Terminal Restriction Fragment Length Polymorphism Analysis of the Gut Microbiota Profiles of Pediatric Patients with Inflammatory Bowel Disease

Aomatsu, Tomoki; Imaeda, Hirotsugu; Fujimoto, Takehide; Takahashi, Kenichiro; Yoden, Atsushi; Tamai, Hiroshi; Fujiyama, Yoshihide; Andoh, Akira

doi:10.1159/000339777

Cited by 28 publications

(22 citation statements)

References 97 publications

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“…Except the AluI-digested T-RF 76-bp that was absent in controls, other OTUs decreased significantly in UC patients, and most of the corresponding bacteria were classified into Bacteroides, Clostridium, or Bifidobacterium ( Table 4). The Clostridium [45] and Bacteroides [46] cluster decreased significantly in fecal samples from UC patients, whereas T-RFs were determined after digestion with BslI. Similar results were also confirmed by quantitative real-time PCR [38].…”

Section: Discussionsupporting

confidence: 61%

Diversity of Microflora in Colonic Mucus from Severe Ulcerative Colitis Patients Analyzed by Terminal Restriction Fragment Length Polymorphism and Clone Libraries of Bacterial 16S rRNA Gene Sequences

Huang¹,

Sato²,

Sakamoto³

et al. 2014

AiM

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Although the gut microflora is thought to be an essential factor in the development of ulcerative colitis (UC), the entire gut microflora occurring in UC remains unknown. Most studies use feces to represent the microflora distribution; however, here we analyzed the bacterial diversity in colonic mucus from UC patients receiving colectomy surgery and control patients. The diversity of microflora was investigated using a combination of terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of the 16S rRNA gene sequences. In the T-RFLP analysis, the number of terminal restriction fragments (T-RFs) decreased significantly in UC patients when compared to control samples. Also in the clone library analysis, the number of operational taxonomic units (OTU) and the Shannon diversity index were reduced significantly in UC patients. These molecular analyses reveal an overall dysbiosis in UC patients. No specific pathogen was found, and a strong negative correlation in relative abundance of bacterial populations was * Corresponding author. IN. Huang et al. 858 observed between the phyla Bacteroidetes and Firmicutes in the UC patients. This is the first report showing a significant correlation between these two phyla, which may be important characteristics in the pathogenesis of UC.

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Section: Discussionsupporting

confidence: 61%

Diversity of Microflora in Colonic Mucus from Severe Ulcerative Colitis Patients Analyzed by Terminal Restriction Fragment Length Polymorphism and Clone Libraries of Bacterial 16S rRNA Gene Sequences

Huang¹,

Sato²,

Sakamoto³

et al. 2014

AiM

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“…Change in gut microbiota Asthma " Clostridium difficile 72 " Bacteroides fragilis subgroup and Clostridium coccoides subcluster XIVa 76 Eczema ↓ Bacterial diversity [91][92][93] " B. pseudocatenulatum, Escherichia coli, and C. difficile 72,90 Food allergy (cow milk allergy) " Total and anaerobic bacteria and ↓ yeast count 100 " C. coccoides group and Atopobium cluster 101 " Bacterial metabolic products, e.g., butyric acid and BCFA 101 NEC " γ-Proteobacteria and ↓ Firmicutes 32 " Citrobacter-like sequences and Enterococcus-like sequences 110 Enterobacter associated with NEC 112 No significant differences between NEC and control 111 IBD " Aerobic and facultative anaerobic bacteria 118 " γ-Proteobacteria, 117 e.g., adhesive-invasive E. coli 119 ↓ Clostridia, e.g., Faecalibacterium, Bacteroides, e.g., B. vulgatus and bifidobacteria 115,116,118 IBS " γ-Proteobacteria, Haemophilus, and infants. 35 Although differences in early microbiota between CsD and VD infants are well documented, the long-term impact of early colonization on subsequent childhood immune development and disease outcomes are not fully understood and shown to be investigated in a long-term prospective cohort study.…”

Section: Immune-mediated Disordersmentioning

confidence: 99%

Early Development of the Gut Microbiome and Immune-Mediated Childhood Disorders

2014

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The human gastrointestinal tract inhabits a complex microbial ecosystem that plays a vital role in host health through its contributions to nutrient synthesis and digestion, protection from pathogens, and promoting maturation of host innate and adapt immune systems. The development of gut microbiota primarily occurs during infancy and is influenced by multiple factors, including prenatal exposure; gestational age; mode of delivery; feeding type; pre-, pro-, and antibiotic use; and host genetics. In genetically susceptible individuals, changes in the gut microbiota induced by environmental factors may contribute to the development of immune-related disorders in childhood, including atopic diseases, inflammatory bowel disease, irritable bowel syndrome, and necrotizing enterocolitis. Pre- and probiotics may be useful in the prevention and treatment of some immune-related diseases by modulating gut microbiota and regulating host mucosal immune function. The review will discuss recent findings on the environmental factors that influence development of gut microbiota during infancy and its potential impact on some immune-related diseases in childhood. The use of pre- and probiotics for prevention and intervention of several important diseases in early life will also be reviewed.

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“…4 The microbiota acquired in early life have longterm implications for host metabolism and gastrointestinal (GI), immune and neurological function. 5,6 Reduced diversity or dysbiosis are linked to childhood and later life disorders, including necrotizing enterocolitis, 7 eczema, 8 asthma, 9 inflammatory bowel diseases, 10 irritable bowel syndrome, 11 obesity, 12 diabetes 13 and autism. 14 Diet is one of the major determinants of GI microbial diversity.…”

Section: Introductionmentioning

confidence: 99%

The role of early life nutrition in the establishment of gastrointestinal microbial composition and function

2017

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The development of the human infant intestinal microbiota is a sequential process that begins in utero and continues during the first 2 to 3 years of life. Microbial composition and diversity are shaped by host genetics and multiple environmental factors, of which diet is a principal contributor. An understanding of this process is of clinical importance as the microbiota acquired in early life influence gastrointestinal, immune and neural development, and reduced microbial diversity or dysbiosis during infancy is associated with disorders in infancy and later childhood. The goal of this article was to review the published literature that used culture-independent methods to describe the development of the gastrointestinal microbiota in breast-and formula-fed human infants as well as the impact of prebiotic and probiotic addition to infant formula, and the addition of solid foods.

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Terminal Restriction Fragment Length Polymorphism Analysis of the Gut Microbiota Profiles of Pediatric Patients with Inflammatory Bowel Disease

Cited by 28 publications

References 97 publications

Diversity of Microflora in Colonic Mucus from Severe Ulcerative Colitis Patients Analyzed by Terminal Restriction Fragment Length Polymorphism and Clone Libraries of Bacterial 16S rRNA Gene Sequences

Diversity of Microflora in Colonic Mucus from Severe Ulcerative Colitis Patients Analyzed by Terminal Restriction Fragment Length Polymorphism and Clone Libraries of Bacterial 16S rRNA Gene Sequences

Early Development of the Gut Microbiome and Immune-Mediated Childhood Disorders

The role of early life nutrition in the establishment of gastrointestinal microbial composition and function

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