A20 in dendritic cells restrains intestinal anti-bacterial peptide expression and preserves commensal homeostasis.

Microbial dysbiosis commonly occurs in patients with inflammatory bowel diseases (IBD). Exogenous causes of dysbiosis such as antibiotics and diet are well described, but host derived causes are understudied. A20 is a potent regulator of signals triggered by microbial pattern molecules, and A20 regulates susceptibility to intestinal inflammation in mice and in humans. We now report that mice lacking A20 expression in dendritic cells, A20FL/FL CD11c-Cre mice (or A20dDC mice), spontaneously develop colitogenic intestinal dysbiosis that is evident upon weaning and precedes the onset of colitis. Intestines from A20dDC mice express increased amounts of Reg3ß and Reg3γ, but not Ang4. A20 deficient DCs promote gut microbiota perturbation in the absence of adaptive lymphocytes. Moreover, A20 deficient DCs directly induce expression of Reg3ß and Reg3γ but not Ang 4 in normal intestinal epithelial cell enteroid cultures in the absence of other cell types. These findings reveal a pathophysiological pathway in which defective expression of an IBD susceptibility gene in DCs drives aberrant expression of anti-bacterial peptides and luminal dysbiosis that in turn confers host susceptibility to intestinal inflammation.

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis.

BACKGROUND: Upper respiratory infections (URI) and their complications are a major healthcare burden for pediatric populations. Although the microbiology of the nasopharynx is an important determinant of the complications of URI, little is known of the nasopharyngeal (NP) microbiota of children, the factors that affect its composition, and its precise relationship with URI. RESULTS: Healthy children (n = 47) aged 49-84 months from a prospective cohort study based in Wisconsin, USA, were examined. Demographic and clinical data and NP swab samples were obtained from participants upon entry to the study. All NP samples were profiled for bacterial microbiota using a phylogenetic microarray, and these data were related to demographic characteristics and upper respiratory health outcomes. The composition of the NP bacterial community of children was significantly related prior to the history of acute sinusitis (R (2) = 0.070, P < 0.009). History of acute sinusitis was associated with significant depletion in relative abundance of taxa including Faecalibacterium prausnitzii and Akkermansia spp. and enrichment of Moraxella nonliquefaciens. Enrichment of M. nonliquefaciens was also a characteristic of baseline NP samples of children who subsequently developed acute sinusitis over the 1-year study period. Time to develop URI was significantly positively correlated with NP diversity, and children who experienced more frequent URIs exhibited significantly diminished NP microbiota diversity (P ≤ 0.05). CONCLUSIONS: These preliminary data suggest that previous history of acute sinusitis influences the composition of the NP microbiota, characterized by a depletion in relative abundance of specific taxa. Diminished diversity was associated with more frequent URIs.

Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition.

Inflammatory bowel diseases encompass gastrointestinal illnesses typified by chronic inflammation, loss of epithelial integrity and gastrointestinal microbiota dysbiosis. In an effort to counteract these characteristic perturbations, we used stem cells and/or a probiotic therapy in a murine model of Dextran Sodium Sulfate induced colitis to examine both their efficacy in ameliorating disease and impact on niche-specific microbial communities of the lower GI tract. Colitis was induced in C57BL/6 mice by administering 3% DSS in drinking water for 10 days prior to administering one of three treatment plans: daily probiotic (VSL#3) supplementation for 3 days, a single tail vein injection of 1x10 (6) murine mesenchymal stem cells, or both. Ileal, cecal and colonic sections were collected for microbiota and histological analyses. Microbiota profiling revealed distinct bacterial community compositions in the ileum, cecum and colon of control untreated animals, all of which were predicted in silico to be enriched for a number of discrete KEGG pathways, indicating compositional and functional niche specificity in healthy animals. DSS-treatment perturbed community composition in all three niches with ileal communities exhibiting the greatest change relative to control animals. Each treatment group exhibited treatment-specific alterations in microbiota composition in the lower GI tract, though disease scores were only improved in VSL#3-treated animals. The ileal microbiota were most profoundly altered in composition in this group of animals and characterized by significant Enterobacteriaceae enrichment compared with colitic mice (P<0.05).

Probiotic strategies for treatment of respiratory diseases.

Recent advances in next-generation sequencing and phylogenetic microarray technologies have identified diverse, niche-specific microbial communities that comprise the human superorganism. Mucosal microbiome perturbation is a prominent feature of an increasing number of chronic inflammatory disorders, including respiratory diseases, and efforts are now focused on identifying novel microbe-based strategies to treat or manage these conditions. Considering the evidence for niche-specificity and the diversity of function that human microbial communities afford, the range of therapeutic species used to date in probiotic supplements is strikingly narrow and is limited to species typically of gastrointestinal origin. Although the field is still relatively nascent, the potential for identifying novel microbe-based therapeutics in the human microbiome is great. This article focuses primarily on the respiratory tract, its associated microbiome, potential interactions with the gastrointestinal microbiota, and the possibilities for microbiome-manipulation strategies in the treatment and prevention of respiratory disease.

The effects of intestinal microbial community structure on disease manifestation in IL-10-/- mice infected with Helicobacter hepaticus.

BACKGROUND: The aberrant inflammation that is the hallmark of the inflammatory bowel diseases (IBD) is associated with several factors, including changes in the intestinal microbiota. Here, we confirmed that an intestinal microbiota is needed for development of typhlocolitis in Helicobacter hepaticus infected IL-10-/- C57BL/6 mice, and investigated the role of the microbiota in modulating disease. RESULTS: We altered the murine microbiota by treatment with the antibiotics vancomycin or cefoperazone prior to H. hepaticus infection. Through surveys of the 16S rRNA encoding-gene, analyses of histology and changes in expression of host mediators, we correlated alterations in the microbiota with host responses. We found that resident microbes are essential for initiation of disease, as animals mono-associated with H. hepaticus did not develop colitis. Despite the requirement for an indigenous microbiota for the initiation of disease, the severity of disease was independent of antibiotic-induced changes in the microbial community structure. Despite differences in the expression of host inflammatory mediators associated with shifts in the microbiota, H. hepaticus infection led to similar histopathologic lesions in microbial communities exposed to either cefoperazone or vancomycin. CONCLUSION: In conclusion, we demonstrate that colitis due to H. hepaticus infection can be initiated and progress in the presence of several different microbial communities. Furthermore, H. hepaticus is the main driver of inflammation in this model, while the specific structure of the microbiota may modulate the host pathways that lead to chronic inflammation.

Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis.

Persistent mucosal inflammation and microbial infection are characteristics of chronic rhinosinusitis (CRS). Mucosal microbiota dysbiosis is found in other chronic inflammatory diseases; however, the relationship between sinus microbiota composition and CRS is unknown. Using comparative microbiome profiling of a cohort of CRS patients and healthy subjects, we demonstrate that the sinus microbiota of CRS patients exhibits significantly reduced bacterial diversity compared with that of healthy controls. In our cohort of CRS patients, multiple, phylogenetically distinct lactic acid bacteria were depleted concomitant with an increase in the relative abundance of a single species, Corynebacterium tuberculostearicum. We recapitulated the conditions observed in our human cohort in a murine model and confirmed the pathogenic potential of C. tuberculostearicum and the critical necessity for a replete mucosal microbiota to protect against this species. Moreover, Lactobacillus sakei, which was identified from our comparative microbiome analyses as a potentially protective species, defended against C. tuberculostearicum sinus infection, even in the context of a depleted sinus bacterial community. These studies demonstrate that sinus mucosal health is highly dependent on the composition of the resident microbiota as well as identify both a new sino-pathogen and a strong bacterial candidate for therapeutic intervention.

Role of the microbiota in inflammatory bowel diseases.

Studying the role of the human microbiome as it relates to human health status has revolutionized our view of microbial community contributions to a large number of diseases, particularly chronic inflammatory disorders. The lower gastrointestinal (GI) tract houses trillions of microbial cells representing a large diversity of species in relatively well-defined phylogenetic ratios that are associated with maintenance of key aspects of host physiology and immune homeostasis. It is not surprising, therefore, that many GI inflammatory diseases, including inflammatory bowel disease (IBD), are associated with substantial changes in the composition of these microbial assemblages, either as a cause or consequence of host inflammatory response. Here we review current knowledge in the emerging field of human microbiome research as it relates to IBD, specifically focusing on Crohn's disease (CD) and ulcerative colitis (UC). We discuss bacteriotherapeutic efforts to restore GI microbial assemblage integrity via probiotic supplementation of IBD patients, and speculate on future directions for the field.

Microbial ecology of the murine gut associated with the development of dextran sodium sulfate-induced colitis.

BACKGROUND: Dextran sodium sulfate (DSS) is used to induce murine colitis. Although the exact mechanism by which DSS administration causes disease is unknown, evidence suggests that the resident bacteria play a role in the development of murine DSS colitis, analogous to their role in human inflammatory bowel diseases. METHODS: C57BL/6 mice received 5% DSS in the drinking water and were euthanized 3 days and 14 days after the initiation of DSS treatment. Culture-independent methods were used to follow changes in the community structure of the gut's microbiota following DSS treatment. Histologic evidence of disease and changes in host gene expression were assessed. RESULTS: Histologic colitis was minimal in DSS-treated animals at 3 days, but severe after 14 days. Analysis of 16S rRNA-encoding gene clone libraries demonstrated that the microbial communities in the ceca of DSS-treated mice were distinct from those in control mice. The microbiota in the cecum of DSS-treated animals was characterized by an overall decrease in microbial richness, an increase in members of the phylum Verrucomicrobia, and decrease in Tenericutes. Changes in the host's inflammatory response and microbial communities occurred before the histologic appearance of severe disease in the colon, but were seen concurrently in the cecum. CONCLUSIONS: DSS administration is associated with reproducible changes in the gut microbial diversity of mice. Microbial and immunological changes appeared before the development of severe inflammation in the colon. This indicates that these changes in microbial community may play role in the potentiation of the abnormal inflammatory response seen in DSS-treated animals.

A cross-sectional study of isolates from sputum samples from bacterial pneumonia patients in Trinidad.

We determined the frequency of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, and Gram-negative enteric bacteria (GNEB) in pneumonia patients, determined the antibiograms of these pathogens, and investigated the relationship between pneumonia and selected risk factors. Sputum and demographic data were collected from 124 pneumonia patients. Sputum was cultured for S. aureus, GNEB, H. influenzae and S. pneumoniae. The disc diffusion method was used to determine resistance to eight antimicrobial agents. Among the 124 sputum samples, eight (6.5%) were positive for S. aureus, 15 (12.1%) for GNEB, two (1.6%) for S. pneumoniae and one (0.8%) for H. influenzae. Hospitals, gender, ethnicity, co-morbidities and symptoms did not significantly (p > 0.05; chi2) affect the prevalence of these bacteria. GNEB infection was most prevalent (47%) in patients over 70 years old. Gentamicin and levofloxacin were the most effective against these bacteria.

A cross-sectional study of isolates from sputum samples from bacterial pneumonia patients in Trinidad

We determined the frequency of Streptococcus pneumoniae, Haemophilus influenzae,Staphylococcus aureus, and Gram-negative enteric bacteria (GNEB) in pneumonia patients,determined the antibiograms of these pathogens, and investigated the relationship between pneumonia and selected risk factors. Sputum and demographic data were collected from 124pneumonia patients. Sputum was cultured for S. aureus, GNEB, H. influenzae and S. pneumoniae.The disc diffusion method was used to determine resistance to eight antimicrobial agents. Amongthe 124 sputum samples, eight (6.5%) were positive for S. aureus, 15 (12.1%) for GNEB, two(1.6%) for S. pneumoniae and one (0.8%) for H. influenzae. Hospitals, gender, ethnicity, comorbidities and symptoms did not significantly (p > 0.05; ö2) affect the prevalence of these bacteria.GNEB infection was most prevalent (47%) in patients over 70 years old. Gentamicin and levofloxacin were the most effective against these bacteria.

A cross-sectional study of isolates from sputum samples from bacterial pneumonia patients in Trinidad

We determined the frequency of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, and Gram-negative enteric bacteria (GNEB) in pneumonia patients, determined the antibiograms of these pathogens, and investigated the relationship between pneumonia and selected risk factors. Sputum and demographic data were collected from 124 pneumonia patients. Sputum was cultured for S. aureus, GNEB, H. influenzae and S. pneumoniae. The disc diffusion method was used to determine resistance to eight antimicrobial agents. Among the 124 sputum samples, eight (6.5 percent) were positive for S. aureus, 15 (12.1 percent) for GNEB, two (1.6 percent) for S. pneumoniae and one (0.8 percent) for H. influenzae. Hospitals, gender, ethnicity, co-morbidities and symptoms did not significantly (p > 0.05; chi2) affect the prevalence of these bacteria. GNEB infection was most prevalent (47 percent) in patients over 70 years old. Gentamicin and levofloxacin were the most effective against these bacteria.