The murine female intestinal microbiota does not shift throughout the estrous cycle.

Pregnancy is accompanied by maternal physiological adaptations including metabolic, endocrine, immune, cardiovascular, skeletomuscular and neurological modifications that facilitate fetal and placental growth and development. Emerging evidence suggests that the maternal intestinal microbiota is modified over the course of healthy pregnancy. We have recently identified a maternal intestinal microbial shift within hours of conception; a shift that continued with advancing gestation. It is possible that maternal gut bacterial profiles might be associated with the known endocrine changes that accompany the female reproductive (estrous) cycle. METHODS:To determine whether the estrous cycle influenced the shifts in the maternal intestinal microbiota, time-matched fecal pellets were collected daily for 3 consecutive estrous cycles from individually housed, non-pregnant female C57BL/6J mice (n = 10) fed a control diet. Estrous stage was identified by cell type predominance in vaginal cytological samples. The corresponding fecal pellets for each estrous stage were processed for bacterial 16S rRNA sequencing of the variable 3 (V3) region. RESULTS:Estrous cycle stage accounted for a very small and not statistically significant proportion of the variation in the fecal microbiota according to PERMANOVA testing performed on Bray-Curtis dissimilarity scores. These values displayed no significant clustering of fecal microbial communities by estrous stage. CONCLUSION:The estrous cycle does not result in any significant shift in the intestinal microbial community in the reproductively mature, regularly cycling female mouse

Effect of Exclusive Enteral Nutrition and Corticosteroid Induction Therapy on the Gut Microbiota of Pediatric Patients with Inflammatory Bowel Disease

Introduction: Exclusive enteral nutrition (EEN) and corticosteroids (CS) are effective induction therapies for pediatric Crohn’s Disease (CD). CS are also therapy for ulcerative colitis (UC). Host–microbe interactions may be able to explain the effectiveness of these treatments. This is the first prospective study to longitudinally characterize compositional changes in the bacterial community structure of pediatric UC and CD patients receiving EEN or CS induction therapy. Methods: Patients with diagnoses of CD or UC were recruited from McMaster Children’s Hospital (Hamilton, Canada). Fecal samples were collected from participants aged 5–18 years old undergoing 8 weeks of induction therapy with EEN or CS. Fecal samples were submitted for 16S rRNA sequencing. The Shannon diversity index and the relative abundance of specific bacterial taxa were compared using a linear mixed model. Results: The clustering of microbiota was the highest between patients who achieved remission compared to patients still showing active disease (p = 0.029); this effect was independent of the diagnosis or treatment type. All patients showed a significant increase in Shannon diversity over the 8 weeks of treatment. By week 2, a significant difference was seen in Shannon diversity between patients who would go on to achieve remission and those who would not. Conclusion: The gut microbiota of pediatric UC and CD patients was most influenced by patients’ success or failure to achieve remission and was largely independent of the choice of treatment or disease type. Significant differences in Shannon diversity indices occurred as early as week 2 between patients who went on to achieve remission and those who continued to have active disease

Relationship between circulating reproductive hormones (arbitaray units), reproductive cycle stage, and vaginal cytological outcomes throughout the reproductive cycle in the female mouse.

<p>Scale bar represents 100 μm.</p

Intestinal microbial differences are driven by mouse-related differences rather than by reproductive cycle stage.

<p><b>A.</b> Principle Coordinate Analysis using the Bray-Curtis dissimilarity metric showed no clustering of intestinal microbial communities present at diestrous, proestrous or estrus in female mice (n = 7). <b>B.</b> Principle Coordinate Analysis using the Bray-Curtis dissimilarity metric shows significant clustering of microbial communities present in each female mouse across 2–3 consecutive estrous cycles (n = 7).</p

The female intestinal microbiota appears consistent throughout the reproductive cycle.

<p><b>A.</b> Taxonomic classifications of the 25 most abundant bacterial taxa resolved to the class (c), order (o), family (f) and genus (g) level at diestrous, proestrous and estrus for 2–3 consecutive estrous cycles in female mice (n = 7). <b>B.</b> Taxonomic classifications of bacterial phyla at diestrous, proestrous, and estrus for 3 consecutive estrous cycles in female mice (n = 7).</p

Biogeographic Variation and Functional Pathways of the Gut Microbiota in Celiac Disease

Background & Aims: Genes and gluten are necessary but insufficient to cause celiac disease (CeD). Altered gut microbiota has been implicated as an additional risk factor. Variability in sampling site may confound interpretation and mechanistic insight, as CeD primarily affects the small intestine. Thus, we characterized CeD microbiota along the duodenum and in feces and verified functional impact in gnotobiotic mice. Methods: We used 16S rRNA gene sequencing (Illumina) and predicted gene function (PICRUSt2) in duodenal biopsies (D1, D2 and D3), aspirates, and stool from patients with active CeD and controls. CeD alleles were determined in consented participants. A subset of duodenal samples stratified according to similar CeD risk genotypes (controls DQ2–/– or DQ2+/– and CeD DQ2+/–) were used for further analysis and to colonize germ-free mice for gluten metabolism studies. Results: Microbiota composition and predicted function in CeD was largely determined by intestinal location. In the duodenum, but not stool, there was higher abundance of Escherichia coli (D1), Prevotella salivae (D2), and Neisseria (D3) in CeD vs controls. Predicted bacterial protease and peptidase genes were altered in CeD and impaired gluten degradation was detected only in mice colonized with CeD microbiota. Conclusions: Our results showed luminal and mucosal microbial niches along the gut in CeD. We identified novel microbial proteolytic pathways involved in gluten detoxification that are impaired in CeD but not in controls carrying DQ2, suggesting an association with active duodenal inflammation. Sampling site should be considered a confounding factor in microbiome studies in CeD.Fil: Constante, Marco. Mc Master University; CanadáFil: Libertucci, Josie. Mc Master University; CanadáFil: Galipeau, Heather J.. Mc Master University; CanadáFil: Szamosi, Jake C.. Mc Master University; CanadáFil: Rueda, Gaston. Mc Master University; CanadáFil: Miranda, Pedro M.. Mc Master University; CanadáFil: Pinto Sanchez, Maria Ines. Mc Master University; CanadáFil: Southward, Carolyn M.. Mc Master University; CanadáFil: Rossi, Laura. Mc Master University; CanadáFil: Fontes, Michelle E.. Mc Master University; CanadáFil: Chirdo, Fernando Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Estudios Inmunológicos y Fisiopatológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Estudios Inmunológicos y Fisiopatológicos; ArgentinaFil: Surette, Michael G.. Mc Master University; CanadáFil: Bercik, Premysl. Mc Master University; CanadáFil: Caminero, Alberto. Mc Master University; CanadáFil: Verdu, Elena F.. Mc Master University; Canad

Microbial dysbiosis and mortality during mechanical ventilation: a prospective observational study

Abstract Background Host-associated microbial communities have important roles in tissue homeostasis and overall health. Severe perturbations can occur within these microbial communities during critical illness due to underlying diseases and clinical interventions, potentially influencing patient outcomes. We sought to profile the microbial composition of critically ill mechanically ventilated patients, and to determine whether microbial diversity is associated with illness severity and mortality. Methods We conducted a prospective, observational study of mechanically ventilated critically ill patients with a high incidence of pneumonia in 2 intensive care units (ICUs) in Hamilton, Canada, nested within a randomized trial for the prevention of healthcare-associated infections. The microbial profiles of specimens from 3 anatomical sites (respiratory, and upper and lower gastrointestinal tracts) were characterized using 16S ribosomal RNA gene sequencing. Results We collected 65 specimens from 34 ICU patients enrolled in the trial (29 endotracheal aspirates, 26 gastric aspirates and 10 stool specimens). Specimens were collected at a median time of 3 days (lower respiratory tract and gastric aspirates; interquartile range [IQR] 2–4) and 6 days (stool; IQR 4.25–6.75) following ICU admission. We observed a loss of biogeographical distinction between the lower respiratory tract and gastrointestinal tract microbiota during critical illness. Moreover, microbial diversity in the respiratory tract was inversely correlated with APACHE II score (r = − 0.46, p = 0.013) and was associated with hospital mortality (Median Shannon index: Discharged alive; 1.964 vs. Deceased; 1.348, p = 0.045). Conclusions The composition of the host-associated microbial communities is severely perturbed during critical illness. Reduced microbial diversity reflects high illness severity and is associated with mortality. Microbial diversity may be a biomarker of prognostic value in mechanically ventilated patients. Trial registration ClinicalTrials.gov ID NCT01782755. Registered February 4 2013