Variability of core microbiota in newly diagnosed treatment-naïve paediatric inflammatory bowel disease patients

Meij, Tim G. J. de; Groot, E. F. J. de; Peeters, Carel F.W.; Boer, Nanne K. H. de; Kneepkens, C. M. F.; Eck, Anat; Benninga, Marc A.; Savelkoul, Paul H. M.; Bodegraven, Ad A. van; Budding, Andries E.

doi:10.1371/journal.pone.0197649

Cited by 49 publications

(47 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Patient and disease characteristics, and clinical and biochemical response are shown in Fig. 1 B and Table 1 and were partially described previously 19 . In addition to EEN, all patients were started on concomitant thiopurines (i.e.…”

Section: Resultsmentioning

confidence: 99%

Exclusive enteral nutrition mediates gut microbial and metabolic changes that are associated with remission in children with Crohn’s disease

Diederen

Donachie

et al. 2020

Sci Rep

View full text Add to dashboard Cite

A nutritional intervention, exclusive enteral nutrition (EEN) can induce remission in patients with pediatric Crohn’s disease (CD). We characterized changes in the fecal microbiota and metabolome to identify the mechanism of EEN. Feces of 43 children were collected prior, during and after EEN. Microbiota and metabolites were analyzed by 16S rRNA gene amplicon sequencing and NMR. Selected metabolites were evaluated in relevant model systems. Microbiota and metabolome of patients with CD and controls were different at all time points. Amino acids, primary bile salts, trimethylamine and cadaverine were elevated in patients with CD. Microbiota and metabolome differed between responders and non-responders prior to EEN. EEN decreased microbiota diversity and reduced amino acids, trimethylamine and cadaverine towards control levels. Patients with CD had reduced microbial metabolism of bile acids that partially normalized during EEN. Trimethylamine and cadaverine inhibited intestinal cell growth. TMA and cadaverine inhibited LPS-stimulated TNF-alpha and IL-6 secretion by primary human monocytes. A diet rich in free amino acids worsened inflammation in the DSS model of intestinal inflammation. Trimethylamine, cadaverine, bile salts and amino acids could play a role in the mechanism by which EEN induces remission. Prior to EEN, microbiota and metabolome are different between responders and non-responders.

show abstract

Section: Resultsmentioning

confidence: 99%

Exclusive enteral nutrition mediates gut microbial and metabolic changes that are associated with remission in children with Crohn’s disease

Diederen

Donachie

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…[38][39][40][41] Furthermore, the predominant species of the Bacteroidetes-dominant settler type we identified were previously found as prevalent members of a healthy core microbiota in children, while missing from that of Two distinct settler types determine early life microbial development pediatric IBD patients. [42] While the mechanisms of these associations are yet to be elucidated, it is important to bring into consideration that a perturbed microbial composition in early life may have long term consequences. For example, children that were characterized by a low-Bacteroides signature at the first six months also presented lower overall microbial diversity that persisted even at 36 months, when Bacteroides had become highly abundant in this group.…”

Section: Discussionmentioning

confidence: 99%

Neonatal microbiota development and the effect of early life antibiotics are determined by two distinct settler types

et al. 2020

View full text Add to dashboard Cite

The neonatal period, during which the initial gut microbiota is acquired, is a critical phase. The healthy development of the infant's microbiome can be interrupted by external perturbations, like antibiotics, which are associated with profound effects on the gut microbiome and various disorders later in life. The aim of this study was to investigate the development of intestinal microbiota and the effect of antibiotic exposure during the first three months of life in term infants. Fecal samples were collected from healthy infants and infants who received antibiotics in the first week of life at one week, one month, and three months after birth. Microbial composition was analyzed using IS-pro and compared between antibiotics-treated and untreated infants. In total, 98 infants, divided into four groups based on feeding type and delivery mode, were analyzed. At one week of age, samples clustered into two distinct groups, which were termed "settler types", based on their Bacteroidetes abundance. Caesarean-born infants belonged to the low-Bacteroidetes settler type, but vaginally-born infants were divided between the two groups. The antibiotics effect was assessed within a subgroup of 45 infants, vaginally-born and exclusively breastfed, to minimize the effect of other confounders. Antibiotics administration resulted in lower Bacteroidetes diversity and/ or a delay in Bacteroidetes colonization, which persisted for three months, and in a differential development of the microbiota. Antibiotics resulted in pronounced effects on the Bacteroidetes composition and dynamics. Finally, we hypothesize that stratification of children's cohorts based on settler types may reveal group effects that might otherwise be masked. PLOS ONE | https://doi.org/10.1371/journal.pone.0228133 February 5, 2020 1 / 15 OPEN ACCESS Citation: Eck A, Rutten NBMM, Singendonk MMJ, Rijkers GT, Savelkoul PHM, Meijssen CB, et al. (2020) Neonatal microbiota development and the effect of early life antibiotics are determined by two distinct settler types. PLoS ONE 15(2): e0228133.

show abstract

“…The majority of published papers concerned small cohorts which were heterogeneous in terms of diagnosis and phenotype of IBD, treatment and duration of the disease. Also, the results of two big paediatric CD studies from North America 12 and Netherland 13 are not fully compatible.…”

Section: Introductionmentioning

confidence: 94%

Differences in the intestinal microbiome of healthy children and patients with newly diagnosed Crohn’s disease

Kowalska-Duplaga

Gosiewski

Kapusta

et al. 2019

Sci Rep

104

View full text Add to dashboard Cite

The aetiology of inflammatory bowel diseases (IBD) seems to be strongly connected to changes in the enteral microbiome. The dysbiosis pattern seen in Crohn’s disease (CD) differs among published studies depending on patients’ age, disease phenotype and microbiome research methods. The aims was to investigate microbiome in treatment-naive paediatric patients to get an insight into its structure at the early stage of the disease in comparison to healthy. Stool samples were obtained from controls and newly diagnosed patients prior to any intervention. Microbiota was analysed by 16SrRNAnext-generation-sequencing (NGS). Differences in the within-sample phylotype richness and evenness (alpha diversity) were detected between controls and patients. Statistically significant dissimilarities between samples were present for all used metrics. We also found a significant increase in the abundance of OTUs of the Enterococcus genus and reduction in, among others, Bifidobacterium (B. adolescentis), Roseburia (R.faecis), Faecalibacterium (F. prausnitzii), Gemmiger (G. formicilis), Ruminococcus (R. bromii) and Veillonellaceae (Dialister). Moreover, differences in alpha and beta diversities in respect to calprotectin and PCDAI were observed: patients with calprotectin <100 µg/g and with PCDAI below 10 points vs those with calprotectin >100 µg/g and mild (10–27.7 points), moderate (27.5–40 points) or severe (>40 points) CD disease activity had higher richness and diversity of gut microbiota. The results of our study highlight reduced diversity and dysbiosis at the earliest stage of the disease. Microbial imbalance and low abundance of butyrate-producing bacteria, including Bifidobacterium adolescentis, may suggest benefits of microbial modification therapy.

show abstract

Variability of core microbiota in newly diagnosed treatment-naïve paediatric inflammatory bowel disease patients

Cited by 49 publications

References 52 publications

Exclusive enteral nutrition mediates gut microbial and metabolic changes that are associated with remission in children with Crohn’s disease

Exclusive enteral nutrition mediates gut microbial and metabolic changes that are associated with remission in children with Crohn’s disease

Neonatal microbiota development and the effect of early life antibiotics are determined by two distinct settler types

Differences in the intestinal microbiome of healthy children and patients with newly diagnosed Crohn’s disease

Contact Info

Product

Resources

About