic potential likely allowing them to serve as primary degraders of cRG-I. These Bacteroidetes members are able to produce succinate, explaining the consistent increase of an OTU related to the succinate-converting Phascolarctobacterium faecium (+0.47 log10(cells/mL)). While the Bifidobacteriaceae family remained unaffected, a specific OTU related to Bifidobacterium longum increased significantly upon cRG-I treatment (+1.32 log10(cells/mL)). Additional monoculture experiments suggested that Bifidobacterium species are unable to ferment cRG-I structures as such and that B. longum probably feeds on arabinan and galactan side chains of cRG-I, released by aforementioned Bacteroidetes members. Overall, this study confirms the prebiotic potential of cRG-I and additionally highlights the marked consistency of the microbial changes observed across simulated subjects, suggesting the involvement of a specialized consortium in cRG-I fermentation by the human gut microbiome.

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Section: Discussionmentioning

confidence: 99%

Consistent Prebiotic Effects of Carrot RG-I on the Gut Microbiota of Four Human Adult Donors in the SHIME® Model despite Baseline Individual Variability

et al. 2021

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“…This system can be primed with fecal suspensions or engineered with specific microbes to enable specific molecular interactions to be studied under controlled conditions. This model has been used to elucidate the effects of diet and pre-or probiotics on organic acid and short-chain fatty acid (SCFA) production in different GI compartments 36,38,[80][81][82] . Other organ models include the Winogradsky column system, which has been used to study the microbial community interactions underlying pulmonary infections [25][26][27] , and a range of single compartment chemostat reactors that have been used to simulate specific microbiome ecosystems (e.g., the human colon) 37,76,77,79,[83][84][85][86] .…”

Section: Organ Models Of Microbiome Metabolismmentioning

confidence: 99%

“…Diet plays a large role in microbiota-mediated effects in the host. Probiotic and prebiotic (e.g., inulin and stachyose) treatments can be used to stimulate specific strains in the gut microbiome to produce higher levels of SCFAs 21,[36][37][38] . Host nutrition can also be corrected through cross-feeding, where in flies, Lactobacillus and Acetobacter establish a syntrophic relationship to overcome nutrient scarcity due to an imbalanced diet 61 .…”

Section: Examples Of Host-microbiome Dynamics That Are Modulated Thro...mentioning

confidence: 99%

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Moving beyond descriptive studies: harnessing metabolomics to elucidate the molecular mechanisms underpinning host-microbiome phenotypes

et al. 2022

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Advances in technology and software have radically expanded the scope of metabolomics studies and allow us to monitor a broad transect of central carbon metabolism in routine studies. These increasingly sophisticated tools have shown that many human diseases are modulated by microbial metabolism. Despite this, it remains surprisingly difficult to move beyond these statistical associations and identify the specific molecular mechanisms that link dysbiosis to the progression of human disease. This difficulty stems from both the biological intricacies of host-microbiome dynamics as well as the analytical complexities inherent to microbiome metabolism research. The primary objective of this review is to examine the experimental and computational tools that can provide insights into the molecular mechanisms at work in host-microbiome interactions and to highlight the undeveloped frontiers that are currently holding back microbiome research from fully leveraging the benefits of modern metabolomics.

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“…Treatment with B. subtilus HU58, in combination with other probiotic strains, has resulted in health benefits in both humans and animals [27][28][29][30]. In-vitro studies using probiotic treatments that include B. subtilis HU58 have reported increased levels of SCFAs, increased relative abundance of beneficial microbial families, increased microbial diversity [31], and potential benefits to microbial community recovery after antibiotic exposure [32] with treatment versus untreated control.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the Effect of Food Products Containing Prebiotics and Bacillus subtilis HU58 on the Gut Microbial Community Activity and Community Composition Using an In Vitro M-SHIME® Model

Marzorati

Bubeck²,

Bayne³

et al. 2021

Applied Sciences

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GoodBiome™ Foods is a collection of foods infused with prebiotics, including inulin and xylooligosaccharides, and the probiotic Bacillus subtilis HU58. The effects of repeated intake of three predigested GoodBiome™ Foods products and one comparator product on microbial community activity and composition were assessed using the mucosal simulator of the human intestinal microbial system (M-SHIME®) platform with proximal colon (PC) and distal colon (DC) compartments and conducted under healthy gut conditions. Treatment with all test products increased short-chain fatty acid (SCFA) production (acetate, propionate, and butyrate) versus the control period in both the PC and DC. The highest increases were seen with the GoodBiome™ Foods products. Ammonium and branched SCFA levels were also increased (versus the control period) in both compartments. Treatment with all test products enhanced the Simpson diversity index (versus the control period), reaching significance for all test products in the PC (p < 0.05). Treatment with all test products resulted in changes in the microbial community composition. The relative abundance increased for Proteobacteria and decreased for Actinobacteria in the PC and DC. Repeated intake of GoodBiome™ Food products increased SCFA production and microbial diversity in an M-SHIME® model of the human intestinal microbiome.

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Treatment with a spore-based probiotic containing five strains of Bacillus induced changes in the metabolic activity and community composition of the gut microbiota in a SHIME® model of the human gastrointestinal system

Cited by 31 publications

References 66 publications

Consistent Prebiotic Effects of Carrot RG-I on the Gut Microbiota of Four Human Adult Donors in the SHIME® Model despite Baseline Individual Variability

Consistent Prebiotic Effects of Carrot RG-I on the Gut Microbiota of Four Human Adult Donors in the SHIME® Model despite Baseline Individual Variability

Moving beyond descriptive studies: harnessing metabolomics to elucidate the molecular mechanisms underpinning host-microbiome phenotypes

Evaluation of the Effect of Food Products Containing Prebiotics and Bacillus subtilis HU58 on the Gut Microbial Community Activity and Community Composition Using an In Vitro M-SHIME® Model

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