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Inflammatory gut disorders, including inflammatory bowel disease (IBD), can be impacted by dietary, environmental and genetic factors. While the incidence of IBD is increasing worldwide, we still lack a complete understanding of the gene-by-environment interactions underlying inflammation and IBD. Here, we profiled the colon transcriptome of 52 BXD mouse strains fed with a chow or high-fat diet (HFD) and identified a subset of BXD strains that exhibit an IBD-like transcriptome signature on HFD, indicating that an interplay of genetics and diet can significantly affect intestinal inflammation. Using gene co-expression analyses, we identified modules that are enriched for IBD-dysregulated genes and found that these IBD-related modules share cis-regulatory elements that are responsive to the STAT2, SMAD3, and REL transcription factors. We used module quantitative trait locus (ModQTL) analyses to identify genetic loci associated with the expression of these modules. Through a prioritization scheme involving systems genetics in the mouse and integration with external human datasets, we identified Muc4 and Epha6 as the top candidates mediating differences in HFD-driven intestinal inflammation. This work provides insights into the contribution of genetics and diet to IBD risk and identifies two candidate genes, MUC4 and EPHA6, that may mediate IBD susceptibility in humans.

Inflammatory gut disorders, including inflammatory bowel disease (IBD), can be impacted by dietary, environmental and genetic factors. While the incidence of IBD is increasing worldwide, we still lack a complete understanding of the gene-by-environment interactions underlying inflammation and IBD. Here, we profiled the colon transcriptome of 52 BXD mouse strains fed with a chow or high-fat diet (HFD) and identified a subset of BXD strains that exhibit an IBD-like transcriptome signature on HFD, indicating that an interplay of genetics and diet can significantly affect intestinal inflammation. Using gene co-expression analyses, we identified modules that are enriched for IBD-dysregulated genes and found that these IBD-related modules sharecis-regulatory elements that are responsive to the STAT2, SMAD3, and REL transcription factors. We used module quantitative trait locus (ModQTL) analyses to identify genetic loci associated with the expression of these modules. Through a prioritization scheme involving systems genetics in the mouse and integration with external human datasets, we identifiedMuc4andEpha6as the top candidates mediating differences in HFD-driven intestinal inflammation. This work provides insights into the contribution of genetics and diet to IBD risk and identifies two candidate genes,MUC4andEPHA6, that may mediate IBD susceptibility in humans.

Mitohormesis defines the increase in fitness mediated by adaptive responses to mild mitochondrial stress. Tetracyclines inhibit not only bacterial but also mitochondrial translation, thus imposing a low level of mitochondrial stress on eukaryotic cells. We demonstrate in cell and germ-free mouse models that tetracyclines induce a mild adaptive mitochondrial stress response (MSR), involving both the ATF4-mediated integrative stress response and type I interferon (IFN) signaling. To overcome the interferences of tetracyclines with the host microbiome, we identify tetracycline derivatives that have minimal antimicrobial activity, yet retain full capacity to induce the MSR, such as the lead compound, 9-tert-butyl doxycycline (9-TB). The MSR induced by doxycycline (Dox) and 9-TB improves survival and disease tolerance against lethal influenza virus (IFV) infection when given preventively. 9-TB, unlike Dox, did not affect the gut microbiome and also showed encouraging results against IFV when given in a therapeutic setting. Tolerance to IFV infection is associated with the induction of genes involved in lung epithelial cell and cilia function, and with downregulation of inflammatory and immune gene sets in lungs, liver, and kidneys. Mitohormesis induced by non-antimicrobial tetracyclines and the ensuing IFN response may dampen excessive inflammation and tissue damage during viral infections, opening innovative therapeutic avenues.

Increasing evidence suggests that intestinal helminth infection can alter intestinal microbial communities with important impacts on the mammalian host. However, all of the studies to date utilize different techniques to study the microbiome and access different sites of the intestine with little consistency noted between studies. In the present study, we set out to perform a comprehensive analysis of the impact of intestinal helminth infection on the mammalian intestinal bacterial microbiome. For this purpose, we investigated the impact of experimental infection using the natural murine small intestinal helminth, Heligmosomoides polygyrus bakeri and examined possible alterations in both the mucous and luminal bacterial communities along the entire small and large intestine. We also explored the impact of common experimental variables including the parasite batch and pre-infection microbiome, on the outcome of helminth-bacterial interactions. This work provides evidence that helminth infection reproducibly alters intestinal microbial communities, with an impact of infection noted along the entire length of the intestine. Although the exact nature of helminth-induced alterations to the intestinal microbiome differed depending on the microbiome community structure present prior to infection, changes extended well beyond the introduction of new bacterial species by the infecting larvae. Moreover, striking similarities between different experiments were noted, including the consistent outgrowth of a bacterium belonging to the Peptostreptococcaceae family throughout the intestine. (C) 2019 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health. We find that the lung microbiota post-transplant can be categorized into four distinct compositional states, ‘pneumotypes’. The predominant ‘balanced’ pneumotype is characterized by a diverse bacterial community with moderate viral loads, and host gene expression profiles suggesting immune tolerance. The other three pneumotypes are characterized by being either microbiota-depleted, or dominated by potential pathogens, and are linked to increased immune activity, lower respiratory function, and increased risks of infection and rejection. Collectively, our findings establish a link between the lung microbial ecosystem, human lung function, and clinical stability post-transplant., Here, the authors combine 16 S rRNA sequencing, culture and bioinformatics to profile the microbiome in 234 serial bronchoalveolar lavage samples from 64 lung transplant recipients collected over 49-months and identify distinct compositional states, termed pneumotypes, linked to current health status, and establish a collection of primary lung bacterial isolates, LuMiCol.

Intestinal helminths, along with mutualistic microbes, have cohabited the intestine of mammals throughout evolution. Interactions between helminths, bacteria, and their mammalian hosts may shape not only host-helminth and host-microbiome interactions, but also the relationship between helminths and the microbiome. This 'ménage à trois' situation may not be completely balanced in that it may favor either the host or the parasite, possibly at the cost of the other partner. Similarly, helminths may favor the establishment of a particular microbiome with either positive or negative consequences for the overall health and well-being of the host. Recent studies indicate that infection with intestinal helminths can and does impact the intestinal microbiome, with important consequences for each partner in this tripartite relationship.

The microbiota have been shown to play an important role in diverse biological processes including immunity, metabolism, and digestion. Assessing the exact composition of the microbiota has proven challenging due to the often unknown growth specificities of its members, and culture-based approaches typically fail to capture the complete diversity of microorganisms present. Next Generation Sequencing (NGS) methods provide an efficient means to gather information about cultured and uncultured members of the microbiota. This article provides a method to characterize bacterial communities in terms of species composition using high-throughput sequencing. Briefly, by extracting the entire DNA content of a microbiota sample and performing a targeted high-throughput sequencing of the 16S rRNA gene, a phylogenetic marker for prokaryotes, prediction of the composition of the entire bacterial community is made possible. © 2017 by John Wiley & Sons, Inc.

Introduction: Low density bacterial communities reside in the lower airways, however the importance of their stability for complication-free survival after lung transplantion (Tx) is poorly understood. Aims:i) To identify the most common and abundant members of the bacterial lung microbiota post-Tx, and ii) to explore whether disruption of this core community is linked to clinical complications. Methods: We prospectively analyzed 234 serial bronchoalveolar lavage (BAL) samples from 64 recipients up to 49 months post-Tx, using 16S quantification and sequencing. Unsupervised clustering was used to differentiate bacterial communities. Cell differentials were obtained for paired BAL and blood samples. Post-Tx clinical complications were sought from patient charts. Results: The most common and abundant operational taxonomic units, mapping to the genera Prevotella, Streptococcus and Veillonella, were linked to a single cluster that identified the core lung microbiota. We further observed two divergent bacterial communities linked to contrasting clinical pictures. Compared with the core, median differences in the first sample set were a 46-fold lower bacterial load, 2.7-fold higher blood lymphocyte counts, and a 3.3-fold higher rate of either acute rejection, chronic lung allograft dysfunction or presence of donor-specific antibodies, while those in the second set were a 2.6-fold lower diversity, 4-fold higher BAL neutrophil counts, and a 3.3-fold higher infection rate. Conclusions: Complication-free survival post-lung Tx is tied to a stable core microbiota, the disruption of which is related to sub-control (rejection) or excessive control (infection) of host immunity.

Skin allergen sensitization can induce atopic dermatitis (AD), which is considered the starting point of the ‘atopic march’. The ‘atopic march’ is the progression of AD in infancy to allergic rhinitis and allergic asthma in childhood. We hypothesize that the skin microbiome drives immune maturation, and that the maturation state at the time of skin allergen sensitization determines the allergic airway inflammation phenotype following allergen challenge. Neonatal and adult mice were subjected to a 3-week epicutaneous allergen sensitization protocol followed by intranasal allergen challenges. Skin and lung tissue inflammation was assessed using histological and FACS analysis. Skin transcriptome and microbiome was analyzed using RNA-seq and 16S rRNA sequencing. The immune maturation state at the time of first sensitization determines a Th2 vs. a mixed Th2/Th17 driven allergic inflammation in both the skin and the lung. Naive neonatal mouse skin exhibited decreased antigen presenting cell frequencies and a decreased antigen uptake and processing capacity compared to adults. Transcriptome analysis revealed that genes associated with immune response and bacterial response pathways were enriched in adult skin compared to neonatal skin. Similar genes were downregulated in adult germ-free mouse skin, suggesting an important role for the microbiome. Epicutaneous allergen sensitization in adult mice was characterized by increased Staphylococcus aureus abundance on the skin, and neutrophil accumulation and increased IL17 gene expression in both the skin and the lung. Taken together, the skin microbiome drives immune maturation and exacerbation of both skin and airway inflammation.

Increasing evidence suggests that intestinal helminth infection can alter intestinal microbial communities with important impacts on the mammalian host. However, all of the studies to date utilize different techniques to study the microbiome and access different sites of the intestine with little consistency noted between studies. In the present study, we set out to perform a comprehensive analysis of the impact of intestinal helminth infection on the mammalian intestinal bacterial microbiome. For this purpose, we investigated the impact of experimental infection using the natural murine small intestinal helminth,Heligmosomoides polygyrus bakeri(Hpb) and examined possible alterations in both the mucous and luminal bacterial communities along the entire small and large intestine. We also explored the impact of common experimental variables, including the parasite batch and pre-infection microbiome, on the outcome of helminth-bacterial interactions. This work provides evidence that helminth infection reproducibly alters intestinal microbial communities – with an impact of infection noted along the entire length of the intestine. Although the exact nature of helminth-induced alterations to the intestinal microbiome differed depending on the parasite batch and microbiome community structure present prior to infection, changes extended well beyond the introduction of new bacterial species by the infecting larvae. Moreover, striking similarities between different experiments were noted, including the consistent outgrowth of a bacterium belonging to the Peptostreptococcaceae family throughout the intestine.Author SummaryIncreasing evidence indicates a role for interactions between intestinal helminths and the microbiome in regulating mammalian health, and a greater understanding of helminth-microbiota interactions may open the path for the development of novel immunomodulatory therapies. However, such studies are hampered by the inconsistent nature of the data reported so far. Such inconsistancies likely result from variations in the experimental and technological methodologies employed to investigate helminth-microbiota interactions and well has natural variation in the starting microbiome composition and/or worm genetics. We conducted a thorough study in which the reproducibility of helminth-induced alterations of microbial communities was determined and impact of common experimental variables – such as the starting microbiome and parasite batch - was determined. Our work reveals the robust ability of small intestinal helminth infection to alter microbial communities along the entire length of the intestine and additionally identifies a single bacterium that is strongly associated with infection across multiple experiments.

Skin allergen sensitization can induce atopic dermatitis (AD), which is considered the starting point of the ‘atopic march’. The ‘atopic march’ is the progression of AD in infancy to allergic rhinitis and allergic asthma in childhood. We hypothesize that the skin microbiome drives immune maturation, and that the maturation state at the time of skin allergen sensitization determines the allergic airway inflammation phenotype following allergen challenge. Neonatal and adult mice were subjected to a 3-week epicutaneous allergen sensitization protocol followed by intranasal allergen challenges. Skin and lung tissue inflammation was assessed using histological and FACS analysis. Skin transcriptome and microbiome was analyzed using RNA-seq and 16S rRNA sequencing. The immune maturation state at the time of first sensitization determines a Th2 vs. a mixed Th2/Th17 driven allergic inflammation in both the skin and the lung. Naive neonatal mouse skin exhibited decreased antigen presenting cell frequencies and a decreased antigen uptake and processing capacity compared to adults. Transcriptome analysis revealed that genes associated with immune response and bacterial response pathways were enriched in adult skin compared to neonatal skin. Similar genes were downregulated in adult germ-free mouse skin, suggesting an important role for the microbiome. Epicutaneous allergen sensitization in adult mice was characterized by increased Staphylococcus aureus abundance on the skin, and neutrophil accumulation and increased IL17 gene expression in both the skin and the lung. Taken together, the skin microbiome drives immune maturation and exacerbation of both skin and airway inflammation.

Background Allergic skin inflammation often presents in early childhood; however, little is known about the events leading to its initiation and whether it is transient or long-term in nature. Objective We sought to determine the immunologic rules that govern skin inflammation in early life. Methods Neonatal and adult mice were epicutaneously sensitized with allergen followed by airway allergen challenge. Epicutaneous application of labeled allergen allowed for determination of antigen uptake and processing by antigen-presenting cells. RNAseq and microbiome analysis was performed on skin from neonatal and adult specific pathogen-free and germ-free mice. Results A mixed TH2/TH17 inflammatory response in the skin and the lungs of adult mice was observed following sensitization and challenge. Comparatively, neonatal mice did not develop overt skin inflammation, but exhibited systemic release of IL-17a and a TH2-dominated lung response. Mechanical skin barrier disruption was not sufficient to drive allergic skin inflammation, although it did promote systemic immune priming. Skin of neonatal mice and adult germ-free mice was seeded with low numbers of antigen-presenting cells and impaired chemokine and alarmin production. Enhanced chemokine and alarmin production, and seeding of the skin with antigen-presenting cells capable of instructing recruited cells to elicit their effector function, was, at least in part, dependent on formation of the microbiome, and consequently contributed to the development of overt skin disease. Conclusions These data shed light on the principles that underlie allergic inflammation in different tissues and highlight a window of opportunity that might exist for early-life prevention of allergic diseases.

SummaryIntestinal helminths are potent regulators of their host’s immune system and can ameliorate inflammatory diseases such as allergic asthma. In the present study we have assessed whether this anti-inflammatory activity was purely intrinsic to helminths, or whether it also involved crosstalk with the local microbiota. We report that chronic infection with the murine helminth Heligmosomoides polygyrus bakeri (Hpb) altered the intestinal habitat, allowing increased short chain fatty acid (SCFA) production. Transfer of the Hpb-modified microbiota alone was sufficient to mediate protection against allergic asthma. The helminth-induced anti-inflammatory cytokine secretion and regulatory T cell suppressor activity that mediated the protection required the G protein-coupled receptor (GPR)-41. A similar alteration in the metabolic potential of intestinal bacterial communities was observed with diverse parasitic and host species, suggesting that this represents an evolutionary conserved mechanism of host-microbe-helminth interactions.

The microbiota have been shown to play an important role in diverse biological processes including immunity, metabolism, and digestion. Assessing the exact composition of the microbiota has proven challenging due to the often unknown growth specificities of its members, and culture-based approaches typically fail to capture the complete diversity of microorganisms present. Next Generation Sequencing (NGS) methods provide an efficient means to gather information about cultured and uncultured members of the microbiota. This article provides a method to characterize bacterial communities in terms of species composition using high-throughput sequencing. Briefly, by extracting the entire DNA content of a microbiota sample and performing a targeted high-throughput sequencing of the 16S rRNA gene, a phylogenetic marker for prokaryotes, prediction of the composition of the entire bacterial community is made possible. © 2017 by John WileySons, Inc.