Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research

Zhang, Shaocun; Cao, Xiaocang; Huang, He

doi:10.3389/fcimb.2017.00051

Cited by 16 publications

(15 citation statements)

References 206 publications

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“…Analyzing a single body niche to categorize CRC individuals does not enable researchers to comprehensively study the spatial variations of the microbiota in CRC. Therefore, the proposed strategy of characterizing the spatial community structures of CRC microbiota (according to Zhang et al, 2017 ) is crucial to improve our understanding of the mutual interplay between microflora and CRC presence.…”

Section: Discussionmentioning

confidence: 99%

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study

et al. 2018

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In this study Next-Generation Sequencing (NGS) was used to analyze and compare human microbiota from three different compartments, i.e., saliva, feces, and cancer tissue (CT), of a selected cohort of 10 Italian patients with colorectal cancer (CRC) vs. 10 healthy controls (saliva and feces). Furthermore, the Fusobacterium nucleatum abundance in the same body site was investigated through real-time quantitative polymerase chain reaction (qPCR) to assess the association with CRC. Differences in bacterial composition, F. nucleatum abundance in healthy controls vs. CRC patients, and the association of F. nucleatum with clinical parameters were observed. Taxonomic analysis based on 16S rRNA gene, revealed the presence of three main bacterial phyla, which includes about 80% of reads: Firmicutes (39.18%), Bacteroidetes (30.36%), and Proteobacteria (10.65%). The results highlighted the presence of different bacterial compositions; in particular, the fecal samples of CRC patients seemed to be enriched with Bacteroidetes, whereas in the fecal samples of healthy controls Firmicutes were one of the major phyla detected though these differences were not statistically significant. The CT samples showed the highest alpha diversity values. These results emphasize a different taxonomic composition of feces from CRC compared to healthy controls. Despite the low number of samples included in the study, these results suggest the importance of microbiota in the CRC progression and could pave the way to the development of therapeutic interventions and novel microbial-related diagnostic tools in CRC patients.

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Section: Discussionmentioning

confidence: 99%

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study

et al. 2018

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“…Mucosal biopsy is a more accurate, deeper and more complex method for sampling the gut microbiota. The composition of intestinal flora in feces and intestinal mucosal tissues is significantly different . Therefore, multiple intestinal mucosal sites are biopsied in each individual to compare the spatial differences in an individual.…”

Section: Ecological Imbalance Of Intestinal Flora In Ucmentioning

confidence: 99%

Gut microbiota in ulcerative colitis: insights on pathogenesis and treatment

Guo

Liu

Hao

2020

J of Digest Diseases

173

110

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Gut microbiota constitute the largest reservoir of the human microbiome and are an abundant and stable ecosystem—based on its diversity, complexity, redundancy, and host interactions This ecosystem is indispensable for human development and health. The integrity of the intestinal mucosal barrier depends on its interactions with gut microbiota. The commensal bacterial community is implicated in the pathogenesis of inflammatory bowel disease (IBD), including ulcerative colitis (UC). The dysbiosis of microbes is characterized by reduced biodiversity, abnormal composition of gut microbiota, altered spatial distribution, as well as interactions among microbiota, between different strains of microbiota, and with the host. The defects in microecology, with the related metabolic pathways and molecular mechanisms, play a critical role in the innate immunity of the intestinal mucosa in UC. Fecal microbiota transplantation (FMT) has been used to treat many diseases related to gut microbiota, with the most promising outcome reported in antibiotic‐associated diarrhea, followed by IBD. This review evaluated the results of various reports of FMT in UC. The efficacy of FMT remains highly controversial, and needs to be regularized by integrated management, standardization of procedures, and individualization of treatment.

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“…Furthermore, the microbiome tends to be sequenced from fecal samples and while this is non-invasive for the IBD patient, this method could provide inaccurate measures, especially for CD patients where inflammation is often localized to the ileum or other portions of the gastrointestinal tract. This sampling method can also overlook mucosa-associated microbiota, and due to the variations in microbial composition that are apparent across the gastrointestinal tract, sampling methods need to be carefully considered when formulating studies (46). Nonetheless, the research that has been conducted to date has provided a solid foundation upon which future studies can expand to improve our understanding of dysbiosis in IBD.…”

Section: Dysbiosis Of Intestinal Microbiota In Ibdmentioning

confidence: 99%

Links Between Inflammatory Bowel Disease and Chronic Obstructive Pulmonary Disease

et al. 2020

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Inflammatory bowel disease (IBD) and chronic obstructive pulmonary disease (COPD) are chronic inflammatory diseases of the gastrointestinal and respiratory tracts, respectively. These mucosal tissues bear commonalities in embryology, structure and physiology. Inherent similarities in immune responses at the two sites, as well as overlapping environmental risk factors, help to explain the increase in prevalence of IBD amongst COPD patients. Over the past decade, a tremendous amount of research has been conducted to define the microbiological makeup of the intestine, known as the intestinal microbiota, and determine its contribution to health and disease. Intestinal microbial dysbiosis is now known to be associated with IBD where it impacts upon intestinal epithelial barrier integrity and leads to augmented immune responses and the perpetuation of chronic inflammation. While much less is known about the lung microbiota, like the intestine, it has its own distinct, diverse microflora, with dysbiosis being reported in respiratory disease settings such as COPD. Recent research has begun to delineate the interaction or crosstalk between the lung and the intestine and how this may influence, or be influenced by, the microbiota. It is now known that microbial products and metabolites can be transferred from the intestine to the lung via the bloodstream, providing a mechanism for communication. While recent studies indicate that intestinal microbiota can influence respiratory health, intestinal dysbiosis in COPD has not yet been described although it is anticipated since factors that lead to dysbiosis are similarly associated with COPD. This review will focus on the gut-lung axis in the context of IBD and COPD, highlighting the role of environmental and genetic factors and the impact of microbial dysbiosis on chronic inflammation in the intestinal tract and lung.

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Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research

Cited by 16 publications

References 206 publications

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study

Gut microbiota in ulcerative colitis: insights on pathogenesis and treatment

Links Between Inflammatory Bowel Disease and Chronic Obstructive Pulmonary Disease

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