Microbial associations with Microscopic Colitis

BACKGROUND AND OBJECTIVE: Microscopic colitis is a relatively common cause of chronic diarrhea and may be linked to luminal factors. Given the essential role of the microbiome in human gut health, analysis of microbiome changes associated with microscopic colitis could provide insights into the development of the disease. METHODS: We enrolled patients who underwent colonoscopy for diarrhea. An experienced pathologist classified patients as having microscopic colitis (n=52) or controls (n=153). Research biopsies were taken from the ascending and descending colon, and the microbiome was characterized with Illumina sequencing. We analyzed the associations between microscopic colitis and microbiome with a series of increasingly complex models adjusted for a range of demographic and health factors. RESULTS: We found that alpha-diversity was significantly lower in microscopic colitis cases compared to controls in the descending colon microbiome. In the descending colon, a series of models that adjusted for an increasing number of co-variates found taxa significantly associated with microscopic colitis, including Proteobacteria that was enriched in cases and Collinsella enriched in controls. While the alpha-diversity and taxa were not significantly associated with microscopic colitis in the ascending colon microbiome, the inference p-values based on ascending and descending microbiomes were highly correlated. CONCLUSION: Our study demonstrates an altered microbiome in microscopic colitis cases compared to controls. Because both the cases and controls had diarrhea, we have identified candidate taxa that could be mechanistically responsible for the development of microscopic colitis independent of changes to the microbial community caused by diarrhea.

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The Effects of Mediterranean Diet on the Human Gut Microbiota; a Brief Discussion of Evidence in Humans

10.21926/obm.hg.2101056 ◽

2021 ◽

Vol 5 (1) ◽

Author(s):

Anita H Kelleher ◽

Angelos K Sikalidis ◽

Keyword(s):

Gut Microbiota ◽

Mediterranean Diet ◽

Metabolic Diseases ◽

Short Chain Fatty Acids ◽

Gut Health ◽

Omega 3 ◽

Bioactive Components ◽

Human Gut ◽

The Mediterranean

The Mediterranean diet (MD) is considered one of the healthiest dietary patterns due to its rich provision of phytochemicals, antioxidants, vitamins, fiber, polyunsaturated, omega-3, and short-chain fatty acids through a variety of foods. The supply of such nutrients and bioactive components can support gut health and reduce systemic inflammation, with accumulating evidence from several human studies demonstrating the utility of the Mediterranean diet in the prevention of chronic and metabolic diseases. Further studies are needed to explore the role of the Mediterranean diet protecting against such diseases and the related mechanisms, including the interplay between components of the MD and gut microbiota. This brief systematic review specifically explores the recent evidence in humans investigating the link between MD and the human microbiota. Herein, over 50 articles were revised and referenced, after a careful vetting process, to produce this manuscript. Articles were ultimately selected based upon the detail and novelty of their content and contribution to the field.

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Bacteriocins and Bacteriophages: Therapeutic Weapons for Gastrointestinal Diseases?

International Journal of Molecular Sciences ◽

10.3390/ijms20010183 ◽

2019 ◽

Vol 20 (1) ◽

pp. 183 ◽

Cited By ~ 21

Author(s):

Loris Riccardo Lopetuso ◽

Maria Ernestina Giorgio ◽

Angela Saviano ◽

Franco Scaldaferri ◽

Antonio Gasbarrini ◽

...

Keyword(s):

Gastrointestinal Diseases ◽

Gram Negative Bacteria ◽

Bacterial Cells ◽

Gut Health ◽

Complex Environment ◽

Therapeutic Application ◽

Human Gut ◽

Viral Components ◽

Diverse Groups

Bacteriocins are bactericidal peptides, ribosomally synthesized, with an inhibitory activity against diverse groups of undesirable microorganisms. Bacteriocins are produced by both gram-positive and gram-negative bacteria, and to a lesser extent by some archaea. Bacteriophages are viruses that are able to infect bacterial cells and force them to produce viral components, using a lytic or lysogenic cycle. They constitute a large community in the human gut called the phageome, the most abundant part of the gut virome. Bacteriocins and bacteriophages may have an influence on both human health and diseases, thanks to their ability to modulate the gut microbiota and regulate the competitive relationship among the different microorganisms, strains and cells living in the human intestine. In this review, we explore the role of bacteriocins and bacteriophages in the most frequent gastrointestinal diseases by dissecting their interaction with the complex environment of the human gut, analyzing a possible link with extra-intestinal diseases, and speculating on their possible therapeutic application with the end goal of promoting gut health.

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The role of mucosal barriers in human gut health

Archives of Pharmacal Research ◽

10.1007/s12272-021-01327-5 ◽

2021 ◽

Vol 44 (4) ◽

pp. 325-341

Author(s):

Kangseok Seo ◽

Jeongmi Seo ◽

Jiyoun Yeun ◽

Haebin Choi ◽

Young-In Kim ◽

...

Keyword(s):

Gut Health ◽

Human Gut

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Gut microbiome transition across a lifestyle gradient in Himalaya

10.1101/253450 ◽

2018 ◽

Author(s):

Aashish R Jha ◽

Emily R Davenport ◽

Yoshina Gautam ◽

Dinesh Bhandari ◽

Sarmila Tandukar ◽

...

Keyword(s):

Environmental Factors ◽

Gut Microbiome ◽

Alpha Diversity ◽

Water Source ◽

Drinking Water Source ◽

Human Gut ◽

Bacterial Composition ◽

Microbiome Composition ◽

The World

The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle/modernization. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in human lifestyles. These groups led seminomadic hunting-gathering lifestyles until transitioning to varying dependence upon farming. The Tharu began farming 250-300 years ago, the Raute and Raji transitioned 30-40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut microbiota and find that the gut microbiome composition is significantly associated with lifestyle. The Chepang foragers harbor elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. For example, our results show that drinking water source and solid cooking fuel are significantly associated with the gut microbiome. Despite the pronounced differences in gut bacterial composition across populations, we found little differences in alpha diversity across populations. These findings in genetically similar populations living in the same geographical region establish the key role of lifestyle in determining human gut microbiome composition and point to the next challenging steps of isolating dietary effects from other factors that change during modernization.

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Gut health: predictive biomarkers for preventive medicine and development of functional foods

British Journal Of Nutrition ◽

10.1017/s0007114509993400 ◽

2010 ◽

Vol 103 (10) ◽

pp. 1539-1544 ◽

Cited By ~ 17

Author(s):

Raish Oozeer ◽

Maria Rescigno ◽

R. Paul Ross ◽

Jan Knol ◽

Michael Blaut ◽

...

Keyword(s):

Gut Microbiota ◽

Predictive Biomarkers ◽

Gut Health ◽

Human Gut ◽

Observation Study ◽

Industry Collaboration ◽

Health And Disease ◽

Micro Organisms ◽

First Time

There is an urgent need to develop and validate a series of biomarkers, which accurately measure and inform on how the human gut microbiota can affect human health. The human gut hosts a complex community of micro-organisms, with unique features in each individual. The functional role of this gut microbiota in health and disease is increasingly evident, but poorly understood. Comprehension of this ecosystem implies a significant challenge in the elucidation of interactions between all of its components, but promises a paradigm shift in preventive nutrition and medicine. ‘Omics’ technologies for the first time offer tools of sufficient subtlety to tackle this challenge. However, these techniques must be allied with traditional skills of the microbial physiologist, which are in danger of being lost. Targeting these efforts at the identification of biomarkers associated with gut health will require access to a ‘biobank’ from a pan-European or worldwide observation study, which would include samples taken with appropriate frequency from healthy individuals of different ages. This offers a pragmatic opportunity for a unique food and pharmaceutical industry collaboration.

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Faculty Opinions recommendation of Biopsies from ascending and descending colon are sufficient for diagnosis of microscopic colitis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.737454151.793577695 ◽

2020 ◽

Author(s):

Ian Beales

Keyword(s):

Microscopic Colitis ◽

Descending Colon

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Methyl mercury in the dutch rhine delta

Water Science & Technology ◽

10.2166/wst.1994.0530 ◽

1994 ◽

Vol 30 (10) ◽

pp. 213-219 ◽

Cited By ~ 2

Author(s):

Hendrik Pieters ◽

Victor Geuke

Keyword(s):

Suspended Matter ◽

Methyl Mercury ◽

Mercury Contamination ◽

Benthic Organisms ◽

Considerable Decrease ◽

Continuous Sedimentation ◽

Highly Correlated ◽

High Level ◽

Almost All

Samples of yellow eel from various locations in the Dutch Rhine area have been analyzed for trend monitoring of mercury since 1977. In the western Rhine delta mercury levels in eels have hardly changed since the seventies, whereas in the eastern part of the Dutch Rhine area a considerable decrease of mercury concentrations in eel has occurred. Because of continuous sedimentation of contaminated suspended matter transported from upstream regions, accumulation rates and concentrations of mercury in eel in the western Rhine delta remained at a relatively high level. Analyses of methyl mercury in biota have been performed to elucidate the role of methyl mercury in the mercury contamination of the Dutch Rhine ecosystem. Low percentages of methyl mercury were observed in zooplankton (3 to 35%). In benthic organisms (mussels) percentages of methyl mercury ranged from 30 to 57%, while in fish species and liver of aquatic top predator birds almost all the mercury was present in the form of methyl mercury (> 80%). During the period 1970-1990 mercury concentrations of suspended matter in the eastern Rhine delta have drastically decreased. These concentrations seemed to be highly correlated with mercury concentrations of eel (R = 0.84). The consequences of this relation are discussed.

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Gut Mycobiota and Fungal Metabolites in Human Homeostasis

Current Drug Targets ◽

10.2174/1389450119666180724125020 ◽

2018 ◽

Vol 20 (2) ◽

pp. 232-240 ◽

Cited By ~ 3

Author(s):

Izabella Mogilnicka ◽

Marcin Ufnal

Keyword(s):

Wide Spectrum ◽

Biological Effects ◽

Fungal Species ◽

Fungal Metabolites ◽

Human Gut ◽

Fecal Transplantation ◽

Bacterial Microbiota ◽

Bowel Diseases ◽

Inflammatory Bowel

Background:Accumulating evidence suggests that microbiota play an important role in host’s homeostasis. Thus far, researchers have mostly focused on the role of bacterial microbiota. However, human gut is a habitat for several fungal species, which produce numerous metabolites. Furthermore, various types of food and beverages are rich in a wide spectrum of fungi and their metabolites.Methods:We searched PUBMED and Google Scholar databases to identify clinical and pre-clinical studies on fungal metabolites, composition of human mycobiota and fungal dysbiosis.Results:Fungal metabolites may serve as signaling molecules and exert significant biological effects including trophic, anti-inflammatory or antibacterial actions. Finally, research suggests an association between shifts in gut fungi composition and human health. Changes in mycobiota composition have been found in obesity, hepatitis and inflammatory bowel diseases.Conclusion:The influence of mycobiota and dietary fungi on homeostasis in mammals suggests a pharmacotherapeutic potential of modulating the mycobiota which may include treatment with probiotics and fecal transplantation. Furthermore, antibacterial action of fungi-derived molecules may be considered as a substitution for currently used antibacterial agents and preservatives in food industry.

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PPM1G promotes the progression of hepatocellular carcinoma via phosphorylation regulation of alternative splicing protein SRSF3

Cell Death and Disease ◽

10.1038/s41419-021-04013-y ◽

2021 ◽

Vol 12 (8) ◽

Author(s):

Dawei Chen ◽

Zhenguo Zhao ◽

Lu Chen ◽

Qinghua Li ◽

Jixue Zou ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Alternative Splicing ◽

Protein Function ◽

Vital Role ◽

Normal Tissues ◽

Mechanistic Analysis ◽

Highly Correlated ◽

Splicing Patterns

AbstractEmerging evidence has demonstrated that alternative splicing has a vital role in regulating protein function, but how alternative splicing factors can be regulated remains unclear. We showed that the PPM1G, a protein phosphatase, regulated the phosphorylation of SRSF3 in hepatocellular carcinoma (HCC) and contributed to the proliferation, invasion, and metastasis of HCC. PPM1G was highly expressed in HCC tissues compared to adjacent normal tissues, and higher levels of PPM1G were observed in adverse staged HCCs. The higher levels of PPM1G were highly correlated with poor prognosis, which was further validated in the TCGA cohort. The knockdown of PPM1G inhibited the cell growth and invasion of HCC cell lines. Further studies showed that the knockdown of PPM1G inhibited tumor growth in vivo. The mechanistic analysis showed that the PPM1G interacted with proteins related to alternative splicing, including SRSF3. Overexpression of PPM1G promoted the dephosphorylation of SRSF3 and changed the alternative splicing patterns of genes related to the cell cycle, the transcriptional regulation in HCC cells. In addition, we also demonstrated that the promoter of PPM1G was activated by multiple transcription factors and co-activators, including MYC/MAX and EP300, MED1, and ELF1. Our study highlighted the essential role of PPM1G in HCC and shed new light on unveiling the regulation of alternative splicing in malignant transformation.

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