Impact of Ethnicity, Geography, and Disease on the Microbiota in Health and Inflammatory Bowel Disease

Prideaux, Lani; Kang, Seungha; Wagner, Josef; Buckley, Michael; Mahar, Jackie E.; Cruz, Peter De; Wen, Zhiyuan; Chen, Liping; Xia, Bing; Langenberg, Daniel R. van; Lockett, Trevor; Ng, Siew C.; Sung, Joseph J.Y.; Desmond, Paul; McSweeney, Christopher S.; Morrison, Mark; Kirkwood, Carl D.; Kamm, Michael A.

doi:10.1097/01.mib.0000435759.05577.12

Cited by 80 publications

(56 citation statements)

References 52 publications

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“…The importance of these childhood immunological, hygiene, and dietary factors, and their downstream effect on the intestinal microbial milieu cannot be overstated [11]. Indeed, a dysbiosis in IBD patients in Asia with a decrease in butyrate-producing bacterial species was observed [22], a finding similar to recent studies in Caucasian patients with UC [23]. …”

Section: Risk Factorsmentioning

confidence: 72%

The Same Intestinal Inflammatory Disease despite Different Genetic Risk Factors in the East and West?

Lui

2016

Inflamm Intest Dis

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Background: Inflammatory bowel disease (IBD) is a chronic inflammatory disease with unknown etiology. It is likely caused by a complex interplay between genetic, immunologic and environmental factors. Although IBD is still relatively uncommon in Asia, a multitude of studies have shown that it is an emerging disease around the world. Recent insights have highlighted both the similarities and differences amongst Asian and Western IBD patients. Summary: The annual incidence of IBD in the East is still low compared with the West, but there are differences between different regions of Asia. Time trend studies have shown that the incidence of IBD is on the rise. Some notable differences in the clinical manifestations of IBD between the East and West have also been noted. ‘Westernization' of lifestyle may encompass various social and environmental changes that account for the emergence of IBD in our population, although genetics also plays a role in disease pathogenesis. Diagnosis and treatment challenges include limited access to medical care in certain areas, limited availability and high cost of medications, lack of insurance reimbursement, paucity of multidisciplinary teams for the management of complicated IBD cases, and a high prevalence of endemic infections. Currently, the risk of colorectal cancer is lower in the East than in the West, but cancer rates will likely approach that of the West in the future as the prevalence of IBD continues to rise. Key Messages: Measures to improve access to diagnostic tools, increase the availability of medication, and provide adequate multidisciplinary care for IBD patients will become increasingly important in Asia. Differences between the East and West will provide a unique opportunity for global collaboration in basic and clinical research to further our understanding of the disease entity and also provide more locoregional data to healthcare providers and policymakers to make informed decisions and policy changes when tackling the rising burden of IBD in Asia.

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Section: Risk Factorsmentioning

confidence: 72%

The Same Intestinal Inflammatory Disease despite Different Genetic Risk Factors in the East and West?

Lui

2016

Inflamm Intest Dis

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“…The index reflects its richness, that is the number of different species in an environment, and its evenness, that is the relative abundance of each species in that environment (5). A low diversity as measured by the Shannon diversity index has been associated with disease states like inflammatory bowel disease (6). The mean(±SD) Shannon diversity index in the pre-transplantation samples was 3.7±0.3 and 3.1±0.8 in the post-transplantation samples (P=0.22, Wilcoxon signed-rank test).…”

Section: Resultsmentioning

confidence: 99%

Gut Microbial Community Structure and Complications After Kidney Transplantation

et al. 2014

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Background The gut microbiome plays a role in the regulation of the immune system. Methods We prospectively enrolled 26 kidney transplant recipients and collected serial fecal specimens (N=85) during the first three months of transplantation. We characterized bacterial composition by PCR amplification of the 16S rRNA V4-V5 variable region and deep sequencing using the Illumina® MiSeq platform. Results An increase in the relative abundance of Proteobacteria was observed in the post-transplantation specimens compared to pre-transplantation specimens (P=0.04, Wilcoxon signed-rank test). In patients with post-transplant diarrhea, the mean(±SD) Shannon diversity index was lower in those with diarrhea (N=6) than those without diarrhea (N=9) (2.5±0.3 vs. 3.4±0.8, P=0.02, Wilcoxon rank-sum test). Principal coordinate analysis (PCoA) showed clear separation between the two groups, and linear discriminant analysis effect size (LEfSe) method revealed that Bacteroides, Ruminococcus, Coprococcus, and Dorea were significantly lower in the patients with diarrhea. PCoA analysis also showed clear separation between the acute rejection (AR) group (N=3) and the no AR group (N=23) and LEfSe method revealed several significant differences between the two groups. Fecal abundance of Enterococcus was associated with Enterococcus urinary tract infection (UTI). The median Enterococcus fecal abundance was 24% (Range: 8% to 95%) in the 3 patients with Enterococcus UTI compared to 0% in the 23 patients without Enterococcus UTI (Interquartile range: 0.00% to 0.08%)(P=0.005, Wilcoxon rank-sum test). Conclusions Our pilot study identified significant alterations in the gut microbiota following kidney transplantation. Moreover, distinct microbiota structures were observed in allograft recipients with post-transplant diarrhea, AR, and Enterococcus UTI.

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“…These techniques have been applied in ecology to analyze species distribution across many sites and samples, and to visualize sample similarity based on the presence and absence of different species (Prideaux et al , 2013). Other examples of CA use can be found in (Jones et al , 2007), (Perez-Cobas et al , 2014), and (Thureborn et al , 2013).…”

Section: Exploratory Methodsmentioning

confidence: 99%

Application of multivariate statistical techniques in microbial ecology

2016

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Recent advances in high-throughput methods of molecular analyses have led to an explosion of studies generating large scale ecological datasets. Especially noticeable effect has been attained in the field of microbial ecology, where new experimental approaches provided in-depth assessments of the composition, functions, and dynamic changes of complex microbial communities. Because even a single high-throughput experiment produces large amounts of data, powerful statistical techniques of multivariate analysis are well suited to analyze and interpret these datasets. Many different multivariate techniques are available, and often it is not clear which method should be applied to a particular dataset. In this review we describe and compare the most widely used multivariate statistical techniques including exploratory, interpretive, and discriminatory procedures. We consider several important limitations and assumptions of these methods, and we present examples of how these approaches have been utilized in recent studies to provide insight into the ecology of the microbial world. Finally, we offer suggestions for the selection of appropriate methods based on the research question and dataset structure.

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Impact of Ethnicity, Geography, and Disease on the Microbiota in Health and Inflammatory Bowel Disease

Cited by 80 publications

References 52 publications

The Same Intestinal Inflammatory Disease despite Different Genetic Risk Factors in the East and West?

The Same Intestinal Inflammatory Disease despite Different Genetic Risk Factors in the East and West?

Gut Microbial Community Structure and Complications After Kidney Transplantation

Application of multivariate statistical techniques in microbial ecology

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