A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

Background: Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes. Methods: We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn. Results: We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut. Conclusions: This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0490-5) contains supplementary material, which is available to authorized users

Trends in the inpatient burden of alcohol-related liver disease among women hospitalized in the United States

Alcohol-related liver disease (ALD) is the leading indication for liver transplantation in the United States, but disparities for women with ALD exist. We sought to characterize trends in ALD hospitalizations and mortality among women. Using the National Inpatient Sample, we evaluated ALD and non-ALD discharges from 2003 to 2017. Multivariable logistic regression was used to evaluate mortality. ALD increased more rapidly among women, with alcohol hepatitis (AH) rising the most. When stratified by age and sex, changes in alcohol-related cirrhosis (AC) and AH were greater in women in nearly all age groups. Similar increases were present when stratified by race, notably for Native American and Asian women. AH mortality increased in women in almost all age groups. While ALD remains predominantly male, discharges and mortality have disproportionately increased among women, particularly in young women and Native Americans. These findings shed light on populations in need of intensive public health interventions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/172991/1/liv15277.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/172991/2/liv15277_am.pd

Diagnosis and Treatment of Alcohol‐Associated Liver Disease: A Patient‐Friendly Summary of the 2019 AASLD Guidelines

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/169247/1/cld1129.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/169247/2/cld1129_am.pd

Additional file 3: of Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease

De novo and rarefy analysis. Contains a table that compares results from the generalized estimating equation (GEE) analysis performed in the paper (using closed-reference OTU picking) to de novo OTU picking and rarefied closed-reference approaches. (XLSX 10 kb

L'Auto-vélo : automobilisme, cyclisme, athlétisme, yachting, aérostation, escrime, hippisme / dir. Henri Desgranges

26 octobre 19381938/10/26 (A39,N13824)

IBD Serology and Disease Outcomes in African Americans With Crohn\u27s Disease

Backgrounds: Recent studies have identified the role of serologic markers in characterizing disease phenotype, location, complications, and severity among Northern Europeans (NE) with Crohn\u27s disease (CD). However, very little is known about the role of serology in CD among African Americans (AA). Our study explored the relationship between serology and disease phenotype in AA with CD, while controlling for genetic ancestry. Methods: AAs with CD were enrolled as participants through multicenter collaborative efforts. Serological levels of IgA anti-Saccharomyces cervisiae antibody (ASCA), IgG ASCA, E. coli outermembrane porin C, anti-CBir1, and ANCA were measured using enzyme-linked immunosorbent assays. Genotyping was performed using Illumina immunochip technology; an admixture rate was calculated for each subject. Multiple imputation by chained equations was performed to account for data missing at random. Logistic regression was used to calculate adjusted odds ratio (OR) for associations between serological markers and both complicated disease and disease requiring surgery. Results: A total of 358 patients were included in the analysis. The majority of our patients had inflammatory, noncomplicated disease (58.4%), perianal disease (55.7%), and documented colonic inflammation (86.8%). On multivariable analysis, both IgG ASCA and OmpC were associated with complicated disease (OR, 2.67; 95% CI, 1.67-4.28; OR, 2.23; 95% CI, 1.41-3.53, respectively) and disease requiring surgery (OR, 2.51; 95% CI, 1.49-4.22; OR, 3.57; 95% CI, 2.12-6.00). NE admixture to the African genome did not have any associations or interactions in relation to clinical outcome. Conclusions: Our study comprises the largest cohort of AAs with CD. The utility of serological markers for the prognosis of CD in NE applies equally to AA populations

IBD Serology and Disease Outcomes in African Americans With Crohn\u27s Disease

Backgrounds: Recent studies have identified the role of serologic markers in characterizing disease phenotype, location, complications, and severity among Northern Europeans (NE) with Crohn\u27s disease (CD). However, very little is known about the role of serology in CD among African Americans (AA). Our study explored the relationship between serology and disease phenotype in AA with CD, while controlling for genetic ancestry. Methods: AAs with CD were enrolled as participants through multicenter collaborative efforts. Serological levels of IgA anti-Saccharomyces cervisiae antibody (ASCA), IgG ASCA, E. coli outermembrane porin C, anti-CBir1, and ANCA were measured using enzyme-linked immunosorbent assays. Genotyping was performed using Illumina immunochip technology; an admixture rate was calculated for each subject. Multiple imputation by chained equations was performed to account for data missing at random. Logistic regression was used to calculate adjusted odds ratio (OR) for associations between serological markers and both complicated disease and disease requiring surgery. Results: A total of 358 patients were included in the analysis. The majority of our patients had inflammatory, noncomplicated disease (58.4%), perianal disease (55.7%), and documented colonic inflammation (86.8%). On multivariable analysis, both IgG ASCA and OmpC were associated with complicated disease (OR, 2.67; 95% CI, 1.67-4.28; OR, 2.23; 95% CI, 1.41-3.53, respectively) and disease requiring surgery (OR, 2.51; 95% CI, 1.49-4.22; OR, 3.57; 95% CI, 2.12-6.00). NE admixture to the African genome did not have any associations or interactions in relation to clinical outcome. Conclusions: Our study comprises the largest cohort of AAs with CD. The utility of serological markers for the prognosis of CD in NE applies equally to AA populations

Additional file 7: Table S6. of A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

Gene annotations for the selected R. gnavus IBD-specific genes mentioned in the main text. (XLSX 9 kb