scholarly journals Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels

Gut Pathogens ◽  
2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Mohammad Tauqeer Alam ◽  
Gregory C. A. Amos ◽  
Andrew R. J. Murphy ◽  
Simon Murch ◽  
Elizabeth M. H. Wellington ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Gut Microbiota ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Global Scale ◽  
Rrna Gene ◽  
Healthy Individuals ◽  
Bacterial Phyla ◽  
Inflammatory Bowel ◽  
Bacterial Groups

Abstract Background Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. Results In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute > 98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of > 22,000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database (Mitchell et al. in Nucleic Acids Res 46:D726–D735, 2018). By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. Conclusions IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD.

scholarly journals P832 Gastrointestinal infections are associated with unique gut microbiome signatures in patients with inflammatory bowel disease

2020 ◽  
Vol 14 (Supplement_1) ◽  
pp. S644-S645
Author(s):  
J Axelrad ◽  
A Hine ◽  
J Devlin ◽  
P Loke ◽  
K Cadwell
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Gastrointestinal Symptoms ◽  
Serum Biomarkers ◽  
Rrna Gene ◽  
Enteric Infection ◽  
Gastrointestinal Infections ◽  
E Coli ◽  
Inflammatory Bowel

Abstract Background Stool PCR pathogen panel assays have implicated enteric infection in nearly 30% of inflammatory bowel disease (IBD) flares, most commonly with Clostridioides difficile, Escherichia coli, and norovirus. Many questions remain about the interpretation of a positive stool PCR result, and the similar presentations of infection and flare present a clinical challenge. We aimed to characterise the gut microbiome during an infection with C. difficile, E. coli, or norovirus in patients with and without IBD to microbially differentiate patients with an enteric infection, flare of IBD, and flare of IBD complicated by a pathogen. Methods We performed a cross-sectional study of patients with a stool PCR panel positive for C. difficile, E. coli subtypes, norovirus, or negative for all pathogens during an episode of gastrointestinal symptoms from September 2018 to February 2019. Clinical data and remnant stool specimens were collected. Our primary outcome was microbiome signature using 16s bacterial rRNA gene sequencing derived from linear discriminant analysis effect size (LEfSe) to identify microbes associated with each pathogen and clinical scenario stratified by IBD. Results We identified 119 patients, 19 (16%) with IBD, with C. difficile (n = 30), an E. coli subtype (n = 30), norovirus (n = 29), or negative for all pathogens (n = 30; Table). Hematochezia on presentation and recent antibiotic or hospitalisation exposure was more common in pathogen negative patients compared with pathogen positive patients (p = 0.045, p = 0.007, respectively). Patients with IBD without a pathogen or with C. difficile tended to have higher serum biomarkers of inflammation (median CRP 24 and 28, respectively) compared with patients with an E. coli subtype (CRP 5) or norovirus (CRP 11). On LEfSe, patients with C. difficile were enriched in Enterobacteriaceae and Clostridioides, E. coli subtypes in Faecalibacterium, norovirus in Roseburia, and negative for a pathogen in Bacteroides. Stratifying by IBD and pathogen, there were several differentially abundant microbes denoting a specific gut microbial signature associated with each pathogen and IBD (Figure). Conclusion In this study of patients with C. difficile, E. coli, norovirus, or negative for pathogens during an episode of gastrointestinal symptoms, there were major differences in presentation and gut microbiota between patients with and without an enteric pathogen and IBD. These data demonstrate that gut microbiomes distinguish and differentially respond to pathogens. In patients with IBD, coupled with a unique microbiota, serum biomarkers of inflammation were lower in patients with E. coli or norovirus, suggesting a milder subset of IBD flare.

scholarly journals Analysis of the gut microbiome of Japanese inflammatory bowel disease patients

2019 ◽  
Author(s):  
Yuto Fukui ◽  
Hitoshi Nakajima ◽  
Kotaro Aoki ◽  
Ohmori Toshihide ◽  
Kazuhiro Tateda ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Illumina Miseq ◽  
Japanese Patients ◽  
Amplicon Sequencing ◽  
Cross Sectional Study ◽  
Healthy Individuals ◽  
Cross Sectional ◽  
Inflammatory Bowel

Abstract Background Gut microbiome dysbiosis has been reported in patients with inflammatory bowel disease (IBD). However, gut microbiome of healthy Japanese individuals differs from that of other populations and gut microbiome of Japanese IBD patients has not been well characterized. We conducted a cross-sectional study to characterize the gut microbiome of Japanese patients with Crohn’s disease (CD) and ulcerative colitis (UC). Methods Two-hundred and eighty-four IBD patients (39 CD patients and 245 UC patients) and 31 healthy participants were enrolled. Gut microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina Miseq. Results Significant differences were observed among the gut microbiome of CD patients, UC patients and healthy individuals. Species richness and evenness were significantly lower in patients with active IBD than in healthy individuals. At the genus level, Bifidobacterium was most abundant genera in all three groups. Pathogenic obligate anaerobes such as Prevotella and Veillonella were increased and commensal bacteria such as Ruminococcus was decreased in IBD patients compared with healthy individuals. Conclusions CD patients and UC patients showed unique patterns of gut microbiome dysbiosis. Patients with active IBD had severe dysbiotic changes. However, characteristic features of the gut microbiome of Japanese individuals, such as high abundance of the genus Bifidobacterium, were maintained in IBD patients.

Gut microbiota pattern in relation to diet, physical activity and malnutrition in patients with inflammatory bowel disease: cases-control study

2019 ◽  
Author(s):  
Isabel Cornejo-Pareja ◽  
Beatriz Garcia-Munoz ◽  
Eduardo Romero-Perez ◽  
Eduardo Garcia-Fuentes ◽  
S Tapia-Paniagua ◽  
...  
Keyword(s):  
Physical Activity ◽  
Inflammatory Bowel Disease ◽  
Gut Microbiota ◽  
Bowel Disease ◽  
Inflammatory Bowel ◽  
Control Study

scholarly journals Tu1789 – Treatment Response to Ustekinumab and Vedolizumab in Inflammatory Bowel Disease: the Predictive Role of Gut Microbiota

2019 ◽  
Vol 156 (6) ◽  
pp. S-1124
Author(s):  
Clara Caenepeel ◽  
Sara Vieira-Silva ◽  
Jorge F. Vázquez-Castellanos ◽  
Bram Verstockt ◽  
Marc Ferrante ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Gut Microbiota ◽  
Treatment Response ◽  
Bowel Disease ◽  
Predictive Role ◽  
Inflammatory Bowel

scholarly journals Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

2021 ◽  
Vol 11 (4) ◽  
pp. 294
Author(s):  
Irina Grigor’eva ◽  
Tatiana Romanova ◽  
Natalia Naumova ◽  
Tatiana Alikina ◽  
Alexey Kuznetsov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Gallstone Disease ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Female Patients ◽  
Composition And Structure ◽  
Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

scholarly journals Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

2021 ◽  
Vol 17 ◽  
pp. 117693432199635
Author(s):  
Daoxin Liu ◽  
Pengfei Song ◽  
Jingyan Yan ◽  
Haijing Wang ◽  
Zhenyuan Cai ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Bacterial Phyla ◽  
In Captivity ◽  
Relative Abundances ◽  
Plateau Zokor

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

Sign in / Sign up

Export Citation Format

Share Document