Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

Wirbel, Jakob; Pyl, Paul Theodor; Kartal, Ece; Zych, Konrad; Kashani, Alireza; Milanese, Alessio; Fleck, Jonas Simon; Voigt, Anita Y.; Pallejà, Albert; Ponnudurai, Ruby; Sunagawa, Shinichi; Coelho, Luís Pedro; Schrotz‐King, Petra; Vogtmann, Emily; Habermann, Nina; Niméus, Emma; Thomas, Andrew Maltez; Manghi, Paolo; Gandini, Sara; Serrano, Davide; Mizutani, Sayaka; Shiroma, Hirotsugu; Shiba, Satoshi; Shibata, Tatsuhiro; Yachida, Shinichi; Yamada, Takuji; Waldron, Levi; Naccarati, Alessio; Segata, Nicola; Sinha, Rashmi; Ulrich, Cornelia M.; Brenner, Hermann; Arumugam, Manimozhiyan; Bork, Peer; Zeller, Georg

doi:10.1038/s41591-019-0406-6

Cited by 781 publications

(847 citation statements)

References 78 publications

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“…However, there is a small portion of microbes changed their abundance in tumor as well as different tumor stages, which probably caused by the inter-species competition in the tumor microenvironment ( Figure 4-5; Supplementary Figure S5). The findings of cancer-associated microbiome through mining small RAN sequencing data are similar to prior reports (Figure 4) (7,8,(12)(13)(14)31,(33)(34)(35)(36)(37). Interestingly the genera in Cluster_Fuso exhibited different pattern from previous studies (8,13,33,41,42).…”

Section: Discussionsupporting

confidence: 86%

“…The 25 genera previously reported as cancer-associated bacteria were used to examine the consistency of our results with other studies (Figure 4) (7,8,(12)(13)(14)31,(33)(34)(35)(36)(37). Several genera, such as Porphyromonas, Roseburia, Ruminococcus, Subdoligranulum, Bacterodies, and Prevotella, were reportedly increased as well as decreased in CRC;…”

Section: Detection Of Cancer-associated Bacteriasupporting

confidence: 75%

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Characterizing the Cancer-Associated Microbiome with Small RNA Sequencing Data

Lee

Chen

Wang

et al. 2019

Preprint

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The microbiome is recognized as a quasi-organ in the human body. In particular, the gut microbiome is correlated with immune function, metabolism, and tumorigenesis. When dysbiosis of the microbiome occurs, this variation may contribute to alterations in the microenvironment, potentially inducing an inflammatory immune response and providing a niche for neoplastic growth. However, there is limited evidence regarding the correlation and interaction between the microbiome and tumorigenesis. By utilizing microRNA sequencing data of patients with colon and rectal cancer from The Cancer Genome Atlas, we designed a novel analytical process to extract non-human small RNA sequences and align them with the microbial genome to obtain a comprehensive view of the cancer-associated microbiome. In the present study, we identified > 1000 genera among 630 colorectal samples and clustered these samples into three distinctive colorectal enterotypes. Each cluster has its own distinctive microbial composition and interactions. Furthermore, we found 12 genera from these clusters that are associated with cancer stages and revealed their putative functions. Our results indicate that the proposed analytical approach can effectively determine the cancer-associated microbiome. It may be readily applied to explore other types of cancer, in which specimens of the microbiome are difficult to collect.

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Section: Discussionsupporting

confidence: 86%

Section: Detection Of Cancer-associated Bacteriasupporting

confidence: 75%

Characterizing the Cancer-Associated Microbiome with Small RNA Sequencing Data

Lee

Chen

Wang

et al. 2019

Preprint

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“…A cross-cohort study by another group also revealed an enrichment of amino acid degradation pathways in CRC metagenomes. 23 Collectively, these findings suggest that changes in intestinal bacteria and fecal metabolites may occur from the very early stages of CRC development, and may be useful in elucidating and diagnosing carcinogenic mechanisms.…”

Section: Is Tin C T S Tag E-s Pecific Phenot Ype S Of the G Ut Mimentioning

confidence: 93%

“…16S ribosomal RNA gene and whole shotgun metagenome sequencing technologies have facilitated the quantitative profiling of the intestinal microbiota in human fecal and tissue samples. Large cohort studies have identified several species associated with adenoma and CRC, [19][20][21][22][23][24] including gram-positive anaerobic cocci, such as Peptostreptococcus anaerobius, Peptostreptococcus stomatis and Parvimonas micra ( Table 1).…”

Section: Identific Ation Of Colorec Tal C An Cer-a Sso Ciated Mi Crmentioning

confidence: 99%

Significance of the gut microbiome in multistep colorectal carcinogenesis

2020

Self Cite

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Colorectal cancer (CRC) is highly prevalent worldwide. In 2018, there were over 1.8 million new cases. Most sporadic CRC develop from polypoid adenomas and are preceded by intramucosal carcinoma (stage 0), which can progress into more malignant forms. This developmental process is known as the adenoma‐carcinoma sequence. Early detection and endoscopic removal are crucial for CRC management. Accumulating evidence suggests that the gut microbiota is associated with CRC development in humans. Comprehensive characterization of this microbiota is of great importance to assess its potential as a diagnostic marker in the very early stages of CRC. In this review, we summarized recent studies on CRC‐associated bacteria and their carcinogenic mechanisms in animal models, human cell lines and human cohorts. High‐throughput technologies have facilitated the identification of CRC‐associated bacteria in human samples. We have presented our metagenome and metabolome studies on fecal samples collected from a large Japanese cohort that revealed stage‐specific phenotypes of the microbiota in CRC. Furthermore, we have discussed the potential carcinogenic mechanisms of the gut microbiota, from which we can infer whether changes in the gut microbiota are a cause or effect in the multi‐step process of CRC carcinogenesis.

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“…The gut is colonized with 10 13 of microbes belonging to thousands of species. Alterations of microbiome composition are linked to lifestyle changes, short-and long-term diet [1], probiotics intake [1,2], medications including antibiotics [3] and diseases including obesity, type 2 diabetes [4], colorectal cancer [5], Crohn's disease [6] and others. Based on the discovered associations, a number of microbial taxa have been proposed as potential biomarkers.…”

Section: Introductionmentioning

confidence: 99%

Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa

Kurina

Popenko

Klimenko

et al. 2020

Molecular and Cellular Probes

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A B S T R A C TNowadays the advent of innovative high-throughput sequencing allows obtaining high-quality microbiome profiling. However, PCR-based tests are still considered the "golden standard" for many clinical applications. Here, we designed a qPCR-based platform with fluorescent-labeled oligonucleotide probes for assessing human gut microbiome composition. The system allows conducting qualitative and semiquantitative analysis for 12 prokaryotic taxa that are prevalent in the human gut and associated with diseases, diet, age and other factors. The platform was validated by comparing microbiome profile data obtained with two different methods -the platform and high-throughput 16S rRNA sequencing -across 42 stool samples. The test can form the basis for precise and cost-efficient microbiome assay for large-scale surveys including clinical trials with interventions related to diet and disease risks.

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Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

Cited by 781 publications

References 78 publications

Characterizing the Cancer-Associated Microbiome with Small RNA Sequencing Data

Characterizing the Cancer-Associated Microbiome with Small RNA Sequencing Data

Significance of the gut microbiome in multistep colorectal carcinogenesis

Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa

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