Primary human colonic mucosal barrier crosstalk with super oxygen-sensitive Faecalibacterium prausnitzii in continuous culture

Fecal luminal factors from patients with irritable bowel syndrome induce distinct gene expression of colonoids

BACKGROUND

Alteration of the host-microbiota cross talk at the intestinal barrier may participate in the pathophysiology of irritable bowel syndrome (IBS). Therefore, we aimed to determine effects of fecal luminal factors from IBS patients on the colonic epithelium using colonoids.

METHODS

Colon-derived organoid monolayers, colonoids, generated from a healthy subject, underwent stimulation with fecal supernatants from healthy subjects and IBS patients with predominant diarrhea, phosphate-buffered saline (PBS), or lipopolysaccharide (LPS). Cytokines in cell cultures and fecal LPS were measured by ELISA and mRNA gene expression of monolayers was analyzed using Qiagen RT² Profiler PCR Arrays. The fecal microbiota profile was determined by the GA-map^™ dysbiosis test and the fecal metabolite profile was analyzed by untargeted liquid chromatography/mass spectrometry.

KEY RESULTS

Colonoid monolayers stimulated with fecal supernatants from healthy subjects (n = 7), PBS (n = 4) or LPS (n = 3) presented distinct gene expression profiles, with some overlap (R² Y = 0.70, Q²  = 0.43). Addition of fecal supernatants from healthy subjects and IBS patients (n = 9) gave rise to different gene expression profiles of the colonoid monolayers (R² Y = 0.79, Q²  = 0.64). Genes (n = 22) related to immune response (CD1D, TLR5) and barrier integrity (CLDN15, DSC2) contributed to the separation. Levels of proinflammatory cytokines in colonoid monolayer cultures were comparable when stimulated with fecal supernatants from either donor types. Fecal microbiota and metabolite profiles, but not LPS content, differed between the study groups.

CONCLUSIONS

Fecal luminal factors from IBS patients induce a distinct colonic epithelial gene expression, potentially reflecting the disease pathophysiology. The culture of colonoids from healthy subjects with fecal supernatants from IBS patients may facilitate the exploration of IBS related intestinal micro-environmental and barrier interactions.

Cultivation of gastrointestinal microbiota in a new growth system revealed dysbiosis and metabolic disruptions in carcinoma-bearing rats

A challenge in the study of gastrointestinal microbiota (GITm) is the validation of the genomic data with metabolic studies of the microbial communities to understand how the microbial networks work during health and sickness. To gain insights into the metabolism of the GITm, feces from healthy and sick rats with cancer were inoculated in a defined synthetic medium directed for anaerobic prokaryote growth (INC-07 medium). Significant differences between cultures of healthy and sick individuals were found: 1) the consumption of the carbon source and the enzyme activity involved in their catabolism (e.g., sucrase, lactase, lipases, aminotransferases, and dehydrogenases); 2) higher excretion of acetic, propionic, isobutyric, butyric, valeric, and isovaleric acids; 3) methane production; 4) ability to form biofilms; and 5) up to 500 amplicon sequencing variants (ASVs) identified showed different diversity and abundance. Moreover, the bowel inflammation induced by cancer triggered oxidative stress, which correlated with deficient antioxidant machinery (e.g., NADPH-producing enzymes) determined in the GITm cultures from sick individuals in comparison with those from control individuals. Altogether, the data suggested that to preserve the microbial network between bacteria and methanogenic archaea, a complete oxidation of the carbon source may be essential for healthy microbiota. The correlation of 16S rRNA gene metabarcoding between cultures and feces, as well as metabolomic data found in cultures, suggest that INC-07 medium may be a useful tool to understand the metabolism of microbiota under gut conditions.

Limnospira indica PCC 8005 or Lacticaseibacillus rhamnosus GG Dietary Supplementation Modulate the Gut Microbiome in Mice

While dietary supplements can have beneficial effects on the health of the intestine, these effects can come with unresolved issues in terms of therapeutic efficacy and mechanisms of action. In this study, the model probiotic Lacticaseibacillus rhamnosus GG ATCC 53103 and the anciently used dietary supplement Limnospira indica strain PCC 8005 were compared for their effects on murine intestinal ecology. Healthy male mice received either saline or suspensions of living cells of L. indica PCC 8005 or L. rhamnosus GG daily along a two-week intervention period, followed by a two-week washout period. Both bacteria-based solutions appeared able to transiently shift the microbial community, which were characterized by a higher relative abundance of members of the butyrate producing Lachnospiraceae and Porphyromonadaceae families.

Bacterial-fungal metabolic interactions within the microbiota and their potential relevance in human health and disease: a short review

The composition of the microbiota is the focus of many recent publications describing the effects of the microbiota on host health. In recent years, research has progressed further, investigating not only the diversity of genes and functions but also metabolites produced by microorganisms composing the microbiota of various niches and how these metabolites affect and shape the microbial community. While an abundance of data has been published on bacterial interactions, much less data are available on the interactions of bacteria with another component of the microbiota: the fungal community. Although present in smaller numbers, fungi are essential to the balance of this complex microbial ecosystem. Both bacterial and fungal communities produce metabolites that influence their own population but also that of the other. However, to date, interkingdom interactions occurring through metabolites produced by bacteria and fungi have rarely been described. In this review, we describe the major metabolites produced by both kingdoms and discuss how they influence each other, by what mechanisms and with what consequences for the host.

A Platform for Co-Culture of Primary Human Colonic Epithelium With Anaerobic Probiotic Bacteria

An in vitro platform was designed and optimized for the co-culture of probiotic anaerobic bacteria with a primary human colonic epithelium having a goal of assessing the anti-inflammatory impact of the probiotic bacteria. The device maintained a luminal O2 concentration at <1% while also supporting an oxygenated basal compartment at 10% for at least 72 h. Measurement of the transepithelial resistance of a confluent colonic epithelium showed high monolayer integrity while fluorescence assays demonstrated that the monolayer was comprised primarily of goblet cells and colonocytes, the two major differentiated cell subtypes of the colonic epithelium. High monolayer barrier function and viability were maintained during co-culture of the epithelium with the probiotic obligate anaerobe Anaerobutyricum hallii (A. hallii). Importantly the device supported a static co-culture of microbes and colonic epithelium mimicking the largely static or low flow conditions within the colonic lumen. A model inflamed colonic epithelium was generated by the addition of tumor necrosis factor-α (TNF-α) and lipopolysaccharide (LPS) to the basal and luminal epithelium sides, respectively. Co-culture of A. hallii with the LPS/TNF-α treated intestine diminished IL-8 secretion by ≥40% which could be mimicked by co-culture with the A. hallii metabolite butyrate. In contrast, co-culture of the inflamed epithelium with two strains of lactic acid-producing bacteria, Lactobacillus rhamnosus GG (LGG) and Bifidobacterium adolescentis (B. adolescentis), did not diminish epithelial IL-8 secretion. Co-culture with colonic epithelial cells from different donors demonstrated a consistent anti-inflammatory effect by A. hallii, but distinct responses to co-culture with LGG and B. adolescentis. The demonstrated system offers a simple and easily adopted platform for examining the physiologic impact of alterations in the intestinal epithelium that occur in the presence of probiotic bacteria and their metabolites.

Modeling microbiota-associated human diseases: from minimal models to complex systems

Alterations in the intestinal microbiota are associated with various human diseases of the digestive system, including obesity and its associated metabolic diseases, inflammatory bowel diseases (IBD), and colorectal cancer (CRC). All three diseases are characterized by modifications of the richness, composition, and metabolic functions of the human intestinal microbiota. Despite being multi-factorial diseases, studies in germ-free animal models have unarguably identified the intestinal microbiota as a causal driver of disease pathogenesis. However, for an increased mechanistic understanding of microbial signatures in human diseases, models require detailed refinement to closely mimic the human microbiota and reflect the complexity and range of dysbiosis observed in patients. The transplantation of human fecal microbiota into animal models represents a powerful tool for studying the causal and functional role of the dysbiotic human microbiome in a pathological context. While human microbiota-associated models were initially employed to study obesity, an increasing number of studies have applied this approach in the context of IBD and CRC over the past decade. In this review, we discuss different approaches that allow the functional validation of the bacterial contribution to human diseases, with emphasis on obesity and its associated metabolic diseases, IBD, and CRC. We discuss the utility of simple models, such as in vitro fermentation systems of the human microbiota and ex vivo intestinal organoids, as well as more complex whole organism models. Our focus here lies on human microbiota-associated mouse models in the context of all three diseases, as well as highlighting the advantages and limitations of this approach.

Oxygen control: the often overlooked but essential piece to create better in vitro systems

Variations in oxygen levels play key roles in numerous physiological and pathological processes, but are often not properly controlled in in vitro models, introducing a significant bias in experimental outcomes. Recent developments in microfluidic technology have introduced a paradigm shift by providing new opportunities to better mimic physiological and pathological conditions, which is achieved by both regulating and monitoring oxygen levels at the micrometre scale in miniaturized devices. In this review, we first introduce the nature and relevance of oxygen-dependent pathways in both physiological and pathological contexts. Subsequently, we discuss strategies to control oxygen in microfluidic devices, distinguishing between engineering approaches that operate at the device level during its fabrication and chemical approaches that involve the active perfusion of fluids oxygenated at a precise level or supplemented with oxygen-producing or oxygen-scavenging materials. In addition, we discuss readout approaches for monitoring oxygen levels at the cellular and tissue levels, focusing on electrochemical and optical detection schemes for high-resolution measurements directly on-chip. An overview of different applications in which microfluidic devices have been utilized to answer biological research questions is then provided. In the final section, we provide our vision for further technological refinements of oxygen-controlling devices and discuss how these devices can be employed to generate new fundamental insights regarding key scientific problems that call for emulating oxygen levels as encountered in vivo. We conclude by making the case that ultimately emulating physiological or pathological oxygen levels should become a standard feature in all in vitro cell, tissue, and organ models.

Possible Benefits of Faecalibacterium prausnitzii for Obesity-Associated Gut Disorders

Metabolic disorders are an increasing concern in the industrialized world. Current research has shown a direct link between the composition of the gut microbiota and the pathogenesis of obesity and diabetes. In only a few weeks, an obesity-inducing diet can lead to increased gut permeability and microbial dysbiosis, which contributes to chronic inflammation in the gut and adipose tissues, and to the development of insulin resistance. In this review, we examine the interplay between gut inflammation, insulin resistance, and the gut microbiota, and discuss how some probiotic species can be used to modulate gut homeostasis. We focus primarily on Faecalibacterium prausnitzii, a highly abundant butyrate-producing bacterium that has been proposed both as a biomarker for the development of different gut pathologies and as a potential treatment due to its production of anti-inflammatory metabolites.

Versatile human in vitro triple coculture model coincubated with adhered gut microbes reproducibly mimics pro-inflammatory host-microbe interactions in the colon

The colonic epithelial barrier is vital to preserve gut and host health by maintaining the immune homeostasis between host and microbes. The mechanisms underlying beneficial or harmful host-microbe interactions are poorly understood and impossible to study in vivo given the limited accessibility and ethical constraints. Moreover, existing in vitro models lack the required cellular complexity for the routine, yet profound, analysis of the intricate interplay between different types of host and microbial cells. We developed and characterized a broadly applicable, easy-to-handle in vitro triple coculture model that combines chemically-induced macrophage-like, goblet and epithelial cells covered by a mucus layer, which can be coincubated with complex human-derived gut microbiota samples for 16 h. Comparison with a standard epithelial monolayer model revealed that triple cocultures produce thicker mucus layers, morphologically organize in a network and upon exposure to human-derived gut microbiota samples, respond via pro-inflammatory cytokine production. Both model systems, however, were not suffering from cytotoxic stress or different microbial loads, indicating that the obtained endpoints were caused by the imposed conditions. Addition of the probiotic Lactobacillus rhamnosus GG to assess its immunomodulating capacity in the triple coculture slightly suppressed pro-inflammatory cytokine responses, based on transcriptomic microarray analyses. TNF conditioning of the models prior to microbial exposure did not cause shifts in cytokines, suggesting a strong epithelial barrier in which TNF did not reach the basolateral side. To conclude, the triple coculture model is tolerable towards manipulations and allows to address mechanistic host-microbe research questions in a stable in vitro environment.

Mucosa-associated specific bacterial species disrupt the intestinal epithelial barrier in the autism phenome

Gut-Brain Axis provides a bidirectional communicational route, an imbalance of which can have pathophysiological consequences. Differential gut microbiome studies have become a frontier in autism research, affecting 85% of autistic children. The present study aims to understand how gut microbiota of autism subjects differ from their neurotypical counterparts. This study would help to identify the abundance of bacterial signature species in autism and their associated metabolites.

16S rRNA metagenomic sequence datasets of 30 out of 206 autism subjects were selected from the American Gut Project Archive. First, the taxonomic assignment was inferred by similarity-based methods using the Quantitative Insights into Microbial Ecology (QIIME) toolkit. Next, species abundance was characterized, and a co-occurrence network was built to infer species interaction using measures of diversity. Thirdly, statistical parameters were incorporated to validate the findings. Finally, the identification of metabolites associated with these bacterial signature species connects with biological processes in the host through pathway analysis.

Gut microbiome data revealed Akkermansia sp. and Faecalibacterium prausnitzii to be statistically lower in abundance in autistic children than their neurotypical peers with a five and two-fold decrease, respectively. While Prevotella sp. and Sutterella sp. showed a five and a two-fold increase in cases, respectively. The constructed pathway revealed succinate and butyrate as the significant metabolites for the bacterial signature species identified.

The present study throws light on the role of mucosa-associated bacterial species: Veillonella sp., Prevotella sp., Akkermansia sp., Sutterella sp., Faecalibacterium prausnitzii, Lactobacillus sp., which can act as diagnostic criteria for detection of gut dysbiosis in autism.

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Bacteroidetes/Firmicutes ratio is significantly higher in autistic children due to differential lifestyle habits in the present study.

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Mucosal associated bacteria, namely Prevotella, Akkermansia, Veillonella, Sutterella, and Faecalibacterium are indicated as potential diagnostic criteria for gut dysbiosis in autism.

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Elevated Proteobacteria levels is contrasting with reported inclinations towards gut related functionality in mouse models.

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The authors report unique link for autism and Prevotella sp. phylotype with higher relative abundance in autism cases.

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Pathway revealed succinate and butyrate as the significant metabolites for the identified bacterial signatures.

Bioderived materials that disarm the gut mucosal immune system: Potential lessons from commensal microbiota

Over the course of evolution, mammals and gut commensal microbes have adapted to coexist with each other. This homeostatic coexistence is dependent on an intricate balance between tolerogenic and inflammatory responses directed towards beneficial, commensal microbes and pathogenic intruders, respectively. Immune tolerance towards the gut microflora is largely sustained by immunomodulatory molecules produced by the commensals, which protect the bacteria from immune advances and maintain the gut's unique tolerogenic microenvironment, as well as systemic homeostasis. The identification and characterization of commensal-derived, tolerogenic molecules could lead to their utilization in biomaterials-inspired delivery schemes involving nano/microparticles or hydrogels, and potentially lead to the next generation of commensal-derived therapeutics. Moreover, gut-on-chip technologies could augment the discovery and characterization of influential commensals by providing realistic in vitro models conducive to finicky microbes. In this review, we provide an overview of the gut immune system, describe its intricate relationships with the microflora and identify major genera involved in maintaining tolerogenic responses and peripheral homeostasis. More relevant to biomaterials, we discuss commensal-derived molecules that are known to interface with immune cells and discuss potential strategies for their incorporation into biomaterial-based strategies aimed at culling inflammatory diseases. We hope this review will bridge the current findings in gut immunology, microbiology and biomaterials and spark further investigation into this emerging field. STATEMENT OF SIGNIFICANCE: Despite its tremendous potential to culminate into revolutionary therapeutics, the synergy between immunology, microbiology, and biomaterials has only been explored at a superficial level. Strategic incorporation of biomaterial-based technologies may be necessary to fully characterize and capitalize on the rapidly growing repertoire of immunomodulatory molecules derived from commensal microbes. Bioengineers may be able to combine state-of-the-art delivery platforms with immunomodulatory cues from commensals to provide a more holistic approach to combating inflammatory disease. This interdisciplinary approach could potentiate a neoteric field of research - "commensal-inspired" therapeutics with the promise of revolutionizing the treatment of inflammatory disease.

Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology

The profound impact of the gut microbiome on host health has led to a revolution in biomedical research, motivating researchers from disparate fields to define the specific molecular mechanisms that mediate host-beneficial effects. The advent of genomic technologies allied to the use of model microbiomes in gnotobiotic mouse models has transformed our understanding of intestinal microbial ecology and the impact of the microbiome on the host. However, despite incredible advances, our understanding of the host-microbiome dialogue that shapes host physiology is still in its infancy. Progress has been limited by challenges associated with developing model systems that are both tractable enough to provide key mechanistic insights while also reflecting the enormous complexity of the gut ecosystem. Simplified model microbiomes have facilitated detailed interrogation of transcriptional and metabolic functions of the microbiome but do not recapitulate the interactions seen in complex communities. Conversely, intact complex communities from mice or humans provide a more physiologically relevant community type, but can limit our ability to uncover high-resolution insights into microbiome function. Moreover, complex microbiomes from lab-derived mice or humans often do not readily imprint human-like phenotypes. Therefore, improved model microbiomes that are highly defined and tractable, but that more accurately recapitulate human microbiome-induced phenotypic variation are required to improve understanding of fundamental processes governing host-microbiome mutualism. This improved understanding will enhance the translational relevance of studies that address how the microbiome promotes host health and influences disease states. Microbial exposures in wild mice, both symbiotic and infectious in nature, have recently been established to more readily recapitulate human-like phenotypes. The development of synthetic model communities from such "wild mice" therefore represents an attractive strategy to overcome the limitations of current approaches. Advances in microbial culturing approaches that allow for the generation of large and diverse libraries of isolates, coupled to ever more affordable large-scale genomic sequencing, mean that we are now ideally positioned to develop such systems. Furthermore, the development of sophisticated in vitro systems is allowing for detailed insights into host-microbiome interactions to be obtained. Here we discuss the need to leverage such approaches and highlight key challenges that remain to be addressed.

High resolution stereolithography fabrication of perfusable scaffolds to enable long-term meso-scale hepatic culture for disease modeling

Microphysiological systems (MPS), comprising human cell cultured in formats that capture features of the three-dimensional (3D) microenvironments of native human organs under microperfusion, are promising tools for biomedical research. Here we report the development of a mesoscale physiological system (MePS) enabling the long-term 3D perfused culture of primary human hepatocytes at scales of over 10⁶cells per MPS. A central feature of the MePS, which employs a commercially-available multiwell bioreactor for perfusion, is a novel scaffold comprising a dense network of nano- and micro-porous polymer channels, designed to provide appropriate convective and diffusive mass transfer of oxygen and other nutrients while maintaining physiological values of shear stress. The scaffold design is realized by a high resolution stereolithography fabrication process employing a novel resin. This new culture system sustains mesoscopic hepatic tissue-like cultures with greater hepatic functionality (assessed by albumin and urea synthesis, and CYP3A4 activity) and lower inflammation markers compared to comparable cultures on the commercial polystyrene scaffold. To illustrate applications to disease modeling, we established an insulin-resistant phenotype by exposing liver cells to hyperglycemic and hyperinsulinemic media. Future applications of the MePS include the co-culture of hepatocytes with resident immune cells and the integration with multiple organs to model complex liver-associated diseases.

Critical Considerations for the Design of Multi-Organ Microphysiological Systems (MPS)

Identification and approval of new drugs for use in patients requires extensive preclinical studies and clinical trials. Preclinical studies rely on in vitro experiments and animal models of human diseases. The transferability of drug toxicity and efficacy estimates to humans from animal models is being called into question. Subsequent clinical studies often reveal lower than expected efficacy and higher drug toxicity in humans than that seen in animal models. Microphysiological systems (MPS), sometimes called organ or human-on-chip models, present a potential alternative to animal-based models used for drug toxicity screening. This review discusses multi-organ MPS that can be used to model diseases and test the efficacy and safety of drug candidates. The translation of an in vivo environment to an in vitro system requires physiologically relevant organ scaling, vascular dimensions, and appropriate flow rates. Even small changes in those parameters can alter the outcome of experiments conducted with MPS. With many MPS devices being developed, we have outlined some established standards for designing MPS devices and described techniques to validate the devices. A physiologically realistic mimic of the human body can help determine the dose response and toxicity effects of a new drug candidate with higher predictive power.

Organ-on-a-chip platforms for evaluation of environmental nanoparticle toxicity

Despite showing a great promise in the field of nanomedicine, nanoparticles have gained a significant attention from regulatory agencies regarding their possible adverse health effects upon environmental exposure. Whether those nanoparticles are generated through intentional or unintentional means, the constant exposure to nanomaterials can inevitably lead to unintended consequences based on epidemiological data, yet the current understanding of nanotoxicity is insufficient relative to the rate of their emission in the environment and the lack of predictive platforms that mimic the human physiology. This calls for a development of more physiologically relevant models, which permit the comprehensive and systematic examination of toxic properties of nanoparticles. With the advancement in microfabrication techniques, scientists have shifted their focus on the development of an engineered system that acts as an intermediate between a well-plate system and animal models, known as organ-on-a-chips. The ability of organ-on-a-chip models to recapitulate in vivo like microenvironment and responses offers a new avenue for nanotoxicological research. In this review, we aim to provide overview of assessing potential risks of nanoparticle exposure using organ-on-a-chip systems and their potential to delineate biological mechanisms of epidemiological findings.

Causative Microbes in Host-Microbiome Interactions

Despite identification of numerous associations between microbiomes and diseases, the complexity of the human microbiome has hindered identification of individual species and strains that are causative in host phenotype or disease. Uncovering causative microbes is vital to fully understand disease processes and to harness the potential therapeutic benefits of microbiota manipulation. Developments in sequencing technology, animal models, and bacterial culturing have facilitated the discovery of specific microbes that impact the host and are beginning to advance the characterization of host-microbiome interaction mechanisms. We summarize the historical and contemporary experimental approaches taken to uncover microbes from the microbiota that affect host biology and describe examples of commensals that have specific effects on the immune system, inflammation, and metabolism. There is still much to learn, and we lay out challenges faced by the field and suggest potential remedies for common pitfalls encountered in the hunt for causative commensal microbes. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Coculture of primary human colon monolayer with human gut bacteria

The presence of microbes in the colon impacts host physiology. Therefore, microbes are being evaluated as potential treatments for colorectal diseases. Humanized model systems that enable robust culture of primary human intestinal cells with bacteria facilitate evaluation of potential treatments. Here, we describe a protocol that can be used to coculture a primary human colon monolayer with aerotolerant bacteria. Primary human colon cells maintained as organoids are dispersed into single-cell suspensions and then seeded on collagen-coated Transwell inserts, where they attach and proliferate to form confluent monolayers within days of seeding. The confluent monolayers are differentiated for an additional 4 d and then cocultured with bacteria. As an example application, we describe how to coculture differentiated colon cells for 8 h with four strains of Bacteroides thetaiotaomicron, each engineered to detect different colonic microenvironments via genetically embedded logic circuits incorporating deoxycholic acid and anhydrotetracycline sensors. Characterization of this coculture system reveals that barrier function remains intact in the presence of engineered B. thetaiotaomicron. The bacteria stay close to the mucus layer and respond in a microenvironment-specific manner to the inducers (deoxycholic acid and anhydrotetracycline) of the genetic circuits. This protocol thus provides a useful mucosal barrier system to assess the effects of bacterial cells that respond to the colonic microenvironment, and may also be useful in other contexts to model human intestinal barrier properties and microbiota-host interactions.

Changes in the fecal microbiota in dogs with acute hemorrhagic diarrhea during an outbreak in Norway

Background

A severe form of acute hemorrhagic diarrhea syndrome (AHDS) occurred in dogs in the Oslo region of Norway during autumn 2019.

Objectives

To characterize the fecal microbiota of dogs with AHDS during the outbreak and compare it to that of healthy dogs from the same period and before the outbreak.

Animals

Dogs with AHDS (n = 50), dogs with nonhemorrhagic diarrhea (n = 3), and healthy dogs (n = 11) were sampled during the outbreak. In addition, 78 healthy dogs from the same region were sampled before the outbreak between 2017 and 2018.

Methods

Retrospective case‐control study. The fecal microbiotas were characterized using 16S rRNA gene amplicon sequencing.

Results

Dogs with AHDS had significantly different microbiota composition (R² = .07, P < .001) and decreased intestinal diversity relative to healthy dogs from the outbreak period (median, 2.7; range, 0.9‐3.5 vs median, 3.2; range, 2.6‐4.0; P < .001). The microbiota in dogs with AHDS was characterized by a decrease of Firmicutes and an outgrowth of Proteobacteria, with increased numbers of Clostridium perfringens and Providencia spp. Among the Providencia spp., 1 showed 100% sequence identity with a Providencia alcalifaciens strain that was cultivated and isolated from the same outbreak. No Providencia spp. was found in healthy dogs sampled before the outbreak.

Conclusions and Clinical Importance

Dogs with AHDS had marked changes in fecal microbiota including increased numbers of Providencia spp. and C. perfringens, which may have contributed to the severity of this illness.

Modulation of jejunal mucosa-associated microbiota in relation to intestinal health and nutrient digestibility in pigs by supplementation of β-glucanase to corn-soybean meal-based diets with xylanase

This study aimed to evaluate the effects of increasing levels of β-glucanase on the modulation of jejunal mucosa-associated microbiota in relation to nutrient digestibility and intestinal health of pigs fed diets with 30% corn distiller's dried grains with solubles and xylanase. Forty pigs at 12.4 ± 0.5 kg body weight (BW) were allotted in a randomized complete block design with initial BW and sex as blocks. Dietary treatments consisted of a basal diet with xylanase (1,500 endo-pentosanase units [EPU]/kg) and increasing levels of β-glucanase (0, 200, 400, and 600 U/kg) meeting nutrient requirements and fed to pigs for 21 d. Blood samples were collected on day 19. On day 21, all pigs were euthanized to collect intestinal tissues and digesta. Tumor necrosis factor-alpha, interleukin (IL)-6, and malondialdehyde were measured in the plasma and mid-jejunal mucosa. Viscosity was determined using digesta from the distal jejunum. Ileal and rectal digesta were evaluated to determine apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of nutrients. Mucosa samples from the mid-jejunum were utilized for microbiota sequencing. Data were analyzed using the MIXED procedure on SAS 9.4. Overall, increasing dietary β-glucanase tended to increase (linear; P = 0.077) the average daily gain of pigs. Increasing dietary β-glucanase affected (quadratic; P < 0.05) the relative abundance of Bacteroidetes, reduced (linear; P < 0.05) Helicobacter rappini, and increased (linear, P < 0.05) Faecalibacterium prausnitzii. β-Glucanase supplementation (0 vs. others) tended to increase (P = 0.096) the AID of crude protein in the diet, whereas increasing dietary β-glucanase tended to increase (linear; P = 0.097) the ATTD of gross energy in the diet and increased (linear; P < 0.05) the concentration of IL-6 in the plasma of pigs. In conclusion, increasing β-glucanase up to 600 U/kg feed in a diet containing xylanase (1,500 EPU/kg) modulated mucosa-associated microbiota by increasing the relative abundance of beneficial bacteria and reducing potentially harmful bacteria. Furthermore, increasing β-glucanase up to 600 U/kg feed in a diet containing xylanase (1,500 EPU/kg feed) enhanced the status of the intestinal environment and nutrient utilization, as well as reduced systemic inflammation of pigs, collectively resulting in moderate improvement of growth performance. Supplementing β-glucanase at a range of 312 to 410 U/kg with xylanase at 1,500 EPU/kg feed showed the most benefit on jejunal mucosa-associated microbiota and reduced systemic inflammation of pigs.

Organoids to Dissect Gastrointestinal Virus-Host Interactions: What Have We Learned?

Historically, knowledge of human host-enteric pathogen interactions has been elucidated from studies using cancer cells, animal models, clinical data, and occasionally, controlled human infection models. Although much has been learned from these studies, an understanding of the complex interactions between human viruses and the human intestinal epithelium was initially limited by the lack of nontransformed culture systems, which recapitulate the relevant heterogenous cell types that comprise the intestinal villus epithelium. New investigations using multicellular, physiologically active, organotypic cultures produced from intestinal stem cells isolated from biopsies or surgical specimens provide an exciting new avenue for understanding human specific pathogens and revealing previously unknown host-microbe interactions that affect replication and outcomes of human infections. Here, we summarize recent biologic discoveries using human intestinal organoids and human enteric viral pathogens.

Growth-promoting effect of alginate on Faecalibacterium prausnitzii through cross-feeding with Bacteroides

Faecalibacterium prausnitzii is a commensal gut bacterium that is thought to provide protection against inflammatory diseases. However, this bacterium is extremely oxygen sensitive, which limits its industrial application as a probiotic. The use of prebiotics to increase the abundance of this bacterium in the gut is an alternative strategy to achieve its possible health-promoting effect. We evaluated nine substances as candidate prebiotics for F. prausnitzii using a pH-controlled single-batch fermenter as a human gut microbiota model. Of them, alginate markedly increased the relative abundance of F. prausnitzii, as determined by the significant increase in the number of 16S rRNA sequences corresponding to this bacterial taxon in the fecal fermentation samples detected by real-time PCR. However, F. prausnitzii strains were incapable of utilizing alginate in monoculture, implying that an interaction with another gut microbe was required. There was a positive correlation between the relative abundance of F. prausnitzii and that of Bacteroides when cultured in medium containing alginate as the sole carbon source, indicative of cross-feeding between these bacteria. Interestingly, the ratio of acetic acid, a known substrate for F. prausnitzii, produced by Bacteroides was significantly higher in the alginate-containing medium than in media containing other prebiotic candidates. Bacterially degraded alginate oligosaccharides (AOS) remained in the medium after Bacteroides monoculture, and an isolate of F. prausnitzii was able to utilize a portion of them. Genomic sequencing revealed that the strain that consumed the AOS contained an ATP-binding cassette transporter, an alginate lyase, and AlgQ1/2 homologs encoding solute-binding proteins. Furthermore, in real-time PCR analyses, AlgQ1/2 homologs were detected in fecal samples collected from 309 of 452 (68.4%) Japanese subjects. Thus, the products of alginate assimilation by Bacteroides may promote the growth of F. prausnitzii.

Intestinal Stem Cell-on-Chip to Study Human Host-Microbiota Interaction

The gut is a tubular organ responsible for nutrient absorption and harbors our intestinal microbiome. This organ is composed of a multitude of specialized cell types arranged in complex barrier-forming crypts and villi covered by a mucosal layer controlling nutrient passage and protecting from invading pathogens. The development and self-renewal of the intestinal epithelium are guided by niche signals controlling the differentiation of specific cell types along the crypt-villus axis in the epithelium. The emergence of microphysiological systems, or organ-on-chips, has paved the way to study the intestinal epithelium within a dynamic and controlled environment. In this review, we describe the use of organ-on-chip technology to control and guide these differentiation processes in vitro. We further discuss current applications and forthcoming strategies to investigate the mechanical processes of intestinal stem cell differentiation, tissue formation, and the interaction of the intestine with the microbiota in the context of gastrointestinal diseases.