Bioengineered Co-culture of organoids to recapitulate host-microbe interactions

Kim, Min Beom; Hwangbo, Soonho; Jang, Se Bok; Jo, Young-Woo

doi:10.1016/j.mtbio.2022.100345

Cited by 13 publications

(8 citation statements)

References 175 publications

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“…Advanced human cell culture systems and techniques, such as induced pluripotent stem cells (iPSC) or adult stem cells (ASC) derived from healthy individuals or patients, threedimensional (3D) cultures and organoids, microfluidics, co-culture systems and (multi)organ chips are gaining increasing interest in disease modeling, drug discovery, and toxicity testing. Such systems may mimic more accurately the human in vivo environment than previous conventional culture systems (Kim et al, 2022) and promise more human-relevant information and improved predictive value in comparison to cancer cellular line cultures or experiments using animals. These complex systems often take into account important parameters found in the host, such as tissue architecture and composition, shear stress, or cell motility and communication as well as primary features of cells.…”

Section: Advanced Human Cell Culture Systems and Techniques For The S...mentioning

confidence: 99%

“…Then, gastrointestinal organoid models may provide new insight into gastroenterological pathophysiology and disease mechanisms and to study how the gut microbiota, or its products, interacts with intestinal host cells (Min et al, 2020;Rubert et al, 2020). Whereas organoid co-cultures with bacterial pathogens or commensals have contributed to a better understanding of previously inaccessible interactions between tissues/cells and microbes, the development of organoids co-cultured with archaea, fungi, and protists are still relatively elusive (Kim et al, 2022).…”

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confidence: 99%

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Roadmap for the integration of gastro‐intestinal (GI) tract microbiomes (human and domestic animal) in risk assessments under EFSA's remit

Moreno,

Pazos,

Garrido‐Romero

et al. 2024

EFSA Supporting Publications

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This report describes the work developed during the execution of the Review Impact MICrobiome In Assesment (RIMICIA) project. This project has performed a comprehensive and critical assessment of the evidence-based research about: i) the impact of dietary compounds in the human and some domestic animals (i.e., poultry, ruminants and pigs) gut microbiome; ii) the most representative in vitro and in vivo models of the human gut microbiota currently used in microbiome research studies; and iii) the methodology used to measure changes in the microbiota. This project has also gathered and appraised information www.efsa.europa.eu/publications EFSA Supporting publication 2024:EN-8597The present document has been produced and adopted by the bodies identified above as authors. In accordance with Article 36 of Regulation (EC) No 178/2002, this task has been carried out exclusively by the authors in the context of a grant agreement between the European Food Safety Authority and the authors. The present document is published complying with the transparency principle to which the Authority is subject. It cannot be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the authors.2Organisation for Economic Co-operation and Development (OECD) or other international test guidelines and, ultimately, into regulatory programs.

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Section: Advanced Human Cell Culture Systems and Techniques For The S...mentioning

confidence: 99%

mentioning

confidence: 99%

Roadmap for the integration of gastro‐intestinal (GI) tract microbiomes (human and domestic animal) in risk assessments under EFSA's remit

Moreno,

Pazos,

Garrido‐Romero

et al. 2024

EFSA Supporting Publications

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“…hIOs integrated with human intestinal bacterial cells have been developed. These systems provide a microenvironment to model intestinal diet–microbiota–host interactions, giving new insights into the mechanisms by which microbiome dysbiosis and gut microbial metabolites may prevent or trigger diseases (M. B. Kim et al., 2022; Rubert et al., 2020).…”

Section: Nams For Nutrition Researchmentioning

confidence: 99%

Human‐based new approach methodologies to accelerate advances in nutrition research

Cassotta,

Cianciosi,

Elexpuru‐Zabaleta

et al. 2024

Food Frontiers

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Much of nutrition research has been conventionally based on the use of simplistic in vitro systems or animal models, which have been extensively employed in an effort to better understand the relationships between diet and complex diseases as well as to evaluate food safety. Although these models have undeniably contributed to increase our mechanistic understanding of basic biological processes, they do not adequately model complex human physiopathological phenomena, creating concerns about the translatability to humans. During the last decade, extraordinary advancement in stem cell culturing, three‐dimensional cell cultures, sequencing technologies, and computer science has occurred, which has originated a wealth of novel human‐based and more physiologically relevant tools. These tools, also known as “new approach methodologies,” which comprise patient‐derived organoids, organs‐on‐chip, multi‐omics approach, along with computational models and analysis, represent innovative and exciting tools to forward nutrition research from a human‐biology‐oriented perspective. After considering some shortcomings of conventional in vitro and vivo approaches, here we describe the main novel available and emerging tools that are appropriate for designing a more human‐relevant nutrition research. Our aim is to encourage discussion on the opportunity to explore innovative paths in nutrition research and to promote a paradigm‐change toward a more human biology‐focused approach to better understand human nutritional pathophysiology, to evaluate novel food products, and to develop more effective targeted preventive or therapeutic strategies while helping in reducing the number and replacing animals employed in nutrition research.

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“…Studying microbe-host interaction using intestinal organoids requires the steep oxygen gradient across the epithelium to be accurately recapitulated to ensure adequate oxygen for the host cells and an anaerobic environment for the microbes. Several co-culture systems have recently been developed to facilitate simultaneous growth of anaerobic bacteria and intestinal organoids [68][69][70][71]. My group was involved in engineering the 'organoid-anaerobe co-culture' model, which involves seeding intestinal-derived organoids as monolayers inside an anaerobic chamber, with oxygen diffusing into media basolaterally (Fig.…”

Section: Moving Beyond Associations To Study Diet-microbe-host Intera...mentioning

confidence: 99%

2022 Fleming Prize Lecture: diet–microbe–host interaction in early life

Stewart

2023

Journal of Medical Microbiology

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The last decade has witnessed a meteoric rise in research focused on characterizing the human microbiome and identifying associations with disease risk. The advent of sequencing technology has all but eradicated gel-based fingerprinting approaches for studying microbial ecology, while at the same time traditional microbiological culture is undergoing a renaissance. Although multiplexed high-throughput sequencing is relatively new, the discoveries leading to this are nearly 50 years old, coinciding with the inaugural Microbiology Society Fleming Prize lecture. It was an honour to give the 2022 Fleming Prize lecture and this review will cover the topics from that lecture. The focus will be on the bacterial community in early life, beginning with term infants before moving on to infants delivered prematurely. The review will discuss recent work showing how human milk oligosaccharides (HMOs), an abundant but non-nutritious component of breast milk, can modulate infant microbiome and promote the growth of Bifidobacterium spp. This has important connotations for preterm infants at risk of necrotizing enterocolitis, a devastating intestinal disease representing the leading cause of death and long-term morbidity in this population. With appropriate mechanistic studies, it may be possible to harness the power of breast milk bioactive factors and infant gut microbiome to improve short- and long-term health in infants.

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Bioengineered Co-culture of organoids to recapitulate host-microbe interactions

Cited by 13 publications

References 175 publications

Roadmap for the integration of gastro‐intestinal (GI) tract microbiomes (human and domestic animal) in risk assessments under EFSA's remit

Roadmap for the integration of gastro‐intestinal (GI) tract microbiomes (human and domestic animal) in risk assessments under EFSA's remit

Human‐based new approach methodologies to accelerate advances in nutrition research

2022 Fleming Prize Lecture: diet–microbe–host interaction in early life

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