Peptostreptococcus anaerobius Induces Intracellular Cholesterol Biosynthesis in Colon Cells to Induce Proliferation and Causes Dysplasia in Mice DOI Creative Commons
Ho Tsoi, Eagle SH Chu, Xiang Zhang

et al.

Gastroenterology, Journal Year: 2017, Volume and Issue: 152(6), P. 1419 - 1433.e5

Published: Jan. 23, 2017

Stool samples from patients with colorectal cancer (CRC) have a higher abundance of Peptostreptococcus anaerobius than stool individuals without CRC, based on metagenome sequencing. We investigated whether P contributes to colon tumor formation in mice and its possible mechanisms carcinogenesis.We performed quantitative polymerase chain reaction analyses measure 112 255 biopsies CRC or advanced adenoma healthy (controls) undergoing colonoscopy examination at hospitals Hong Kong Beijing. C57BL/6 were given broad-spectrum antibiotics, followed by single dose azoxymethane, induce formation. Three days later, Esherichia coli MG1655 (control bacteria), via gavage, for 6 weeks. Some also the nicotinamide adenine dinucleotide phosphate oxidase inhibitor apocynin. Intestine tissues collected analyzed histologically. The epithelial cell line NCM460 lines HT-29 Caco-2 exposed control bacteria; cells immunoblot, proliferation, bacterial attachment compared gene expression profiling studies. Gene was knocked down these small interfering RNAs.P significantly enriched controls. Mice depleted bacteria azoxymethane had incidence intestinal dysplasia (63%) not (8.3%; < .01). mainly colonized rest intestine. Colon levels proliferation cells. found genes that regulate cholesterol biosynthesis, Toll-like receptor (TLR) signaling, AMP-activated protein kinase signaling be up-regulated anaerobius. Total increased activation sterol regulatory element-binding 2. interacted TLR2 TLR4 increase intracellular reactive oxidative species, which promoted synthesis proliferation. Depletion species knockdown TLR4, incubation an antioxidant, prevented inducing biosynthesis proliferation.Levels are human adenomas non-tumor tissues; this increases mouse model CRC. interacts promotes

Language: Английский

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 DOI Creative Commons
Francesco Beghini, Lauren J. McIver, Aitor Blanco‐Míguez

et al.

eLife, Journal Year: 2021, Volume and Issue: 10

Published: May 4, 2021

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances methods for biological profiling via shotgun metagenomics. Opportunities improvement continue accelerate, with greater access multi-omics, reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set integrated, improved taxonomic, strain-level, functional, phylogenetic metagenomes newly developed build on largest sequences now available. Compared current alternatives, MetaPhlAn 3 increases accuracy taxonomic profiling, HUMAnN improves that functional potential activity. These detected novel disease-microbiome links applications CRC (1262 metagenomes) IBD (1635 817 metatranscriptomes). Strain-level an additional 4077 StrainPhlAn PanPhlAn unraveled structure common gut microbe Ruminococcus bromii , previously described by only 15 isolate genomes. With open-source implementations cloud-deployable reproducible workflows, platform can help researchers deepen resolution, scale, multi-omic community studies.

Language: Английский

Citations

1374
Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer DOI
Shinichi Yachida, Sayaka Mizutani,

Hirotsugu Shiroma

et al.

Nature Medicine, Journal Year: 2019, Volume and Issue: 25(6), P. 968 - 976

Published: June 1, 2019

Language: Английский

Citations

1044
Gut microbiota in colorectal cancer: mechanisms of action and clinical applications DOI
Sunny H. Wong, Jun Yu

Nature Reviews Gastroenterology & Hepatology, Journal Year: 2019, Volume and Issue: 16(11), P. 690 - 704

Published: Sept. 25, 2019

Language: Английский

Citations

978
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer DOI
Jakob Wirbel, Paul Theodor Pyl, Ece Kartal

et al.

Nature Medicine, Journal Year: 2019, Volume and Issue: 25(4), P. 679 - 689

Published: April 1, 2019

Language: Английский

Citations

973
Regional variation limits applications of healthy gut microbiome reference ranges and disease models DOI
Yan He, Wei Wu, Huimin Zheng

et al.

Nature Medicine, Journal Year: 2018, Volume and Issue: 24(10), P. 1532 - 1535

Published: Aug. 17, 2018

Language: Английский

Citations

744
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation DOI
Andrew Maltez Thomas, Paolo Manghi, Francesco Asnicar

et al.

Nature Medicine, Journal Year: 2019, Volume and Issue: 25(4), P. 667 - 678

Published: April 1, 2019

Language: Английский

Citations

739
Tumour-associated and non-tumour-associated microbiota in colorectal cancer DOI Creative Commons
Burkhardt Flemer, Denise B. Lynch,

Jillian M R Brown

et al.

Gut, Journal Year: 2016, Volume and Issue: 66(4), P. 633 - 643

Published: March 18, 2016

Objective

A signature that unifies the colorectal cancer (CRC) microbiota across multiple studies has not been identified. In addition to methodological variance, heterogeneity may be caused by both microbial and host response differences, which was addressed in this study.

Design

We prospectively studied colonic expression of specific genes using faecal mucosal samples ('ON' 'OFF' tumour, proximal distal) from 59 patients undergoing surgery for CRC, 21 individuals with polyps 56 healthy controls. Microbiota composition determined 16S rRNA amplicon sequencing; involved CRC progression immune quantified real-time quantitative PCR.

Results

The differed controls, but alterations were restricted cancerous tissue. Differences between distal cancers detected only partially reflected CRC. Patients can stratified based on higher level structures mucosal-associated bacterial co-abundance groups (CAGs) resemble previously formulated concept enterotypes. Of these, Bacteroidetes Cluster 1 Firmicutes decreased abundance mucosa, whereas 2, Pathogen Prevotella showed increased mucosa. CRC-associated CAGs differentially correlated immunoinflammatory genes.

Conclusions

profiles differ those subjects are linked distinct gene-expression profiles. Compositional tissue cancers.

Language: Английский

Citations

679
Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries DOI Creative Commons
Tarini Shankar Ghosh, Simone Rampelli, Ian B. Jeffery

et al.

Gut, Journal Year: 2020, Volume and Issue: 69(7), P. 1218 - 1228

Published: Feb. 17, 2020

Objective Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We others have shown that frailty co-varies with alterations in the gut microbiota a manner accelerated consumption restricted diversity diet. The Mediterranean diet (MedDiet) associated health. In NU-AGE project, we investigated if 1-year MedDiet intervention could alter reduce Design profiled 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy Poland) before after administration 12-month long tailored elderly (NU-AGE diet). Results Adherence was specific microbiome alterations. Taxa enriched adherence were positively several markers lower improved cognitive function, negatively inflammatory including C-reactive protein interleukin-17. Analysis inferred microbial metabolite profiles indicated diet-modulated change an increase short/branch chained fatty acid production secondary bile acids, p-cresols, ethanol carbon dioxide. Microbiome ecosystem network analysis showed bacterial taxa responded occupy keystone interaction positions, whereas frailty-associated are peripheral networks. Conclusion Collectively, our findings support feasibility improving habitual modulate turn has potential promote healthier ageing.

Language: Английский

Citations

666
The Intestinal Microbiota in Colorectal Cancer DOI Creative Commons
Herbert Tilg, Timon E. Adolph, Romana R. Gerner

et al.

Cancer Cell, Journal Year: 2018, Volume and Issue: 33(6), P. 954 - 964

Published: April 12, 2018

Language: Английский

Citations

637
Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma DOI Creative Commons
Zhigang Ren, Ang Li, Jianwen Jiang

et al.

Gut, Journal Year: 2018, Volume and Issue: 68(6), P. 1014 - 1023

Published: July 25, 2018

Objective To characterise gut microbiome in patients with hepatocellular carcinoma (HCC) and evaluate the potential of as non-invasive biomarkers for HCC. Design We collected 486 faecal samples from East China, Central China Northwest prospectively finally 419 completed Miseq sequencing. characterised microbiome, identified microbial markers constructed HCC classifier 75 early HCC, 40 cirrhosis healthy controls. validated results 56 controls, 30 45 advanced further verified diagnosis 18 Xinjiang 80 Zhengzhou. Results Faecal diversity was increased to cirrhosis. Phylum Actinobacteria versus Correspondingly, 13 genera including Gemmiger Parabacteroides were enriched Butyrate-producing decreased, while producing-lipopolysaccharide The optimal through a fivefold cross-validation on random forest model achieved an area under curve 80.64% between 105 non-HCC samples. Notably, strong even Importantly, successfully cross-region validation China. Conclusions This study is first report successful establishment Gut microbiota-targeted represent tools

Language: Английский

Citations

592