Toll-Interacting Protein Regulates Immune Cell Infiltration and Promotes Colitis-Associated Cancer.

Expression of Toll-interacting protein (Tollip), a potent TLR modulator, decreases in patients with inflammatory bowel diseases (IBD), whereas Tollip <sup>-/-</sup> mice are susceptible to colitis. Tollip expression was shown to be reduced in sporadic adenoma . In contrast, we found variable Tollip expression in patients with colitis-associated adenomas. In Tollip <sup>-/-</sup> mice challenged to develop colitis-associated cancer (CAC), tumor formation was significantly reduced owing to decreased mucosal proliferative and apoptotic indexes. This protection was associated with blunt inflammatory responses without significant changes in microbial composition. mRNA expression of Cd62l and Ccr5 homing receptors was reduced in colons of untreated Tollip <sup>-/-</sup> mice, whereas CD62L <sup>+</sup> CD8 <sup>+</sup> T cells accumulated in the periphery. In Tollip-deficient adenomas Ctla-4 mRNA expression and tumor-infiltrating CD4 <sup>+</sup> Foxp3 <sup>+</sup> regulatory T cell (Treg) were decreased. Our data show that protection from CAC in Tollip-deficient mice is associated with defects in lymphocyte accumulation and composition in colitis-associated adenomas

Enhanced Mucosal Antibody Production and Protection against Respiratory Infections Following an Orally Administered Bacterial Extract

Secondary bacterial infections following influenza infection are a pressing problem facing respiratory medicine. Although antibiotic treatment has been highly successful over recent decades, fatalities due to secondary bacterial infections remain one of the leading causes of death associated with influenza. We have assessed whether administration of a bacterial extract alone is sufficient to potentiate immune responses and protect against primary infection with influenza, and secondary infections with either Streptococcus pneumoniae or Klebsiella pneumoniae in mice. We show that oral administration with the bacterial extract, OM-85, leads to a maturation of dendritic cells and B-cells characterized by increases in MHC II, CD86, and CD40, and a reduction in ICOSL. Improved immune responsiveness against influenza virus reduced the threshold of susceptibility to secondary bacterial infections, and thus protected the mice. The protection was associated with enhanced polyclonal B-cell activation and release of antibodies that were effective at neutralizing the virus. Taken together, these data show that oral administration of bacterial extracts provides sufficient mucosal immune stimulation to protect mice against a respiratory tract viral infection and associated sequelae

Sperm Microbiota and Its Impact on Semen Parameters

Compared to its female counterpart, the microbiota of the male genital tract has not been studied extensively. With this study, we aimed to evaluate the bacterial composition of seminal fluid and its impact on sperm parameters. We hypothesized that a dysbiotic microbiota composition may have an influence on sperm quality. Semen samples of 26 men with normal spermiogram and 68 men with at least one abnormal spermiogram parameter were included in the study. Samples were stratified based on total sperm count, spermatozoa concentration, progressive motility, total motility and spermatozoa morphology. Microbiota profiling was performed using 16S rRNA gene amplicons sequencing and total bacterial load was determined using a panbacterial quantitative PCR. Semen samples broadly clustered into three microbiota profiles: Prevotella-enriched, Lactobacillus-enriched, and polymicrobial. Prevotellaenriched samples had the highest bacterial load (p < 0.05). Network analysis identified three main co-occurrence modules, among which two contained bacteria commonly found in the vaginal flora. Genera from the same module displayed similar oxygen requirements, arguing for the presence of different ecological niches for bacteria that colonize semen through the passage. Contrary to our hypothesis, shifts in overall microbiota composition (beta-diversity) did not correlate with spermiogram parameters. Similarly, we did not find any difference in microbial richness or diversity (alphadiversity). Differential abundance testing, however, revealed three specific genera that were significantly enriched or depleted in some of the sperm quality groups (p < 0.05). Prevotella relative abundance was increased in samples with defective sperm motility while Staphylococcus was increased in the corresponding control group. In addition, we observed an increased relative abundance of Lactobacillus in samples with normal sperm morphology. Our study indicates that overall bacterial content of sperm might not play a major role in male infertility. Although no major shifts in microbiota composition or diversity were found, the differential abundance of specific bacterial genera in the sperm suggests that a small subset of microbes might impact the spermatozoal physiology during sperm transition, more specifically motility and morphology. Further studies are required to challenge this finding and develop potential strategies to induce the formation of a healthy seminal microbiota

Early life inter-kingdom interactions shape the immunological environment of the airways

Background: There is increasing evidence that the airway microbiome plays a key role in the establishment of respiratory health by interacting with the developing immune system early in life. While it has become clear that bacteria are involved in this process, there is a knowledge gap concerning the role of fungi. Moreover, the inter-kingdom interactions that influence immune development remain unknown. In this prospective exploratory human study, we aimed to determine early post-natal microbial and immunological features of the upper airways in 121 healthy newborns. Results: We found that the oropharynx and nasal cavity represent distinct ecological niches for bacteria and fungi. Breastfeeding correlated with changes in microbiota composition of oropharyngeal samples with the greatest impact upon the relative abundance of Streptococcus species and Candida. Host transcriptome profiling revealed that genes with the highest expression variation were immunological in nature. Multi-omics factor analysis of host and microbial data revealed unique co-variation patterns. Conclusion: These data provide evidence of a diverse multi-kingdom microbiota linked with local immunological characteristics in the first week of life that could represent distinct trajectories for future respiratory health

Early origins of lung disease: Towards an interdisciplinary approach

The prenatal and perinatal environments can have profound effects on the development of chronic inflammatory diseases. However, mechanistic insight into how the early-life microenvironment can impact upon development of the lung and immune system and consequent initiation and progression of respiratory diseases is still emerging. Recent studies investigating the developmental origins of lung diseases have started to delineate the effects of early-life changes in the lung, environmental exposures and immune maturation on the development of childhood and adult lung diseases. While the influencing factors have been described and studied in mostly animal models, it remains challenging to pinpoint exactly which factors and at which time point are detrimental in lung development leading to respiratory disease later in life. To advance our understanding of early origins of chronic lung disease and to allow for proper dissemination and application of this knowledge, we propose four major focus areas: 1) policy and education; 2) clinical assessment; 3) basic and translational research; and 4) infrastructure and tools, and discuss future directions for advancement. This review is a follow-up of the discussions at the European Respiratory Society Research Seminar “Early origins of lung disease: towards an interdisciplinary approach” (Lisbon, Portugal, November 2019)

IPF multi-omics datasets

Metabolomics and lipidomics datasets of IPF and NDC apex and base lung explants.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Virulence Factor Database for 16S metagenomics

Virulence-relevant KOs Database allows the prediction of bacterial virulence factor genes from 16S-based metagenomics using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) algorithm. After normalisation for 16S rDNA copy number and total species count, KEGG Orthologs (KO) abundances can be estimated using PICRUSt pre-computed files and virulence-specific genes parsed using VFDB_KO_unique file

Microbiota Analysis Using an Illumina MiSeq Platform to Sequence 16S rRNA Genes.

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

Butyrate regulates neutrophil homeostasis and impairs early antimicrobial activity in the lung

Short-chain fatty acids (SCFAs) are metabolites that are produced following microbial fermentation of dietary fibre and impact cell metabolism and anti-inflammatory pathways both locally in the gut and systemically. In preclinical models, administration of SCFAs, such as butyrate, ameliorates a range of inflammatory disease models including allergic airway inflammation, atopic dermatitis and influenza infection. Here we report the effect of butyrate on a bacteria-induced acute neutrophil-driven immune response in the airways. Butyrate impacted discrete aspects of haematopoiesis in the bone marrow resulting in the accumulation of immature neutrophils. During Pseudomonas aeruginosa infection, butyrate treatment led to enhanced mobilization of neutrophils to the lungs as a result of increased CXCR2 expression by lung macrophages. Despite this increase in granulocyte numbers and their enhanced phagocytic capacity, neutrophils failed to control early bacterial growth. Butyrate reduced expression of nicotinamide adenine dinucleotide phosphate (NADPH), oxidase complex components required for reactive oxygen species (ROS) production, and reduced secondary granule enzymes, culminating in impaired bactericidal activity. These data reveal that SCFAs tune neutrophil maturation and effector function in the bone marrow under homeostatic conditions, potentially to mitigate against excessive granulocyte-driven immunopathology, but their consequently restricted bactericidal capacity impairs early control of Pseudomonas infection