Characteristics of Faecal Microbiota in Paediatric Crohn’s Disease and Their Dynamic Changes During Infliximab Therapy

Wang, Yizhong; Gao, Xuefeng; Ghozlane, Amine; Hu, Hui; Li, Xiaolu; Xiao, Yunfeng; Li, Dan; Yu, Guangjun; Zhang, Ting

doi:10.1093/ecco-jcc/jjx153

Cited by 137 publications

(154 citation statements)

References 53 publications

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“…Stiemsma et al (2016) reported that the abundance of genus Lachnospira (L) decreased in children with asthma, and opposing shifts in the relative abundance of Lachnospira and Clostridium neonatale (C) in the first 3 months of life were associated with preschool-age asthma, and the L/C ratio might serve as a potential early-life biomarker to predict asthma development. Wang et al (2017) found a significant loss of Lachnospira in pediatric patients with Crohn's disease prior to infliximab treatment. In the present study, the relative abundance of Ruminococcus_gnavus was higher in the CKD group.…”

Section: Discussionmentioning

confidence: 88%

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Altered gut microbiota and microbial biomarkers associated with chronic kidney disease

et al. 2018

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The present study aimed to determine the differences in gut microbiota between patients with chronic kidney disease (CKD) and healthy controls (HC) and search for better microbial biomarkers associated with CKD. The 16S rRNA gene sequencing approach was used to investigate the differences in gut microbiota between the CKD and HC groups. The study found that 12 phylotypes were overrepresented in the CKD group and 19 in the HC group at the genus level. Furthermore, genera Lachnospira and Ruminococcus_gnavus performed the best in differentiating between HC and CKD populations. In addition, this novel study found that the genera Holdemanella, Megamonas, Prevotella 2, Dielma, and Scardovia were associated with the progression of CKD and hemodialysis. In conclusion, the composition of gut microbiota was different in CKD populations compared with healthy populations, and Lachnospira and R._gnavus were better microbial biomarkers. In addition, five phylotypes, including Holdemanella, Megamonas, Prevotella2, Dielma, and Scardovia, served as an indicator of the progression of CKD and hemodialysis. However, large-scale prospective studies should be performed to identify the reliability of the set of these phylotypes as biomarkers.

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Section: Discussionmentioning

confidence: 88%

“…Wang et al. () found a significant loss of Lachnospira in pediatric patients with Crohn's disease prior to infliximab treatment. In the present study, the relative abundance of Ruminococcus_gnavus was higher in the CKD group.…”

Section: Discussionmentioning

confidence: 99%

Altered gut microbiota and microbial biomarkers associated with chronic kidney disease

et al. 2018

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“…DNA was quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA). PCR amplification and library preparation were accomplished using previously reported methods . In brief, amplification of the V3‐V4 hypervariable regions of the ribosomal 16S rRNA genes was performed using universal primers 341F (5′‐CCTACGGGAGGCAGCAG‐3′)/806R (5′‐GGACTACNNGGGTACTAAT‐3).…”

Section: Methodsmentioning

confidence: 99%

“…PCR amplification and library preparation were accomplished using previously reported methods. 18 In brief, amplification of the V3-V4 hypervariable regions of the ribosomal 16S rRNA genes was performed using universal primers 341F (5′-CCTACGGGAGGCAGCAG-3′)/806R (5′-GGACTACNNGGGTACTAAT-3). Purified amplicon libraries were sequenced on the MiSeq platform (Illumina, Inc, San Diego, CA) using the 2 × 300 bp paired-end protocol.…”

Section: Sample Collection Dna Isolation and 16s Rrna Gene Sequenmentioning

confidence: 99%

Helicobacter pylori infection alters gastric and tongue coating microbial communities

et al. 2019

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Objective Infection with Helicobacter pylori ( H pylori ), especially cytotoxin‐associated gene A‐positive (CagA+) strains, has been associated with various gastrointestinal and extragastric diseases. The aim of this study was to characterize H pylori ‐induced alterations in the gastric and tongue coating microbiota and evaluate their potential impacts on human health. Design The gastric mucosa and tongue coating specimens were collected from 80 patients with chronic gastritis, and microbiota profiles were generated by 16S rRNA gene sequencing. Samples were grouped as H pylori negative (n = 32), CagA‐negative H pylori infection (n = 13), and CagA‐positive H pylori infection (n=35). The comparison of bacterial relative abundance was made using a generalized linear model. Functional profiling of microbial communities was predicted with PICRUSt and BugBase. Microbial correlation networks were produced by utilizing SparCC method. Results Significant alterations of the gastric microbiota were found in the H pylori +/CagA+ samples, represented by a decrease in bacterial diversity, a reduced abundance of Roseburia , and increased abundances of Helicobacter and Haemophilus genera. At the community level, functions involved in biofilm forming, mobile element content, and facultative anaerobiosis were significantly decreased in gastric microbiome of the H pylori + subjects. The presence of CagA gene was linked to an increased proportion of Gram‐negative bacteria in the stomach, thereby contributing to an upregulation of lipopolysaccharide (LPS) biosynthesis. The number of bacterial interactions was greatly reduced in networks of both tongue coating and gastric microbiota of the H pylori +/CagA+ subject, and the cooperative bacterial interactions dominated the tongue coating microbiome. Conclusions Infection with H pylori strains possessing CagA may increase the risk of various diseases, by upregulating LPS biosynthesis in the stomach and weakening the defense of oral microbiota against microorganisms with pathogenic potential.

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“…Lachnospira has been reported as depleted with respect to Crohn's disease several times 501 [35,36]. The depletion of tyzzerella has been associated with chronic intestinal 502 inflammation and supplementation suggested as a probiotic for Crohn's disease [37,38].…”

Section: Figure 3 453mentioning

confidence: 99%

BowSaw: inferring higher-order trait interactions associated with complex biological phenotypes

DiMucci

Kon

Segrè

2019

Preprint

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1Machine learning is helping the interpretation of biological complexity by enabling the 2 inference and classification of cellular, organismal and ecological phenotypes based on 3 large datasets, e.g. from genomic, transcriptomic and metagenomic analyses. A number 4 of available algorithms can help search these datasets to uncover patterns associated with 5 specific traits, including disease-related attributes. While, in many instances, treating an 6 algorithm as a black box is sufficient, it is interesting to pursue an enhanced 7 understanding of how system variables end up contributing to a specific output, as an 8 avenue towards new mechanistic insight. Here we address this challenge through a suite 9 of algorithms, named BowSaw, which takes advantage of the structure of a trained 10 random forest algorithm to identify combinations of variables ("rules") frequently used 11 for classification. We first apply BowSaw to a simulated dataset, and show that the 12 algorithm can accurately recover the sets of variables used to generate the phenotypes 13 through complex Boolean rules, even under challenging noise levels. We next apply our 14 method to data from the integrative Human Microbiome Project and find previously 15 unreported high-order combinations of microbial taxa putatively associated with Crohn's 16 disease. By leveraging the structure of trees within a random forest, BowSaw provides a 17 new way of using decision trees to generate testable biological hypotheses. 18 19 20 21 22

show abstract

Characteristics of Faecal Microbiota in Paediatric Crohn’s Disease and Their Dynamic Changes During Infliximab Therapy

Cited by 137 publications

References 53 publications

Altered gut microbiota and microbial biomarkers associated with chronic kidney disease

Altered gut microbiota and microbial biomarkers associated with chronic kidney disease

Helicobacter pylori infection alters gastric and tongue coating microbial communities

BowSaw: inferring higher-order trait interactions associated with complex biological phenotypes

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