Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells

Greenhalgh, Kacy; Ramiro-García, Javier; Heinken, Almut; Ullmann, Pit; Bintener, Tamara Jean Rita; Pacheco, Maria Pires; Bagińska, Joanna; Shah, Pranjul Jaykumar; Frachet, Audrey; Halder, Rashi; Fritz, Joëlle V.; Sauter, Thomas; Thiele, Ines; Haan, Serge; Letellier, Elisabeth; Wilmes, Paul

doi:10.1016/j.celrep.2019.04.001

Cited by 71 publications

(51 citation statements)

References 83 publications

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“…Although this would be a good starting point, such a system would be limited in its ability to provide precise and personalized recommendations that usually need a platform that can create new products or processes on a case-by-case basis. Recent studies simulate a virtual gut microbiome by integrating known metabolic pathways of microbial species with the individual's microbiome and diet (Shoaie et al, 2015;Baldini et al, 2018;Bauer and Thiele, 2018;Greenhalgh et al, 2018). Such mechanistic modeling is very promising, however, it is currently hindered by numerous challenges, such as incomplete characterization of an individual's gut and metabolic pathways of their microbiome.…”

Section: Recommendation Systems and Artificial Intelligencementioning

confidence: 99%

“…Despite our limited understanding regarding its intricate relationship with the host and its environment (Foster et al, 2017), recent discoveries related to the human microbiome have opened new horizons in food science (Barratt et al, 2017), precision medicine (Wishart, 2016), and biotechnology (Taroncher-Oldenburg et al, 2018) among other fields. In parallel, advances in genomics and bioinformatics have provided inexpensive tools to acquire biological and clinical data, as well as the tools to translate the data into knowledge (Shoaie et al, 2015;Zeevi et al, 2015;Thaiss et al, 2016a;Korem et al, 2017;Baldini et al, 2018;Bauer and Thiele, 2018;Gilbert et al, 2018;Greenhalgh et al, 2018;Knight et al, 2018). Given these advances, the integration of diet, gut microbiome, and human health (DGMH) data has the potential to drive a paradigm shift in the way wellness states are measured, diseases are treated, products are designed, and health interventions are administered.…”

Section: Introductionmentioning

confidence: 99%

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The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health

et al. 2020

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Food and human health are inextricably linked. As such, revolutionary impacts on health have been derived from advances in the production and distribution of food relating to food safety and fortification with micronutrients. During the past two decades, it has become apparent that the human microbiome has the potential to modulate health, including in ways that may be related to diet and the composition of specific foods. Despite the excitement and potential surrounding this area, the complexity of the gut microbiome, the chemical composition of food, and their interplay in situ remains a daunting task to fully understand. However, recent advances in high-throughput sequencing, metabolomics profiling, compositional analysis of food, and the emergence of electronic health records provide new sources of data that can contribute to addressing this challenge. Computational science will play an essential role in this effort as it will provide the foundation to integrate these data layers and derive insights capable of revealing and understanding the complex interactions between diet, gut microbiome, and health. Here, we review the current knowledge on diet-health-gut microbiota, relevant data sources, bioinformatics tools, machine learning capabilities, as well as the intellectual property and legislative regulatory landscape. We provide guidance on employing machine learning and data analytics, identify gaps in current methods, and describe new scenarios to be unlocked in the next few years in the context of current knowledge.

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Section: Recommendation Systems and Artificial Intelligencementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health

et al. 2020

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“…Reproducible human organoids have been used to recapitulate irritable bowel syndrome manifestations and the restorative effects of L. rhamnosus GG ( Han et al, 2019 ). Sophisticated organs-on-chips combine advances in human cell culturing with microelectronics and microfluidics to discover the anti-cancer potential of probiotic and synbiotic formulations, however, they are limited due to lack of exposure to host defenses ( Bein et al, 2018 ; Greenhalgh et al, 2019 ). Cervico-vaginal tissue explants and organotypic tissue models circumvent this by combining human epithelial and immune cells and have previously allowed to identify anti-HIV-1 effects of wild type and genetically modified lactobacilli ( Lagenaur et al, 2011 ; Ñahui Palomino et al, 2017 ).…”

Section: Developments In Probiotics and Prebiotics Researchmentioning

confidence: 99%

Future of Probiotics and Prebiotics and the Implications for Early Career Researchers

et al. 2020

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The opportunities in the fields of probiotics and prebiotics to a great degree stem from what we can learn about how they influence the microbiota and interact with the host. We discuss recent insights, cutting-edge technologies and controversial results from the perspective of early career researchers innovating in these areas. This perspective emerged from the 2019 meeting of the International Scientific Association for Probiotics and Prebiotics-Student and Fellows Association (ISAPP-SFA). Probiotic and prebiotic research is being driven by genetic characterization and modification of strains, stateof-the-art in vitro, in vivo, and in silico techniques designed to uncover the effects of probiotics and prebiotics on their targets, and metabolomic tools to identify key molecules that mediate benefits on the host. These research tools offer unprecedented insights into the functionality of probiotics and prebiotics in the host ecosystem. Young scientists need to acquire these diverse toolsets, or form interconnected teams to perform comprehensive experiments and systematic analysis of data. This will be critical to identify microbial structure and co-dependencies at body sites and determine how administered probiotic strains and prebiotic substances influence the host. This and other strategies proposed in this review will pave the way for translating the health benefits observed during research into real-life outcomes. Probiotic strains and prebiotic products can contribute greatly to the amelioration of global issues threatening society. The intent of this article is to provide an early career researcher's perspective on where the biggest opportunities lie to advance science and impact human health.

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“…They will among other things support the development of applications to manipulate microbiome (OECD 2017). Nevertheless, researchers have already identified the potential use of M&S applied to the microbiome field (Moorthy and Eberl 2017; Borenstein 2012; Bauer and Thiele 2018; Greenhalgh et al 2019;Michelini et al 2018). Moorthy et al proposed an in silico platform to investigate host microbiome, its interactions, and its role on the host health (Moorthy and Eberl 2017).…”

Section: New Nonclinical / Clinical Approach: In Silico Modeling and mentioning

confidence: 99%

Microbiome Product Toxicology: Regulatory View on Translational Challenges

Rousseau¹,

Desvignes²,

Kling³

et al. 2020

Regulatory Toxicology

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The recent rise of science in the microbiome field has brought to light new opportunities of health technologies development. Microbiome-derived products are very diverse and encompass several product categories such as foods as well as medicinal products. While some guidance and recommendations are being drawn for very specific microbiome applications, there is no consolidated regulatory framework applicable to all microbiome products. Any specific requirements should be carefully considered on a case-by-case basis in order to demonstrate the safety and efficacy of these new high potential healthcare solutions. Specific challenges due to the nature of microbiome health products must be addressed for toxicology assessment and clinical translation. Colonization and proliferation processes for live microorganisms need to be controlled. Some solutions are already available for microbiome products development, such as dedicated nonclinical models, and emerging tools such as in silico modeling may potentially prove useful. This chapter aims to draw the regulatory landscape for microbiome-derived products prior to debating various nonclinical tests systems to evaluate their toxicology.

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Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells

Cited by 71 publications

References 83 publications

The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health

The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health

Future of Probiotics and Prebiotics and the Implications for Early Career Researchers

Microbiome Product Toxicology: Regulatory View on Translational Challenges

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