Dysbiosis of the Intestinal Microbiota in IBS

Lyra, Anna; Lahtinen, Sampo J.

doi:10.5772/25759

Cited by 6 publications

(6 citation statements)

References 74 publications

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“…This order represents a lot of families whose abundance is directly correlated with a healthy gut (Ruminococcaceae, Eubacteriaceae, Lachnospiraceae [25]). Moreover, it is known that dysbiosis of the intestinal microbiota related to metabolic or infectious diseases like inflammatory bowel syndrome (IBS), inflammatory bowel disease (IBD) or enteric pathogens infections [26,27,28], that is commonly associated with inflammation of the lower gastro-intestinal tract, is typified by a reduction in bacterial diversity, a bloom of facultative anaerobic Gammaproteobacteria like Enterobacteriaceae and a decreased abundance of Clostridia [27,28]. Therefore, using QIIME 1 and kraken mini revealed in Blastocystis -colonized patients a significantly higher abundance of an order which could be essential in our gut health context.…”

Section: Resultsmentioning

confidence: 99%

The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?

et al. 2019

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Targeted metagenomics is the solution of choice to reveal differential microbial profiles (defined by richness, diversity and composition) as part of case-control studies. It is well documented that each data processing step may have the potential to introduce bias in the results. However, selecting a bioinformatics pipeline to analyze high-throughput sequencing data from A to Z remains one of the critical considerations in a case-control microbiota study design. Consequently, the aim of this study was to assess whether the same biological conclusions regarding human gut microbiota composition and diversity could be reached using different bioinformatics pipelines. In this work, we considered four pipelines (mothur, QIIME, kraken and CLARK) with different versions and databases, and examined their impact on the outcome of metagenetic analysis of Ion Torrent 16S sequencing data. We re-analyzed a case-control study evaluating the impact of the colonization of the intestinal protozoa Blastocystis sp. on the human gut microbial profile. Although most pipelines reported the same trends in this case-control study, we demonstrated how the use of different pipelines affects the biological conclusions that can be drawn. Targeted metagenomics must therefore rather be considered as a profiling tool to obtain a broad sense of the variations of the microbiota, rather than an accurate identification tool.

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Section: Resultsmentioning

confidence: 99%

The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?

et al. 2019

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“…Although efforts to define what “normal” gut microbiota means are still progressing, it is well known that the level of diversity and bacterial species composition of the microbiota of healthy individuals differ from those of patients suffering from many metabolic or infectious diseases. The dysbiosis of the intestinal microbiota related to metabolic or infectious diseases like IBS, IBD or enteric pathogens infections 21 22 23 , that is commonly associated with inflammation of the lower GI tract, is typified by a reduction in bacterial diversity, a decreased abundance of Clostridia and a bloom of facultative anaerobic Gammaproteobacteria like Enterobacteriaceae 36 37 .…”

Section: Discussionmentioning

confidence: 99%

“…As a complement to in vitro , in vivo and in silico studies, another way to address the issue of Blastocystis pathogenicity could be to investigate the effects of colonization by this protist on the composition of the gut microbiota. Indeed, it is now well established that alterations in the composition of commensal bacterial populations (a phenomenon known as ‘dysbiosis’) are linked to multiple intestinal diseases, such as IBD or IBS 21 22 , two potential Blastocystis -associated diseases. Furthermore, diverse enteric pathogens can induce significant perturbations in the microbiota or bloom during dysbiosis 23 .…”

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confidence: 99%

Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota

Audebert¹,

Even²,

Cian³

et al. 2016

Sci Rep

233

208

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Alterations in the composition of commensal bacterial populations, a phenomenon known as dysbiosis, are linked to multiple gastrointestinal disorders, such as inflammatory bowel disease and irritable bowel syndrome, or to infections by diverse enteric pathogens. Blastocystis is one of the most common single-celled eukaryotes detected in human faecal samples. However, the clinical significance of this widespread colonization remains unclear, and its pathogenic potential is controversial. To address the issue of Blastocystis pathogenicity, we investigated the impact of colonization by this protist on the composition of the human gut microbiota. For that purpose, we conducted a cross-sectional study including 48 Blastocystis-colonized patients and 48 Blastocystis-free subjects and performed an Ion Torrent 16S rDNA gene sequencing to decipher the Blastocystis-associated gut microbiota. Here, we report a higher bacterial diversity in faecal microbiota of Blastocystis colonized patients, a higher abundance of Clostridia as well as a lower abundance of Enterobacteriaceae. Our results contribute to suggesting that Blastocystis colonization is usually associated with a healthy gut microbiota, rather than with gut dysbiosis generally observed in metabolic or infectious inflammatory diseases of the lower gastrointestinal tract.

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“…In contrast, the diversity of bacterial community decreased in Blastocystis-colonized patients with hepatic encephalopathy [35]. However, a decreased bacterial diversity has been observed in metabolic or infectious diseases, such as IBD or infection with enteric pathogens, which are associated with inflammation of the lower gastrointestinal tract [21,22,42].…”

Section: Discussionmentioning

confidence: 99%

“…Yet, this protozoa-associated dysbiosis remains poorly understood. It was shown that bacterial dysbiosis occurred in subjects with chronic diseases, such as IBD, which are associated with Blastocystis [21,22]. A study showed a direct association between Blastocystis and gut dysbiosis in the absence of gastrointestinal diseases or inflammation [23].…”

Section: Introductionmentioning

confidence: 99%

Blastocystis Colonization Is Associated with Increased Diversity and Altered Gut Bacterial Communities in Healthy Malian Children

et al. 2019

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Blastocystis is the most common protozoan colonizing the gut of vertebrates. It modulates the human digestive microbiota in the absence of inflammation and gastrointestinal disease. Although it has been associated with human diseases, including inflammatory bowel disease, its pathogenicity remains controversial. This study aimed to assess the influence of Blastocystis on the gut bacterial communities in healthy children. We conducted a cross-sectional study on 147 Blastocystis-colonized and 149 Blastocystis-noncolonized Malian children, with Blastocystis colonization assessed by real-time PCR and gut microbial communities characterized via 16S rRNA gene (Illumina MiSeq) sequencing and bioinformatics analysis. The gut microbiota diversity was higher in Blastocystis-colonized compared to Blastocystis-noncolonized children. The phyla Firmicutes, Elusimicrobia, Lentisphaerae, and Euryarchaeota were higher in Blastocystis-colonized children, whereas Actinobacteria, Proteobacteria, unassigned bacteria, and Deinococcus–Thermus were higher in Blastocystis-noncolonized children. Moreover, Faecalibacterium prausnitzii (family Ruminococcaceae) and Roseburia sp. (family Lachnospiraceae) abundance was higher in Blastocystis-colonized children. We conclude that Blastocystis colonization is significantly associated with a higher diversity of the gut bacterial communities in healthy children, while it is not associated with the presence of potentially pathogenic bacteria in the human gut.

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Dysbiosis of the Intestinal Microbiota in IBS

Cited by 6 publications

References 74 publications

The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?

The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical “Microscope” Affect the Biological Interpretation?

Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota

Blastocystis Colonization Is Associated with Increased Diversity and Altered Gut Bacterial Communities in Healthy Malian Children

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