scholarly journals Bacterial community structure alterations within the colorectal cancer gut microbiome

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mark Loftus ◽  
Sayf Al-Deen Hassouneh ◽  
Shibu Yooseph
Keyword(s):  
Colorectal Cancer ◽  
Community Structure ◽  
Bacterial Community ◽  
Gut Microbiome ◽  
Late Stage ◽  
Bacterial Community Structure ◽  
Whole Genome ◽  
Human Gut ◽  
Fecal Samples ◽  
Human Gut Microbiome

Abstract Background Colorectal cancer is a leading cause of cancer-related deaths worldwide. The human gut microbiome has become an active area of research for understanding the initiation, progression, and treatment of colorectal cancer. Despite multiple studies having found significant alterations in the carriage of specific bacteria within the gut microbiome of colorectal cancer patients, no single bacterium has been unequivocally connected to all cases. Whether alterations in species carriages are the cause or outcome of cancer formation is still unclear, but what is clear is that focus should be placed on understanding changes to the bacterial community structure within the cancer-associated gut microbiome. Results By applying a novel set of analyses on 252 previously published whole-genome shotgun sequenced fecal samples from healthy and late-stage colorectal cancer subjects, we identify taxonomic, functional, and structural changes within the cancer-associated human gut microbiome. Bacterial association networks constructed from these data exhibited widespread differences in the underlying bacterial community structure between healthy and colorectal cancer associated gut microbiomes. Within the cancer-associated ecosystem, bacterial species were found to form associations with other species that are taxonomically and functionally dissimilar to themselves, as well as form modules functionally geared towards potential changes in the tumor-associated ecosystem. Bacterial community profiling of these samples revealed a significant increase in species diversity within the cancer-associated gut microbiome, and an elevated relative abundance of species classified as originating from the oral microbiome including, but not limited to, Fusobacterium nucleatum, Peptostreptococcus stomatis, Gemella morbillorum, and Parvimonas micra. Differential abundance analyses of community functional capabilities revealed an elevation in functions linked to virulence factors and peptide degradation, and a reduction in functions involved in amino-acid biosynthesis within the colorectal cancer gut microbiome. Conclusions We utilize whole-genome shotgun sequenced fecal samples provided from a large cohort of late-stage colorectal cancer and healthy subjects to identify a number of potentially important taxonomic, functional, and structural alterations occurring within the colorectal cancer associated gut microbiome. Our analyses indicate that the cancer-associated ecosystem influences bacterial partner selection in the native microbiota, and we highlight specific oral bacteria and their associations as potentially relevant towards aiding tumor progression.

scholarly journals Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0155362 ◽  
Author(s):  
Emily Vogtmann ◽  
Xing Hua ◽  
Georg Zeller ◽  
Shinichi Sunagawa ◽  
Anita Y. Voigt ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gut Microbiome ◽  
Shotgun Sequencing ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Whole Genome Shotgun Sequencing

Tu1716 Evaluation of the Impact of Different Commercially Available DNA Extraction Kits and Laboratories for Assessing Bacterial Community Structure in Fecal Samples - Implications for IBD Research

2013 ◽  
Vol 144 (5) ◽  
pp. S-829
Author(s):  
Nicholas A. Kennedy ◽  
Alan Walker ◽  
UK IBD Microbiota Consortia ◽  
UK IBD Genetics Consortia ◽  
Susan H. Berry ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Dna Extraction ◽  
Bacterial Community Structure ◽  
Fecal Samples ◽  
The Impact

scholarly journals Metaproteomics characterizes human gut microbiome function in colorectal cancer

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Shuping Long ◽  
Yi Yang ◽  
Chengpin Shen ◽  
Yiwen Wang ◽  
Anmei Deng ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome

scholarly journals Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota

mSystems ◽  
2017 ◽  
Vol 2 (5) ◽  
Author(s):  
Eric J. de Muinck ◽  
Knut E. A. Lundin ◽  
Pål Trosvik
Keyword(s):  
Spatial Distribution ◽  
Spatial Structure ◽  
Gut Microbiome ◽  
Spatial Organization ◽  
Biotic Interactions ◽  
Community Level ◽  
Human Gut ◽  
Microbial Composition ◽  
Fecal Samples ◽  
Human Gut Microbiome

ABSTRACT The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention. The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention. Author Video: An author video summary of this article is available.

scholarly journals Human Gut Microbiome and Risk for Colorectal Cancer

2013 ◽  
Vol 105 (24) ◽  
pp. 1907-1911 ◽  
Author(s):  
Jiyoung Ahn ◽  
Rashmi Sinha ◽  
Zhiheng Pei ◽  
Christine Dominianni ◽  
Jing Wu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome

Abstract 2290: Human gut microbiome and risk of colorectal cancer, a case-control study.

2013 ◽  
Author(s):  
Jiyoung Ahn ◽  
Rashmi Sinha ◽  
Zhiheng Pei ◽  
Christine Dominianni ◽  
James J. Goedert ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gut Microbiome ◽  
Case Control Study ◽  
Case Control ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Control Study

scholarly journals Diversity and Distribution of Sulfur Metabolism 1 in the Human Gut Microbiome and its Association with Colorectal Cancer

2021 ◽  
Author(s):  
Patricia G. Wolf ◽  
Elise S. Cowley ◽  
Adam Breister ◽  
Sarah Matatov ◽  
Luke Lucio ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Sulfate Reduction ◽  
Gut Microbiome ◽  
Sulfur Metabolism ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Metabolic Genes ◽  
Comprehensive Knowledge ◽  
Potential Trigger

Abstract Background: Microbial sulfidogenesis produces genotoxic hydrogen sulfide (H2S) in the human gut using inorganic (sulfate) and organic (taurine/cysteine/methionine) substrates, however the majority of studies have focused on sulfate reduction using dissimilatory sulfite reductases (Dsr). Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge of sulfur metabolism within the human gut.Results: Here we show that microbial sulfur metabolism is more abundant and diverse than previously studied and is statistically associated with CRC. Using ~17,000 bacterial genomes from publicly available stool metagenomes, we studied the diversity of sulfur metabolic genes in 667 participants across different health statuses: healthy, adenoma, and carcinoma. Sulfidogenic genes were harbored by 142 bacterial genera and both organic and inorganic sulfidogenic genes were associated with carcinoma. Significantly, anaerobic sulfite reductases were twice as abundant as dsr, demonstrating that this enzyme is likely a more important contributor to sulfate reduction in the human gut. We identified twelve potential pathways for reductive taurine metabolism and discovered novel genera harboring these pathways. Finally, prevalence of metabolic genes for organic sulfur indicate that these understudied substrates may be the most abundant source of microbially derived H2S.Conclusions: Our findings significantly expand knowledge of microbial sulfur metabolism in the human gut. We show that microbial sulfur metabolism in the human gut is more prevalent than previously known, irrespective of health status (i.e., in both healthy and diseased states). Our results significantly increase the diversity of pathways and bacteria that are associated with microbial sulfur metabolism in the human gut. Overall, our results have implications for understanding the role of the human gut microbiome and its potential contributions to the pathogenesis of CRC.

scholarly journals Whole-genome of Mexican-crAssphage isolated from the human gut microbiome

2018 ◽  
Vol 11 (1) ◽  
Author(s):  
Melany Cervantes-Echeverría ◽  
Edgar Equihua-Medina ◽  
Fernanda Cornejo-Granados ◽  
Abigail Hernández-Reyna ◽  
Filiberto Sánchez ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Whole Genome ◽  
Human Gut ◽  
Human Gut Microbiome
Sign in / Sign up

Export Citation Format

Share Document