Gut microbiota community adaption during young children fecal microbiota transplantation by 16s rDNA sequencing

doi:10.1016/j.neucom.2016.01.095

Neurocomputing

Volume 206, 19 September 2016, Pages 66-72

https://doi.org/10.1016/j.neucom.2016.01.095 Get rights and content

Abstract

Fecal microbiota transplantation (FMT) is to restore the intestinal environment of a diseased individual by using of intestinal microbiota from a healthy donor. In recent years, FMT has been developed into a useful treatment method for various chronic gastrointestinal disease. There are already some works attempt to explain the mechanism of this treatment for gastrointestinal diseases in adult patients. However, much less effort has been focused on pediatric gastrointestinal disorders. In this work, we have invited 3 young children with chronic immune-mediated gastrointestinal disorders treated by FMT surgery, and systematically investigated their temporal changes of fecal microbiota after transplantation by 16s rDNA sequencing technology. According to our observations, the fecal microbiota composition of these patients appears obviously interindividual variability and the fecal transplantation significantly increased the species richness in these young patients. The species abundance of Pasteurellaceae was remarkably increased during the FMT treatment in all three patients.

Introduction

The human gut is colonized by a highly diverse community of microorganisms that play a critical symbiosis with their host, including energy metabolism, immunity and nervous system [1], [2]. Studies of the intestinal microbiota imply that an unbalanced microbial community is associated with the pathogenesis of gastrointestinal symptoms. Growing evidence supported that fecal microbiota transplantation could reestablish the balance of gut microbiota community and is an effective treatment against several gastrointestinal symptoms, best known as a treatment for recurrent Clostridium difficile infection (CDI) [3], current studies suggested it is also promising results with many other digestive or auto-immune disease, including inflammatory bowel disease (IBD), Irritable Bowel Syndrome (IBS), and Ulcerative Colitis (UC) [4]. It is reported that intestinal gut microbiota appears various bacterial richness and diversity among different diseases [5], [6]. The microbiota community studies in CDI indicated that compared with healthy controls, the patients had an initial CDI appears a progressive decrease in species diversity and reduction of Bacteroidetes and Firmicutes phylum in their fecal samples [3]. A larger cohort study of pediatric Crohn׳s Disease imply that a set of microorganism taxa associated with disease status, it is might be a bacterial biomarker for early diagnosis [7].

Fecal microbiota transplantation (FMT) is transplantation of a fecal suspension from a healthy donor into the gastrointestinal tract of patient, and to reestablish the balance of intestinal microbiota community of patient. Although FMT has been most accepted treatment for the intestinal microbiota dysbiosis, but the mechanism is still not entirely clear. More research is needed to investigate and understand the dynamic changes of intestinal microbiota community during the FMT treatment, and especially in children patients because children is more impressionable to environmental factors than adult. Gut microbiota studies are commonly performed by analyzing the 16s ribosomal DNA gene (16s rDNA), and it is also current golden standard for microbial community analysis [8], [9]. In present study, we applied 16s rDNA sequencing analysis to profile the fecal microbiota community from 3 young children with Juvenile idiopathic arthritis, Ulcerative colitis or Hemophagocytic syndrome. The aim of this study was to characterize the changes of microbiota community before and after the FMT for these young children.

Section snippets

Patient information and feces sample process

Three young children (1 female, 2 male; aged 19–40 months) with immune-imbalance related chronic diseases were planning to undergo FMT surgery at Department of Gastroenterology at Shanghai Children׳s Hospital, and invited to participate in this study. The Shanghai Children׳s Hospital review board approved this study and we obtained written informed consent for this study from their guardians. Before donating the feces, the two healthy adult donors were screened following test: HIV1/2

Results and discussion

Using Illumina Hiseq 2000 sequencing platform, a total of 1.4 Gb clean data was generated from 14 samples involving 3 young children patients with different sampling time-point for each patient covered pre-FMT to post-FMT treatment and 2 healthy adult donors, the detailed information of samples listed in Table 1. After removing low quality reads, 776 Mb clean sequencing data were produced. These sequencing reads were pre-assembled and then clustered into operational taxonomic units (OTUs) that

Conclusion

From this study, some results have shown that FMT surgeries can change the species richness of the gut microbial community, but the bacterial spectrum of fecal samples exhibit strong stability along with the FMT surgeries. 16s rDNA sequencing reports displayed that some species may change sharply after FMT surgeries. However, only with the 16s rDNA data, the results can’t tell what had happened after FMT surgeries. A number of important questions are also raised by these findings. For example,

Acknowledgments

This work is supported in part by the National Natural Science Foundation of China (Nos. 31071167 and 31370751), Shanghai Municipal Commission of Health and Family Planning (Grant nos. 201440434, 20144Y0179 and 20144Y0175), Shanghai Key Projects for Basic Scientific Research (14JC1405700), Research and Innovation Project of High Level Talents in Putuo District of Shanghai (2014-A-20) and Natural Science Foundation of Shanghai (14ZR1434200), China.

Jianlei Gu is an Assistant Research Fellow at Shanghai Children′s Hospital, Shanghai Jiao Tong University. He obtained his Master degree in Microbiology Science from Fudan University (2008.9–2011.7) and Bachelor degree in Biological Engineering from the China University of Mining and Technology (2004.09–2008.7).

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Yizhong Wang, Ph.D., is an Assistant Professor at Shanghai Children′s Hospital, Shanghai Jiao Tong University. He was a Postdoctoral fellow at Division of Gastroenterology, University of Utah School of Medicine (2009.09–2010.06) and at the Department of Pathology and Laboratory Medicine, Temple University School of Medicine (2010.07–2014.02).

Shiyi Liu is a graduate student at Shanghai Jiaotong University.

Guangjun Yu, Ph.D., is a Professor and the President of Shanghai Children׳s Hospital, Shanghai Jiaotong University.

Ting Zhang, M.D., is the Director of Gastroenterology Department, Shanghai Children׳s Hospital, Shanghai Jiaotong University.

Hui Lu Ph.D. Shanghai Jiao Tong University and Shanghai Children’s Hospital.

¹: These authors contributed equally to this work.

View full text

Gut microbiota community adaption during young children fecal microbiota transplantation by 16s rDNA sequencing

Abstract

Introduction

Section snippets

Patient information and feces sample process

Results and discussion

Conclusion

Acknowledgments

FEBS Lett.

Cell Host Microbe

J. Mol. Biol.

Anaerobe

Gut microbiota composition correlates with diet and health in the elderly

Nature

Durable alteration of the colonic microbiota by the administration of donor fecal flora

J. Clin. Gastroenterol.