Microfluidics gut microbiome. Changc, and Rustem F.

Microfluidics gut microbiome 5% of people will be diagnosed with cancer at some point during their lifetimes. Thousands of bacterial genomes can be covered in 1 h of work, with less than ten micrograms of Here we present a modular, microfluidics-based model (HuMiX, human–microbial crosstalk), which allows co-culture of human and microbial cells under conditions For functional analysis of the microbiota, we will cover state-of-the-art microfluidic devices for microbiota cultivation and functional measurements. Although culture-independent approac Advances in the isolation, cultivation, and identification of gut microfluidics and liberate their DNA, which we then amplify, tag with droplet-specific barcodes, and sequence. Asterisks indicate significantly different prevalence between the two clinical status groups (p value < 10−5) Tauzin et al. Besides supporting the digestive process, protecting the host from endogenous and exogenous infections, and shaping the anatomy and functionality of the entire gastrointestinal tract [1,2,3,4,5], gut microorganisms are also implicated in physiological processes involving other distal organs (e. 44, 45 KEYWORDS: microbiome, microfluidics, bacteria, gut, prebiotics, polysaccharides, diet, droplet, fiber. 2). We used Bacteroides thetaiotaomicron and Bacteroides fragilis, two of the most abundant commensals in the human bowel. Increasing evidence suggests that it plays a crucial role in maintaining overall health. After intestinal epithelial cells form villi Background: Symbiotic gut microbes have a rich genomic and metabolic pool and are closely related to hosts’ health. Recent studies have employed The imbalance in the gut microbiome plays a vital role in the progression of many diseases, including cancer, due to increased inflammation in the body. Although this method has not yet been applied to the generation of SAGs, isolation of individual cells after the screening process could be applied to generate single-cell genomes. In a seminal study, a co-culture of intestinal epithelial cells (Caco-2) and Lactobacillus GG (LGG) provided proof of concept for how the newly designed microfluidic chips could support a prolonged epithelial microbiota co-culture [47]. With the continuous development of microfluidics and organ-on-a-chip, gut-on-a-chip has become a powerful tool for modeling host-microbe interactions. 1186/s40168-022-01333-9. The emerging evidence suggests that the gut microbiome has a role in promoting cancer. A typical platform for anaerobic single-bacterial cultivation is MicDrop, which developed a droplet microfluidic system in an anaerobic chamber, to encapsulate and culture individual gut microbiota members in pico-liter droplets [148]. 2020 Oct 1 little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. , 2022). To understand the pathophysiological role of host-microbiome crosstalk, it is critical to recreate Right from birth to early life, the gut flora is crucial. Herein, we provide a microfluidics-derived encapsulation strategy to address this problem. Since gut microbiome-induced inflammation can serve as a novel therapeutic strategy, there is an increasing need to identify novel approaches to investigate the effect of inflammation instigated by gut SlipChip represents a significant endeavor in applying droplet microfluidics to gut microbes, facilitating automated as well as high-throughput isolation and cultivation of gut microbes. The study of the gut microbiome Paradoxically, gut microbiome can also negatively orchestrate the host responses in diseases or chronic disorders, suggesting that the regulated and balanced host-gut microbiome crosstalk is a salient prerequisite in gastrointestinal physiology. These engineered gut barrier-on-a-chip models enable the reconstruction of the proliferative and differentiated regions of the intestinal epithelium, long-term perfusion of the organoids-derived monolayer, as well as the in The human gut microbiota is a trending research topic. we next tested the functionality of the chip wash method using a model community from the human gut For instance, a microfluidic streak plate was developed by partitioning a microbial population into microfluidic droplets, followed by dispensing each droplet onto an agar plate for subsequent culture and functional analyses, including the growth rate and biofilm formation by imaging-based morphological assessment. Among the different methodologies used to study intestinal microorganisms, new methods based on microfluidic technology have been receiving increasing attention in recent years. Tauzin1, Mariana Rangel Pereira2,3, Liisa D. 00; KCl, 0. As well as interacting with each other, the bacteria in the microbiome interact with our cells and available nutrients. Specific compounds in the gut affect the growth of different bacterial species and the production of beneficial or harmful byproducts. Hananc, Eugene B. Through metagenomic analysis of the gut microbiota, we found that after the long-term use of the EBPB bacteria, the abundance of beneficial bacteria, such as Bifidobacterium, Lactobacillus, and Akkermansia, increased. (A) A photograph (left) and a schematic (right) of a 2-channel, gut-on-a-chip microfluidic device. 13, 14 Drug designers may need to consider the high spatial heterogeneity and complexity of the gut microbiota: going from stomach to large The gut microbiota play critical role in the health of the host, which include but is not limited to the maturation of the immune system, Another interesting innovation in the area of microfluidics in microbiome research is the development of organs on chip. We have also hypothesized new models to help in understanding bacterial pathways involved in the gut-lung axis Our arsenal of tools includes advanced sequencing technologies, high-resolution 3D imaging of gut microbial communities, quantitative analysis of microbial communities, computational modeling, microfluidics, and concepts from engineering and control theory. We recapitulate the intestinal lumen-capillary tissue interface in a microfluidic device, where physiological m Here, we discuss the key components of the gut–liver axis, including the gut epithelium, liver cells, gut microbiota, and their roles in the organ functions. first discusses the development of an intestine-on-a-chip used to simulate the physiological microenvironment of the intestine, facilitating the cultivation of gut microbiota. 1042/BCJ20200426. Introduction In the past decades, various technologies have been developed to better understand and exploit the microbiome. First, we tested whether chip wash can detect microbial growth on SlipChip. 42 This technology has been applied to isolate and Background Symbiotic gut microbes have a rich genomic and metabolic pool and are closely related to hosts’ health. The termite gut microbiome is a model system to investigate microbial interactions and their associations with host. 1A). Emerging research has elucidated that the microbiota mediates a range of modifications of drugs, leading to their activation, inactivation, or even toxication. Here, we outline the importance of the intestinal microbiome in modulating drug metabolism. Polydimethylsiloxane (PDMS) is the most widely used material to produce microfluidic systems []. Search for more papers by this author. Table S1. Authors Riddhi Trivedi Microfluidics and organ on chip model are emerging technologies that can satisfy these needs. Omics-based methods such as metagenomics, metatranscriptomics, and metabolomics are widely used to assess the human gut microbiota [8,9]. ABSTRACT. Background: Cancer is the second leading cause of death globally and ~39. , 2015; Vos and Vos, 2012) and contains at least several thousand species (Almeida et al. Recent advancements in artificial intelligence (AI) have opened new avenues for exploring the intricate functionalities of the gut microbiota. The gut microbiota suspension in the Here, we describe a protocol to perform long-term co-culture of multi-species human gut microbiome with microengineered intestinal villi in a human gut-on-a-chip microphysiological device. According to the microfluidic chip design and the perfusion velocity of the liquid sample, Recent work has shown that strain-level classification of the human gut microbiome is achievable Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. , 2020). Dysbiosis, or a disruption in the balance of the host gut Microbiome. More recently, the development of droplet microfluidics has streamlined the process of screening and targeting specific gut microbiome members (Pryszlak et al. Gut-On-Chip Systems 2. Graphical abstract. Nature Reviews Gastroenterology & Hepatology - In this Review, Motta, Vergnolle and colleagues describe the Abstract. A limited number of bacterial High-throughput amplicon sequencing has generated a wealth of data on microbiome composition from different environments and conditions including the gut microbiome of ~1000 year old preserved human remains, which showed that, similar to modern day humans, Firmicutes was the dominant bacterial phylum within the gut at that time . 12H 2 O, 3. The human microbiome refers to the collection of micro-organisms that live symbiotically in the human body (defined as the “microbiota”), their genetic material, and the surrounding environmental habitat. Keywords: droplet microfluidics, single-cell analysis, genomics, genome, gut microbiome, functional analysis, metagenomics, bacteria. A person's microbiome influences how the body Gut microbiota composition and function are heavily influenced by environmental factors, diet, and age. doi: 10. Table S2. Investigating host-microbiome interactions by droplet based microfluidics Microbiome. Merten 1 7 9 We report a droplet microfluidic method to target and sort individual cells directly from complex microbiome samples and to prepare these cells for bulk whole-genome sequencing without cultivation. Traditional sequencing profiling masks the genomic and phenotypic diversity among strains from the same species. Isolating, characterizing, and identifying gut microbes are crucial for research on the gut microbiome and essential for advancing our understanding and utilization of it. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of In this review, we emphasize the importance of culturomics research on the gut microbiome and provide new theories and insights for expanding microbial diversity via the optimization of cultivation conditions. 1 Fabrication of a human gut on-chip model and CFD simulation analysis. For any specific experiment, the first step is always droplet generation. . Proceedings of the National Academy of Sciences of the United States of America , 111 ( 27 ), 9768–9773. Thus, there is an unmet need to identify novel strategies for early cancer detection and prevention. More recently, a newer version of this ‘gut-on-chip’ was used to study the dynamic interactions between The ability to culture human intestinal epithelium overlaid by complex human gut microbial communities within microfluidic Intestine Chips may enable investigations of host-microbiome interactions In the central channel, over the membrane, fragments of colon organoids obtained from primary colonic epithelial cells derived biopsy specimens, were cultured generating human intestinal epithelium, which were covered by its own mucus and a layer of complex gut microbiota. This review gives an overview of colonic commensals in lung pathology and novel systems that help in alleviating symptoms of lung diseases. Daniel J. , vitamin synthesis, fiber degradation, de- and reactivation of drugs) that humans lack or have limited ability to perform. The Article Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics Anna Pryszlak,1,8 Tobias Wenzel,1,2,8 Kiley West Seitz,1 Falk Hildebrand,1,3,4 Ece Kartal,1 Marco Raffaele Cosenza,1 Vladimir Benes,1 Peer Bork,1,5,6,* and Christoph A. The gut microbiota thus stands out as a source of functional This model was used to analyze how gut microbiome, inflammatory cells, and peristalsis-associated mechanical deformations independently contribute to intestinal bacterial overgrowth and inflammation. Ismagilova,1 Divisions of aChemistry and Chemical Engineering and bGeological and Figure 1: Schematic of intestine-on-a-chip microfluidic devices used for gut microbiome research. The development of these models constitutes a rapidly developing field of research. A new perspective suggests that a dynamic bidirectional communication system, often referred to as the microbiome-gut-brain axis, exists among the gut, its microbiome, and the central nervous system (CNS). 2022 Aug 31;10(1):140. As well as interacting with each other, the bacteria in the microbiome interact with our cells and available Gut-on-a-chip systems represent a promising advancement in microfluidics and tissue engineering, offering a more physiologically relevant alternative to traditional 2D cell cultures and animal models for studying gut function. Various disease states have been linked to dysregulation Fig. 3a,b), first appeared in medical studies on human gut bacteria 30,38 and The gut microbiota plays a crucial role in maintaining human health and influencing disease states. Divisions of a Chemistry and Chemical Engineering and. Background: Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. a, Jungwoo Kim. Machine Learning and Gut Microbiome. 20; Na 2 HPO 4. Innovative droplet-based microfluidic cultivation may help to elucidate the Microfluidics in Microbiome and Cancer Research. The gastrointestinal (GI) tract is a complex system responsible for nutrient absorption, digestion, secretion, and elimination of waste products that also hosts immune surveillance, the intestinal microbiome, and interfaces with the nervous system. Please cite this article in press as: Pryszlak et al. Changes in the composition of the gut microbiome, due to diet or medication, disrupts homeostasis and can induce pathogenesis [18]. 11 Organs-on-a-chip technology used to simulate Later, this method was simplified by sorting the agarose droplets in microwell plates, therefore reducing the microfluidic processing steps. Innovative droplet-based microfluidic cultivation may help to elucidate the inter-strain interactions. pdf Available via license: CC BY 4. g. This Background Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. , Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet micro- fluidics, Cell Reports Methods (2021 Research on the gut microbiome is progressing through several steps that mirror those of other fields on other biological systems: (1) compilation of parts lists, (2) association of the system or its components to external factors, (3) establishment of functional knowledge, and (4) translation of that knowledge into applications. A growing body of research is beginning to elucidate the diverse impacts the gut microbiota plays in human Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. They further applied a similar gut inflammation-on-a-chip model to identify the initiator of inflammatory host-microbiome cross-talk Shin & Kim, 2018). To resolve the coupling between flow and social interaction in microbiota communities, we leveraged anaerobic microfluidics. Open in a new tab . Changc, and Rustem F. 43 Molecular signals from the gut can modify a breadth of neurodevelopmental processes in the enteric system and the CNS. 0 Content may be subject to copyright. Gut microbiome a promising target for management of respiratory diseases Biochem J. Recent advancements in artificial intelligence (AI) have opened new avenues for exploring the intricate The gut microbiome is closely associated with human health and the development of diseases. Dysregulation of the human microbiome has been linked to various disease states, which has galvanized the efforts to modulate human health through microbiomes. Background: Symbiotic gut microbes have a rich genomic and metabolic pool and are closely related to hosts' health. 3). Slade, Daniel J. Our new protocol for creating an AOI in a microfluidic gut-on-a-chip may enable to demonstrate the key physiological interactions of obligate anaerobic gut microbiome with the host cells associated DoTA-seq leverages a microfluidic droplet system to isolate and lyse diverse microbes and amplify target genetic loci, enabling high-throughput single-cell sequencing of microbial populations. Fig. Gene abundance (a, relative abundance of genes in samples that contain them) and prevalence (b A new perspective suggests that a dynamic bidirectional communication system, often referred to as the microbiome-gut-brain axis, exists among the gut, its microbiome, and the central nervous system (CNS). We characterize this approach by recovering bacteria spiked into human stool samples at a ratio as low The human gut is responsible for food digestion and absorption. S5 Abundance and prevalence in the human gut microbiome of European healthy and IBD affected individuals of the genes encoding the characterized GH123s. In this review, we present a brief history of microfluidics technology and describe its applications in gut microbiome research, with a specific emphasis on the 3. , the microbiota-gut-brain axis) [6, 7]. This article aims to provide an overview of the current state-of-the-art applications of AI in microbiome analysis, with examples related The guts from 40 termites were removed aseptically with fine-tipped forceps onto a sterilized glass slide and the gut microbiota were squeezed out of the guts and were transferred into a tube with 1mL of PBS buffer (PBS buffer, g/L: NaCl, 8. Highlights • Rare microbial high-quality genomes can be obtained by culture-free enrichment • Microfluidic workflow benchmarked to work directly with complex microbiome samples • Genomic DNA In vitro models of the human gut help compensate for the limitations of animal models in studying the human gut–microbiota interaction and are indispensable in the clarification the mechanism of microbial action or in the high-throughput screening and functional evaluation of probiotics. A zoom-in schematic shows the intestinal microenvironment undergoing complex crosstalk between commensal gut microbiome, bacterial pathogens, and immune The majority of human gut microbiome is comprised of obligate anaerobic bacteria that exert essential metabolic functions in the human colon. We explore the human gut microbiome, sequencing more than 20,000 microbial single-amplified genomes (SAGs) from a single human donor and coassembling genomes of almost 100 bacterial species, including several with multiple subspecies of gut communities is unclear. present an ultra-high-throughput droplet microfluidic workflow to enrich target bacteria from the complex background of millions of gut microbiota, including steps to clean their genomic DNA for whole-genome sequencing. , 2014; Nobu et al. , 2019). 1 It is now appreciated that the microbiome plays an important role in human health and diseases. This interest has been due not only to the importance of the intestine's proper functions but also to the relationship that this organ and the microbiota that inhabits it has with the rest of the body's organs. Download Citation | Microfluidics: A new tool for microbial single cell analyses in human microbiome studies | Microbial cells behave differently in colonies and when singled out. By taking advantage of microfluidic technologies, inherited shortcomings of traditional methods such as low throughput, labor-consuming, and The gut microbiota plays a crucial role in maintaining human health and influencing disease states. This system may influence brain health and various brain-related diseases, especially in the r Effect of gut microbiota-derived metabolites and extracellular The role of the host–biofilm relationship in gut homeostasis and disease is discussed. Here, Unlike other microfluidics-based gut-on-chip models, this chip can be assembled and dissembled for the culture and collections of cells after the completion of the cell interactions in the device for microscopic analysis and extraction of intracellular biomolecules such as DNA, RNA, proteins). Microbiome (2020) 8:141 Highly abundant host glycan degradation pathways in the gut microbiome The clone 1, clone 2, and clone 3 genes encoding CAZymes are highly abundant and prevalent in the human gut microbiome The MSP platform provided a powerful tool in isolating the rare species from complex environmental samples, including soil [42], termite gut microbiome [43] and deep-sea sediments [41]. In diverse individuals, variations in Recently, advances in nanofabrication and microfluidics have led to the development of in vitro modular gut barrier-on-a-chip models. Studies report patterns of gut microbes that not only influence aging but can also predict age-associated decline (Bosco and Noti, 2021). This adaptation, named SAG-gel, was applied to study the gut microbiome of mice, In this project, you will study the effect of novel sweeteners on intestinal microbes. 1073/pnas. 3D Printed Multi-material Microfluidic Valve; Gut-On-A-Chip 'Human gut-on-a-chip inhabited by microbial The termite gut microbiome is a model system to investigate microbial interactions and their associations with host. we next tested the functionality of the chip wash method using a model community from the human gut microbiome (Fig. 2021), sustaining intestinal The gut microbiome is shaped early in life by dietary and lifestyle factors. However, no host-microbiota co-culture system has been developed for depression, which hinders the controlled study of the interaction between depression and gut microbiota. Harnessing microfluidic streak plate technique to investigate the gut microbiome of Here, a general workflow of floating droplet microfluidics for microbiome research is shown in Figure 1. This indicates that the EBPB bacteria could regulate the microbiota composition, promoting the growth of beneficial Beyond the use of microfluidics for lab-on-a-chip platforms with microbiome applications, gut-on-chip technology can also be employed to investigate host-microbiome interactions and provide useful tools for elucidating the relationship between the composition of Microfluidics is a system involving the treatment or manipulation of microscale (10 -9 to 10 -18 L) fluids using microchannels (10 to 100 μm) contained on a microfluidic chip. Endothelium was cultured in the bottom layer of the central chambre. Food Compromised host–microbiome interactions may contribute to disease development (Box 1), including dysregulated multi-organ interactions in the gut–brain axis 18 and gut–liver axis 19. For the gut microbiome, this is reflected in 2. utilized droplet microfluidics in an anaerobic chamber to isolate and cultivate gut microbiota [44]. The microbiome is a complex and increasingly important research target. (A) Human villus intestinal epithelium and vascular endothelium are lined on opposite sides of a flexible porous membrane under fluid flows and peristalsis-like strains. The gut microbiome has emerged as an important factor affecting human health and disease. Watterson et al. We demonstrated that they form biofilms and engage in metabolite More recently, the development of droplet microfluidics has streamlined the process of screening and targeting specific gut microbiome members (Pryszlak et al. Yet, many bacterial gro Harnessing microfluidic streak plate technique to investigate the gut The gut microbiome contains approximately a hundredfold more genes than its human host, Citation 20, Citation 21 and has a variety of metabolic capacities (e. Here, we will highlight a few possibilities of using microfluidic technology in organ-specific microbiome Research on the gut microbiome is progressing through several steps that mirror those of other fields on other biological systems: (1) compilation of parts lists, (2) association of the system or its components to external factors, (3) establishment of functional knowledge, and (4) translation of that knowledge into applications. (B) Schematic diagrams of the procedure of host-gut microbiome co-culture in the gut-on-a-chip. This review gives an overview of colonic commensals in lung pathology and novel Introduction. A person's microbiome influences how the body Abundance and prevalence in the human gut microbiome of the newly discovered CAZymes encoding genes. This complex mixture of bacteria is part of the gut microbiome, along with other lifeforms such as viruses, archaea and fungi. 2019 the extended coculture of living human intestinal epithelium with stable communities of aerobic and anaerobic human gut microbiota, using a microfluidic intestine-on-a-chip that permits the control and real-time assessment of physiologically Different microbiota can interact with pharmaceutical drugs in different ways. These A microfluidic chip incorporating oxygen gradients, a diverse human microbiota and patient-derived cells, mimics interactions between microorganisms and host tissue in the human gut. Liang Ma. 1. Its ease of production and ability to be molded into different shapes revolutionized microfluidics and made it accessible to most labs. However, effective delivery and in situ colonization are limited by the harsh environment of the gastrointestinal tract. The study of the gut microbiome The goal of this paper is to discuss and highlight the opportunities of applying different microfluidic technologies to specific areas of microbiome research as well as unique challenges that The human gut is inhabited with hundreds of billions of bacterial cells from a wide range of families. However, recent evidence suggests that supplementation of Microfluidics and organ on chip model are emerging technologies that can satisfy these needs. This chip allowed for the quantification of the effect of bacteria on the growth of colorectal cancer cells, showing that certain bacteria can promote RESEARCH Open Access Investigating host-microbiome interactions by droplet based microfluidics Alexandra S. A unique feature of this system was the Microfluidics is a system involving the treatment or manipulation of microscale (10−9 to 10−18 L) fluids using microchannels (10 to 100 μm) contained on a microfluidic chip. The gut-on-a-chip consisted of three parallel microchannels Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project’s Most Wanted taxa Liang Ma a, Jungwoo Kim , Roland Hatzenpichlerb, Mikhail A. A robust longitudinal co-culture of obligate anaerobic gut microbiome with human intestinal A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip Nat Biomed Eng. Previous work has developed a gut-on-a-chip system that As for the relevance of organotypic slices cultures for investigating gut microbiota‐dependent molecular mechanisms, we can find in literature a few very recent examples suggesting possible interesting applications: mouse's hippocampal slices culture was performed to reveal gut microbiome‐derived metabolites having a significant impact on Additionally, by employing precise injection pumps and microfluidic channels, researchers can quantitatively introduce specific amounts of microorganisms and control their distribution and concentration within the chip, thus simulating the colonization and dynamic changes of microbes in the gut. This adaptation, named SAG-gel, was applied to study the gut microbiome of mice, where a total of 346 SAGs was generated from two independent samples (Chijiiwa et al. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel The position is embedded in a PPS project called Sweetspot funded by TKI and private partners which investigates the effects of non-nutritive sweeteners (NNS) and novel sugars on the gut microbiome and food-products. Although culture-independent approac Request PDF | Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa | Significance Obtaining cultures of microbes Article Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics Anna Pryszlak,1,8 Tobias Wenzel,1,2,8 Kiley West Seitz,1 Falk Hildebrand,1,3,4 Ece Kartal,1 Marco Raffaele Cosenza,1 Vladimir Benes,1 Peer Bork,1,5,6,* and Christoph A. Find articles by Liang Ma. 2020 Jul 31;477(14):2679-2696. Merten1,7,9,* 1European Molecular Biology Laboratory, Heidelberg, Germany 2Institute for The human gut is a complex ecosystem harboring rich microbes that play a key role in the nutrient absorption, drug metabolism, and immune responses. However, the sliding operation limits the throughput of droplet generation, manipulating only hundreds of microbial cells in a single assay. Finally, we highlight the use of Background Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans While microbiome maturation during development and ageing is naturally occurring and results in desirable compositional and functional changes with protective effects against inflammation and other disorders , a scrutiny of studies has revealed recently the connection between several pathophysiological conditions with an impaired gut microbiome, the effects of which extend Gut Microbiome. These systems simulate the complex microenvironment of the gastrointestinal tract, including the gut’s structural, immunological, and endocrine roles. Oral administration of probiotics orchestrates the balance between intestinal microbes and the immune response. A microfluidic chip was developed to test the effects of bacteria and inflammatory stress on cancer cells in vitro. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient Pryszlak et al. S6 Illustrations for the microfluidics-based screening. Material. Gene‐targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. Merten1,7,9,* 1European Molecular Biology Laboratory, Heidelberg, Germany 2Institute for Keywords: microphysiological model, gut-on-a-chip, organ chip, microbiome, intestinal tissue, organoid, microfluidics Citation: Steinway SN, Saleh J, Koo B-K, Delacour D and Kim D-H (2020) Human Microphysiological Models of Intestinal Tissue and Gut Microbiome. However, while many studies have found a correlation between certain diseases and changes in the microbiome, the impact of different microbial compositions on the gut and the mechanisms The concept of microbiome types, which are defined by the discrete or semi-discrete nature of microbiome structures (Fig. The gut microbiome is closely associated with human health and the development of diseases. For example, food is inextricably linked to our well-being, health, and diseases. Qi et al. Virginia Polytechnic Institute and State University – Wake Forest University, School of Biomedical Engineering and Sciences, 325 Stanger Street, Blacksburg, VA, 24061 USA . Acquiring target microorganisms from the vast array of intestinal microbes for in vitro culture poses a technical challenge High-throughput amplicon sequencing has generated a wealth of data on microbiome composition from different environments and conditions including the gut microbiome of ~1000 year old preserved human remains, which showed that, similar to modern day humans, Firmicutes was the dominant bacterial phylum within the gut at that time . 10. Keywords: Culturomics, gut microbiome, cultivation conditions, medium optimization, cultivation techniques. 2. 16S rRNA gene sequencing and quantitative PCR were applied for downstream analysis, enabling to characterize The gut microbiota is vital for maintaining homeostasis and nutrient absorption, regulating the intestinal epithelial mucosal barrier, and protecting against pathogens and drug metabolism. Defining the composition and spatial heterogeneity of the microbiome is critical to facilitate further understanding of the gut microbiome ecology. Dysbiosis of Introduction. Karymova, Nathaniel Hubertc, Ira M. NNS are commonly integrated into products and presumed to be inert. A model of the gut microbiome inside microfluidic droplets would allow us to test drugs at very high throughput either by screening many drugs through a single Our new protocol for creating an AOI in a microfluidic gut-on-a-chip may enable to demonstrate the key physiological interactions of obligate anaerobic gut microbiome with the host cells The gut microbiota is vital for maintaining homeostasis and nutrient absorption, regulating the intestinal epithelial mucosal barrier , and protecting against pathogens and drug metabolism. You will study if specific microbes can grow on these, how microbial growth is impacted by these sweeteners and how sweeteners will affect trophic interactions between intestinal microbes and the intestinal microbiome in general. It will be of interest to identify the effect of diet and age on gut microbiome in immunocompromised The gut microbiota is of particular interest in pharmacology due to the manner in which gastrointestinal (GI) microbes are associated with a multitude of diseases 11, 12 and interact with xenobiotics. While attempts to identify a common pattern of microbial Gut Microbiome. This system may influence brain health and various brain-related diseases, especially in the realms of neurodevelopmental and neurodegenerative conditions. The human gut is inhabited with hundreds of billions of bacterial cells from a wide range of families. For the gut microbiome, this is reflected in the following Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics Author links open overlay panel Anna Pryszlak 1 8 , Tobias Wenzel 1 2 8 , Kiley West Seitz 1 , Falk Hildebrand 1 3 4 , Ece Kartal 1 , Marco Raffaele Cosenza 1 , Vladimir Benes 1 , Peer Bork 1 5 6 , Christoph A. 2012), promoting immune system development (Ge et al. We then explore the potential of gut–liver-on-a-chip models to Diverse microfluidic approaches for phenotype screening and sorting. While fish microbiome research, particularly in their gut, dates back to pioneer studies in the early half of the 20th century [2] and to later descriptive papers [3], knowledge on fish-associated microbes Later, this method was simplified by sorting the agarose droplets in microwell plates, therefore reducing the microfluidic processing steps. A novel synergistic delivery system Over the last few years, the intestine has been extensively studied using in vitro microfluidic systems, commonly known as gut-on-a-chip (GOC) devices. And the applications of gut-related multichip coupling and disease modelling in the context of drug development is systematically reviewed. The recent development of –omics approaches, including phylogenetic marker-based microbiome profiling, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics, has enabled efficient characterization of microbial communities. Virginia Polytechnic Institute and State One can appreciate the complexity of the human‐microbiome relationship by studying how the microbiome evolves after birth and affects maturation of the GI epithelium during the establishment of the normal symbiotic relationship. . Advances in microfluidic technologies have made a significant Isolation and culture of gut bacteria enable testing for microbial roles in disease and may also lead to novel therapeutics. With an estimated 100 trillion microorganisms, the gut is an extraordinarily complex system of microbe-microbe and microbe-host interactions. This study demonstrated the co-culture of caco-2 cells with Lactobacillus The gut microbiota, known as the second human genome, plays a vital role in modulating drug metabolism, significantly impacting therapeutic outcomes and adverse effects. However, the diversity of human gut microbial communities (microbiota Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics. Van Vliet2,4, Pierre-Yves Colin2, Elisabeth Laville1, Jeremy Esque1, Sandrine Laguerre1, Bernard Henrissat5,6,7, Nicolas Terrapon5,6, Vincent Lombard5,6, Marion Leclerc8, Joël Doré8,9, Florian Hollfelder2* and As a result, focus over the last few years has shifted from analyzing the diversity of gut microbiome by sequencing of the entire microbial community, towards understanding the gut microbiome in spatial context. In the past decade, researchers have enhanced To allow better insights into host–microbe interactions and develop a more physiological relevant model, co-culturing gut microbiome with intestinal epithelial cells in Here, we gathered publications on the co-culturing of host and microbial cells in microfluidic platforms and discussed the main findings and the key parameters to consider in developing In this review, we present a brief history of microfluidics technology and describe its applications in gut microbiome research, with a specific emphasis on the microfluidic Here, we introduce an ultra-high-throughput metagenomic approach based on droplet microfluidics, to screen fosmid libraries. The diverse commensal microbiome of the human intestine has been considered to play a central role in depression. Traditional <i>in vitro</i> systems cannot harness Beyond the use of microfluidics for lab-on-a-chip platforms with microbiome applications, gut-on-chip technology can also be employed to investigate host-microbiome interactions and provide useful tools for elucidating the relationship between the composition of Article Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics Anna Pryszlak,1,8 Tobias Wenzel,1,2,8 Kiley West Seitz,1 Falk Hildebrand,1,3,4 Ece Kartal,1 Marco Raffaele Cosenza,1 Vladimir Benes,1 Peer Bork,1,5,6,* and Christoph A. The chapter examines select organ-on-chip devices that recapitulate salient features of the gut epithelium This paper outlines the characteristics of the different cell types most frequently used to construct microfluidic gut-on-a-chip models and the microfluidic devices employed for the study of drug absorption. In particular, microfluidics has demonstrated its strength and prominence in the microbiome research. Advances in technology and cost reduction have made it possible to study the previously unexplored landscape of the human gut microbiome at a large scale. For decades, extensive research with molecular tools and conventional cultivation method has been carried out to define the microbial diversity in termite gut. Fish have unique and relatively stable interactions with the vast variety of microorganisms that surround them, inhabit their skin, gills, and gastrointestinal tract [1 •]. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. To investigate the interactions between microbiomes and human Caco-2 cells in a human intestinal microenvironment, we developed a microfluidic-based gut-on-a-chip embedding with microelectrode arrays (Fig. Features of gut-on-chip models to study host-microbial interactions. Culture and screening of gut bacteria enable testing of microbial function and therapeutic potential. Traditional sequencing proling masks the genomic and phenotypic diversity among strains from the same Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts Thus, there is an urgent need for a novel hydrogel microcapsule system that targets inflamed gut tissue and enables programmable stem cell release during gut inflammation and microbiome dysbiosis. The human gut microbiota is one of the most densely populated ecosystems of microorganisms on earth. However To explore the precise role of the gut microbiome in disease progression , design synthetic microbial communities , and ultimately translate the gut microbiome research into clinical applications, it is essential to initially obtain viable gut microbes. Unintended adverse pharmacological responses can occur because of the gut microbiota’s impact on drug metabolism . The standard Specifically, the gut microbiome composition and function has been shown to play a critical role in the etiology of different intestinal and extra-intestinal diseases. Microfluidics can be used to study gut bacteria by simulating the gut microbiome and its interaction with cancer cells. Health of neonatal may be impacted by gut microbiome populations because they guard against harmful pathogens (Martin and Sela 2013), assisting in the metabolisation as well as digestion of breast milk but also formula milk (Koropatkin et al. Recent progress in microfluidic technology has made it possible to mimic characteristics and responses of the human gut as seen in vivo. We also highlight how novel microfluidics-based tissue models could provide novel insights into the signaling along the gut–liver axis and help to advance our understanding in drug-induced toxicity and its underlying mechanisms. Recently, growing evidence has shown its vital role in the proper functioning of other organs. 24; pH 7. Merten1,7,9,* 1European Molecular Biology Laboratory, Heidelberg, Germany 2Institute for The gut microbiome plays a crucial role in cancer development and progression, by influencing the host immune system and metabolism. Slade. Their cultivation-free method enables the recovery of high-quality genomes from rare target cells (<1%) in microbiome samples. Summary of the clonal redundancy identified by Sanger sequencing of the metagenomic DNA extremities. , 2016; Louis et al. Arrows indicate the direction of culture medium flow (blue, top microchannel; red, bottom microchannel). (A) Screening microbes with antimicrobial ability, double emulsion droplets are detected and sorted by flow cytometer Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. 1404753111 [ Europe PMC free article ] [ Abstract ] [ CrossRef ] [ Google Scholar ] The intestine contains the largest microbial community in the human body, the gut microbiome. 58; KH 2 PO 4, 0. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of 2022). In particular, the gut microbiome is linked to over 100 disease states or syndromes (Gupta et al. The mechanically active human Gut Chip. Microfluidics, referred to as one of the powerful cell encapsulation techniques, enables the rapid and consistent production of highly uniform A multi-chamber microfluidic intestinal barrier model using Caco-2 cells for drug transport studies. 1 Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics Anna Pryszlak1,*, Tobias Wenzel1,2,*, Kiley West Seitz1, Falk Hildebrand1,3,3a, Ece Kartal1, Marco Raffaele Cosenza1, Vladimir Benes1, Peer Bork1,4a,4b,+ and Christoph Merten1,5,+ 1 European Molecular Biology Laboratory, Heidelberg, DE 2 Institute for Biological Additionally, the gut microbiome’s makeup can influence how the body reacts to medicines, most notably those used to treat cancer. We designed Summary This chapter provides an introduction to the role of microbiome in human in microfluidic device development and 3D tissue microenvironment engineering that enable the dissection of key microscale host-microbiome interactions. 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