Emerging Technologies for Gut Microbiome Research

Arnold, Jason W.; Roach, Jeffrey; Azcárate-Peril, M. Andrea

doi:10.1016/j.tim.2016.06.008

Cited by 158 publications

(98 citation statements)

References 135 publications

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“…Alternatively, a controlled microfluidics-based co-culture system such as HuMiX [49] allows growth of bacteria, intestinal epithelial cells, and human immune cells in different chambers separated by membranes. Other in vitro systems such as the gut-on-the-chip with stem cell-derived organoids supporting co-cultures with the microbiome could facilitate the study of the interactions of the microbial cultures with human gut cells [50]. Another area of major focus will be in situ noninvasive sampling from different parts of the gut to extend the current knowledge on the compartmentalization of the microbiota.…”

Section: Perspectives For Therapeutic Strategies Involving the Gut MImentioning

confidence: 99%

“…Another area of major focus will be in situ noninvasive sampling from different parts of the gut to extend the current knowledge on the compartmentalization of the microbiota. A device allowing the isolation and identification of uncultivable microorganisms is the iChip, and its derivative iTip could provide further coverage of the human gut microbiota [50]. …”

Section: Perspectives For Therapeutic Strategies Involving the Gut MImentioning

confidence: 99%

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The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials

et al. 2018

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The human gut microbiota gained tremendous importance in the last decade as next-generation technologies of sequencing and multiomics analyses linked the role of the microbial communities to host physiology and pathophysiology. A growing number of human pathologies and diseases are linked to the gut microbiota. One of the main mechanisms by which the microbiota influences the host is through its interactions with the host immune system. These interactions with both innate and adaptive host intestinal and extraintestinal immunity, although usually commensalistic even mutualistic with the host, in some cases lead to serious health effects. In the case of allogenic hematopoietic stem cell transplantation (allo-HSCT), the disruption of the intestinal microbiota diversity is associated with acute graft-versus-host disease (GvHD). Causing inflammation of the liver, skin, lungs, and the intestine, GvHD occurs in 40–50% of patients undergoing allo-HSCT and results in significant posttransplantation mortality. In this review, we highlight the impact of the gut microbiota on the host immunity in GvHD and the potential of microbiota in alleviation or even prevention of GvHD.

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Section: Perspectives For Therapeutic Strategies Involving the Gut MImentioning

confidence: 99%

Section: Perspectives For Therapeutic Strategies Involving the Gut MImentioning

confidence: 99%

The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials

et al. 2018

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“…A well-balanced gut microbiota is critical for maintaining general health. Alterations in the composition of gut microbiota have been linked to a range of disorders including inflammatory, metabolic, neurologic, and oncologic (reviewed in 8 ). Research on human disease and the gut microbiota is a relatively new field, and so far, most studies have treated the disease as a single predictor, disregarding the wide range of variables that could also affect the microbiome and obscure the disease signature.…”

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confidence: 99%

Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome

et al. 2017

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Background There is mounting evidence for a connection between the gut and Parkinson’s disease (PD). Dysbiosis of gut microbiota could explain several features of PD. Objective To determine if PD involves dysbiosis of gut microbiome, disentangle effects of confounders, and identify candidate taxa and functional pathways to guide research. Methods 197 PD cases and 130 controls were studied. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from stool. Metadata were collected on 39 potential confounders including medications, diet, gastrointestinal symptoms, and demographics. Statistical analyses were conducted while controlling for potential confounders and correcting for multiple testing. We tested differences in the overall microbial composition, taxa abundance, and functional pathways. Results Independent microbial signatures were detected for PD (P=4E-5), subjects’ region of residence within the United States (P=3E-3), age (P=0.03), sex (P=1E-3) and dietary fruits/vegetables (P=0.01). Among patients, independent signals were detected for catechol-O-methyltransferase-inhibitors (P=4E-4), anticholinergics (P=5E-3), and possibly carbidopa/levodopa (P=0.05). We found significantly altered abundance of Bifidobacteriaceae, Christensenellaceae, [Tissierellaceae], Lachnospiraceae, Lactobacillaceae, Pasteurellaceae and Verrucomicrobiaceae families. Functional predictions revealed changes in numerous pathways including metabolism of plant-derived compounds and xenobiotics degradation. Conclusion PD is accompanied by dysbiosis of gut microbiome. Results coalesce divergent findings of prior studies, reveal altered abundance of several taxa, nominate functional pathways, and demonstrate independent effects of PD medications on the microbiome. The findings provide new leads and testable hypotheses on the pathophysiology and treatment of PD.

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“…A recent study has examined the transcriptional response of organoids upon exposure to short-chain fatty acids (SCFAs) and products generated by two abundant microbiota constituents, Akkermansia muciniphila and Faecalibacterium prausnitzii (Arnold, Roach et al 2016). A. muciniphila metabolites affect various transcription factors and genes involved in cellular lipid metabolism and growth, supporting previous in vivo findings.…”

Section: Feasibility and Application Of Organoids In Studying Host-mimentioning

confidence: 99%

Intestinal organoid as an in vitro model in studying host-microbial interactions

Sun

2017

Front. Biol.

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Background: Organoid is an in vitro three-dimensional organ-bud that shows realistic microanatomy and physiologic relevance. The progress in generating organoids that faithfully recapitulate human in vivo tissue composition has extended organoid applications from being just a basic research tool to a translational platform with a wide range of uses. Study of host-microbial interactions relies on model systems to mimic the in vivo infection. Researchers have developed various experimental models in vitro and in vivo to examine the dynamic host-microbial interactions. For some infectious pathogens, model systems are lacking whereas some of the used systems are far from optimal. Objective: In the present work, we will review the brief history and recent findings using organoids for studying host-microbial interactions. Methods: A systematic literature search was performed using the PubMed search engine. We also shared our data and research contribution to the field. Results: we summarize the brief history of 3D organoids. We discuss the feasibility of using organoids in studying host-microbial interactions, focusing on the development of intestinal organoids and gastric organoids. We highlight the advantage and challenges of the new experimental models. Further, we discuss the future direction in using organoids in studying host-microbial interactions and its potential application in biomedical studies. Conclusion: In combination with genetic, transcriptome and proteomic profiling, both murine- and human-derived organoids have revealed crucial aspects of development, homeostasis and diseases. Specifically, human organoids from susceptible host will be used to test their responses to pathogens, probiotics, and drugs. Organoid system is an exciting tool for studying infectious disease, microbiome, and therapy.

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Emerging Technologies for Gut Microbiome Research

Cited by 158 publications

References 135 publications

The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials

The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials

Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome

Intestinal organoid as an in vitro model in studying host-microbial interactions

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