Development of human colonic microbiota in the computer-controlled dynamic SIMulator of the GastroIntestinal tract SIMGI

Barroso, Elvira; Cueva, Carolina; Peláez, Carmen; Martínez-Cuesta, M. Carmen; Requena, Teresa

doi:10.1016/j.lwt.2014.12.014

Cited by 92 publications

(77 citation statements)

References 41 publications

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“…The evolution of the gut microbiota in the AC, TC and DC compartments of the SIMGI model was followed during a 2-week stabilization period (Barroso et al 2015 ). Results indicated that from day 8 onwards the microbial DGGE fi ngerprints of samples from the same compartment clustered together and that at 14 days the microbial communities reached the steady state.…”

Section: Stability and Reproducibility Of The Systemmentioning

confidence: 99%

The Computer-Controlled Multicompartmental Dynamic Model of the Gastrointestinal System SIMGI

Barroso

Cueva

Peláez

et al. 2015

The Impact of Food Bioactives on Health

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The SIMGI (SIMulator Gastro-Intestinal) is an automated gastrointestinal in vitro model designed to dynamically simulate the physiological processes taking place during digestion in the stomach and small intestine, as well as to reproduce the colonic microbiota responsible for metabolic bioconversions in the large intestine. This computer-controlled system is a fl exible modulating system that combines a gastric compartment that operates with peristaltic mixing movements, a reactor simulating the small intestine and three-stage continuous reactors that reproduce the colon region-specifi c microbiota. The compartments designed for digestion (stomach and small intestine) and fermentation (colon) can be connected to operate jointly. Alternatively, the digestion and fermentation processes can proceed independently. This section describes the conditions needed to inoculate, stabilize and differentiate the fecal microbiota in the SIMGI system, as well as the steps to follow in order to test the stabilized colonic microbiota with different food ingredients and/or by modifying the caloric intake in the nutrition media.

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Section: Stability and Reproducibility Of The Systemmentioning

confidence: 99%

The Computer-Controlled Multicompartmental Dynamic Model of the Gastrointestinal System SIMGI

Barroso

Cueva

Peláez

et al. 2015

The Impact of Food Bioactives on Health

Self Cite

View full text Add to dashboard Cite

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“…Also note that spatially separated 285 microbial compositions, corresponding to the trophic levels in our model, could in principle be 286 tested in artificial gut systems (such as in Refs. [31,32]).…”

mentioning

confidence: 99%

Evidence for a multi-level trophic organization of the human gut microbiome

Wang

Goyal

Dubinkina

et al. 2019

Preprint

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1The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and 2 metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, 3 both the large-scale trophic organization of this ecosystem, and its effects on the underlying 4 metabolic flow, remain unexplored. Here, using a simplified model, we provide quantitative 5 support for a multi-level trophic organization of the human gut microbiome, where microbes 6 consume and secrete metabolites in multiple iterative steps. Using a manually-curated set of 7 metabolic interactions between microbes, our model suggests about four trophic levels, each 8 characterized by a high level-to-level metabolic transfer of byproducts. It also quantitatively 9 predicts the typical metabolic environment of the gut (fecal metabolome) in approximate 10 agreement with the real data. To understand the consequences of this trophic organization, we 11 quantify the metabolic flow and biomass distribution, and explore patterns of microbial and 12 metabolic diversity in different levels. The hierarchical trophic organization suggested by our 13 model can help mechanistically establish causal links between the abundances of microbes and 14 metabolites in the human gut. 15 Introduction 16 The human gut microbiome is a complex ecosystem with several hundreds of microbial species 17 [1,2] consuming, producing and exchanging hundreds of metabolites [3,4,5,6,7]. With 18 the advent of high-throughput genomics and metabolomics techniques, it is now possible to 19 simultaneously measure the levels of individual metabolites (the fecal metabolome), as well as 20 the abundances of individual microbial species [8]. Quantitatively connecting these levels with 21 each other, requires knowledge of the relationships between microbes and metabolites in their 22 shared environment: who produces what, and who consumes what? [9,10] In recent studies, 23 information about these relationships for all of the common species and metabolites in the human 24 gut has been gathered using both manual curation from published studies [6] and automated 25 genome reconstruction methods [3]. This has laid the foundation for mechanistic models which 26 would allow one to relate metabolome composition to microbiome composition [11,12]. 27More generally, the construction of mechanistic models has been hindered by the complexity 28 of dynamical processes taking place in the human gut, which in addition to cross-feeding and 29 2 competition, includes differential spatial distribution and species motility, interactions of microbes 30 with host immune system and bacteriophages, changes in activity of metabolic pathways in 31 individual species in response to environmental parameters, etc. This complexity can be tackled 32 on several distinct levels. For 2-3 species it is possible to construct a detailed dynamical model 33 taking into account the spatial organization and flow of microbes and nutrients within the lower 34 gut [13,14], or optimizing the intracellular metabol...

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“…Una vez establecidas las variables de funcionamiento, se llevó a cabo la inoculación de los fermentadores colónicos con microbiota fecal humana. Los resultados de este estudio demostraron que el simgi ® permite obtener una microbiota colónica estable y diferenciada tanto en composición como en funcionalidad (24). Alcanzado este objetivo, el siguiente paso fue definir los modos de operación del simgi ® , quedando establecidos en 3 (Tabla II), lo que permite una gran versatilidad experimental.…”

Section: Modelos De Simulación De La Microbiota Intestinal: Caso Espeunclassified

Simulador gastrointestinal dinámico (simgi®): una herramienta potencialmente útil en nutrición clínica

Tamargo¹,

Gil‐Sánchez²,

Miralles³

et al. 2017

Nutr Hosp

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Dentro de la microbiota humana, el tracto gastrointestinal alberga el ecosistema más complejo y abundante del cuerpo humano, siendo el colon donde se encuentra la concentración más alta de microrganismos (1012cél/g). La microbiota intestinal desempeña funciones metabólicas, tróficas y de protección que son de gran importancia para el hospedador. Durante las últimas décadas, son numerosos los estudios que han tratado de aportar evidencias científicas acerca de los factores que, a través de cambios en la composición de la microbiota intestinal, influyen en la salud humana. Sin embargo, esta aproximación está cambiando, y son cada vez más los expertos que apuestan por evaluar cambios a nivel de funcionalidad de la microbiota. Si aplicamos este enfoque dual al papel desempeñado por la dieta, resulta obvia la necesidad de disponer de modelos dinámicos de simulación gastrointestinal, como es el simgi®, que permitan evaluar las transformaciones que sufren los alimentos y/o ingredientes alimentarios durante el tránsito por el tracto gastrointestinal, así como para determinar los posibles cambios en la composición y funcionalidad de la microbiota intestinal derivados de la ingesta de alimentos. Los estudios llevados a cabo hasta el momento con el simgi® constatan sus potenciales aplicaciones en el área de los alimentos como paso previo a su aplicación en nutrición clínica, para prevenir y/o tratar enfermedades asociadas a disbiosis intestinal, así como trastornos metabólicos. Así mismo, esta revisión recoge posibles perspectivas de utilización del simgi® en la investigación clínica relativa a enfermedades relacionadas con disfunciones de la microbiota intestinal

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Development of human colonic microbiota in the computer-controlled dynamic SIMulator of the GastroIntestinal tract SIMGI

Cited by 92 publications

References 41 publications

The Computer-Controlled Multicompartmental Dynamic Model of the Gastrointestinal System SIMGI

The Computer-Controlled Multicompartmental Dynamic Model of the Gastrointestinal System SIMGI

Evidence for a multi-level trophic organization of the human gut microbiome

Simulador gastrointestinal dinámico (simgi®): una herramienta potencialmente útil en nutrición clínica

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