Gut microbiome in Crohn's disease and EEN therapy, China

AbstractBackgroundInflammatory bowel diseases (IBD), with Crohn’s disease (CD) being one of the primary types, have been extensively studied for genetic and gut microbial factors leading to its epidemic in the modern world. However, limited information using metagenomic shotgun-sequencing to pinpoint the gut microbial species and functions involved. Exclusive enteral nutrition (EEN) is a nutritional therapy used for disease-modifying treatment of CD, but its impact on the gut microbiome remains unclear. ResultsWe collected 123 stool samples from 49 CD patients, 14 of whom were resampled after 2 weeks of EEN, and 56 subjects with no disease. Metagenomic shotgun sequencing and analyses confirmed a decreased diversity in the gut microbiota of CD patients, and identified microbial species and potential functions altered in CD, most notably an increased ratio of hexa- to penta-acylated lipopolysaccharide (LPS). Some co-abundance gene groups (CAGs) including Parabacteroides distasonis, Bacteroides intestinalis, Ruminococcus sp. showed strong correlation with clinical indicators such as hs.CRP, Prealbumin, platelets and BMI. The entire cohort could be divided into three types according to their species composition, with Type A largely consisting of healthy controls and Type C containing exclusively CD or after EEN samples. Although compositional changes were generally mild after 2 weeks of EEN, remodeling of the gut microbial network could be observed.ConclusionsOur metagenomic dataset unlock the gut microbiome in CD for functional investigations. Microbiome-based stratification of CD patients before EEN might help optimize the therapy for wider applications.

Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

• host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
• body site study.title · “The gut microbiome in Crohn's”
• body site study.description · “for genetic and gut microbial factors leading”
• life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”

122 runs over 122 samples · mean 5.44 Gbp per run (median 5.40 Gbp, total 663.83 Gbp; 122 runs with a base count) · layout PAIRED 122 · platform ILLUMINA 122 · models Illumina HiSeq 2000 (122) · 91% of runs with a Sandpiper profile · first public 2016-11-11

Pasolli E first · Asnicar F · Manara S · Zolfo M · Karcher N · Armanini F · Beghini F · Manghi P · Tett A · Ghensi P · Collado MC · Rice BL · DuLong C · Morgan XC · Golden CD · Quince C · Huttenhower C · Segata N last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Xu J first · Li P · Li Z · Liu S · Guo H · Lesser CF · Ke J · Zhao W · Mou X last · Li L first · Liu Z · Qin J · Xiong G · Yang C · Cai F · Huang J last · Wu F first · Wang Y · Mai Z · Xu Z · Li S · Li Y · Yin R · Li J · Yu Z · Wu Y · Tian X · Feng X · Huo X · Wang C · Ma X last · Ivanov A first · Popov V · Morozov M · Olekhnovich E · Ulyantsev V last · Zhou K first · Kosmopoulos JC · Anantharaman K last

PRJEB15371.csv.gz (4.5 KB) · parquet (75.5 KB) — all 122 samples, every field with route and confidence · PRJEB15371_determinations.csv.gz (10.0 KB) — 750 evidence rows