Review
Immunology
Hanghang Yuan, Ruirui Gui, Zhicheng Wang, Fang Fang, Hongguang Zhao
Summary: Colorectal cancer (CRC) is a common and deadly cancer that poses a major burden on human health. Gut microbiota regulate human immunity and metabolism through producing numerous metabolites, but the specific mechanisms by which gut microbiota interact with immunotherapy and radiotherapy remain incongruent. This review discusses recent advances and the potential of targeting gut microbiota to enhance the efficacy of radioimmunotherapy in CRC, providing references and fresh ideas for the clinical application of this novel strategy.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Cell Biology
Yanmin Li, Hong Cao, Bojian Fei, Qizhong Gao, Wanya Yi, Weifeng Han, Chuanqing Bao, Jianmin Xu, Wei Zhao, Feng Zhang
Summary: By studying the microbiota of colorectal mucosa and feces in CRC patients, we found significant differences between the microbiota of tumor mucosa and normal mucosa, while the microbiota of para-cancerous mucosa served as a transitional state. Furthermore, we discovered a strong correlation between FOBT positivity and the genus Fusobacterium, and identified six key genera that were consistently over-represented in tumor mucosa compared to normal mucosa and/or in mucosa compared to feces.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Ling Wang, Yi-Xuan Tu, Lu Chen, Yuan Zhang, Xue-Ling Pan, Shu-Qiao Yang, Shuai-Jie Zhang, Sheng-Hui Li, Ke-Chun Yu, Shuo Song, Hong-Li Xu, Zhu-Cheng Yin, Jun-Qiu Yue, Qian-Lin Ni, Tang Tang, Jiu-Liang Zhang, Min Guo, Shuai Zhang, Fan Yao, Xin-Jun Liang, Zhen-Xia Chen
Summary: Men have higher incidence and mortality rates of colorectal cancer (CRC) than women. This study explains the sexual dimorphism in CRC by examining sex-biased gut microbiota and metabolites. The results show that male mice and pseudo-germ mice receiving fecal samples from males have larger tumors and impaired gut barrier function. Changes in gut microbiota composition, including increased pathogenic bacteria and decreased probiotic bacteria, were observed in male mice and pseudo-germ mice. Sex-biased gut metabolites contribute to the sex dimorphism in CRC through glycerophospholipids metabolism pathway. Modulating sex-biased gut microbiota and metabolites could be a potential therapeutic strategy for CRC.
Article
Oncology
P. H. A. Wisse, W. de Klaver, F. van Wifferen, L. Meiqari, M. Bierkens, M. J. E. Greuter, B. Carvalho, M. E. van Leerdam, M. C. W. Spaander, E. Dekker, V. M. H. Coupe, M. de Wit, G. A. Meijer
Summary: This study aims to validate the relative sensitivity of mtFIT compared to FIT in colorectal cancer (CRC) screening, and predict the lifetime health effects and costs using the Adenoma and Serrated Pathway to Colorectal CAncer model. The results of this study will provide important clinical utility information for the Dutch national CRC screening program.
Article
Gastroenterology & Hepatology
Stefanie Brezina, Martin Borkovec, Andreas Baierl, Fabienne Bastian, Andreas Futschik, Nikolaus Gasche, Thomas Gruenberger, Michael Hallas, Christian Jannsen, Gernot Leeb, Rebecca Lutz, Barbara Sladek, Andrea Gsur
Summary: The study evaluated the usability of FIT cartridges for microbiome analysis and compared it to Stool Collection and Preservation Tubes. The FIT and Preservation Tube samples had highly similar microbiome profiles, with minor differences between abundances of some bacterial taxa. The results indicate that FIT cartridges are suitable for gut microbiome analysis within CRC screening programs.
Article
Oncology
Travis J. Gates, Ce Yuan, Mihir Shetty, Thomas Kaiser, Andrew C. Nelson, Aastha Chauhan, Timothy K. Starr, Christopher Staley, Subbaya Subramanian
Summary: Inflammation of the colon (colitis) increases the risk of colorectal cancers, and gut microbiota may be involved in cancer development. Manipulating the bacteria community in the colon could be a potential way to prevent cancer. A study using mice found that transferring bacteria from healthy mice to those with colitis increased the presence of Akkermansia, which may alleviate colon inflammation, while untreated mice had an increase in other bacteria types, such as Anaeroplasma and Alistipes, which could contribute to inflammation. These findings suggest that specific bacteria types may help reduce colon inflammation and prevent cancer.
Article
Multidisciplinary Sciences
James J. Goedert, Zhenyi Wu, Cyndee H. Yonehara, Timothy B. Frankland, Rashmi Sinha, Gieira S. Jones, Yunhu Wan, Jacques Ravel, Ni Zhao, Stacey A. Honda
Summary: This study used FIT samples to analyze the fecal microbiome and found no consistent association between CRA/CRC and fecal microbiome diversity or composition. Men had a higher risk of being FIT positive. The findings of this study have important implications for future microbiome research design and sample size determination.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
Jihye Park, Nam-Eun Kim, Hyuk Yoon, Cheol Min Shin, Nayoung Kim, Dong Ho Lee, Jae Yong Park, Chang Hwan Choi, Jae Gyu Kim, Yoon-Keun Kim, Tae-Seop Shin, Jinho Yang, Young Soo Park
Summary: The study found significant differences in the microbial composition, evenness, and diversity of fecal microbiota and gut microbe-derived EVs in colorectal cancer (CRC) subjects compared to control subjects. Additionally, there were noticeable changes in microbial composition, evenness, and diversity between late-stage and early-stage CRC subjects in both fecal microbiota and gut microbe-derived EVs. EVs derived from certain microbes could serve as novel biomarkers for diagnosing CRC and predicting CRC stages.
FRONTIERS IN ONCOLOGY
(2021)
Review
Immunology
Lena Van Dingenen, Charlotte Segers, Shari Wouters, Mohamed Mysara, Natalie Leys, Samir Kumar-Singh, Surbhi Malhotra-Kumar, Rob Van Houdt
Summary: Colorectal cancer is a common and burdensome disease. Current treatment includes surgery, chemotherapy, radiotherapy, and immunotherapy. The gut microbiome may influence treatment efficacy and toxicity, and fecal microbiota transplantation can reduce toxicity and enhance efficacy.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Review
Oncology
Mong-Hong Lee
Summary: Research has shown that gut microbiota dysbiosis is linked to physiological changes and various diseases, including cancers. Advances in metagenome sequencing and multiomics studies have provided insights into the composition, taxonomic alterations, and host interactions of gut microbiota during tumorigenesis. However, the complexity of gut microbiota interactions still presents challenges in fully understanding the microbiota-cancer connections and their implications for cancer diagnosis, treatment, and prevention.
CANCER COMMUNICATIONS
(2021)
Article
Oncology
Shaobo Mo, Hui Wang, Lingyu Han, Wenqiang Xiang, Weixing Dai, Pengfei Zhao, Fengchun Pei, Zhixi Su, Chengcheng Ma, Qi Li, Zhimin Wang, Sanjun Cai, Hao Wang, Rui Liu, Guoxiang Cai
Summary: The multidimensional assay combining FIT and stool DNA tests enhances the diagnostic sensitivity for CRC, especially in patients with stage II and III. Furthermore, the detection rate of CRC increases with tumor size and age, with a slightly higher detection rate in smokers.
FRONTIERS IN ONCOLOGY
(2021)
Letter
Biochemistry & Molecular Biology
Einar Birkeland, Giulio Ferrero, Barbara Pardini, Sinan U. Umu, Sonia Tarallo, Sara Bulfamante, Geir Hoff, Carlo Senore, Trine B. Rounge, Alessio Naccarati
Summary: Fecal microRNAs have potential clinical interest as non-invasive diagnostic and prognostic biomarkers in colorectal cancer (CRC) screening. This study assessed the feasibility of using small RNA sequencing to measure human miRNAs in FIT samples and demonstrated the stability and consistency of this method for detecting CRC and advanced adenoma in large scale screening.
Article
Gastroenterology & Hepatology
Wen-Feng Hsu, Chi-Yang Chang, Chun-Chao Chang, Li-Chun Chang, Chien-Hua Chen, Chun-Che Lin, Yu-Min Lin, Chia-Long Lee, Hong-Yuan Wu, Hsin-Chung Lee, Yi-Chia Lee, Ming-Yao Su, Li-Ju Lin, Shu-Li Chia, Ming-Shiang Wu, Han-Mo Chiu
Summary: The study found that FIT-colonoscopy was associated with more than two-fold risk of significant bleeding, especially when polypectomy was performed.
Review
Biology
Ruqaiyyah Siddiqui, Anania Boghossian, Ahmad M. Alharbi, Hasan Alfahemi, Naveed Ahmed Khan
Summary: The gut microbiome may play a pivotal role in the development and progression of colorectal cancer. Changes in diet and alcohol consumption can alter the microbiome and impact the development of colorectal cancer. Potential therapies such as fecal microbiota transfer and pre/postbiotics can help restore gut microbial dysbiosis.
Article
Microbiology
Jingjing Liu, Mingyang Qi, Chengchao Qiu, Feng Wang, Shaofei Xie, Jian Zhao, Jing Wu, Xiaofeng Song
Summary: The gut microbiome and its interaction with the host play important roles in the pathogenesis of colorectal cancer (CRC). This study investigated the compositions of gut bacteria and their interactions with the host during the early stages of inflammation and CRC. The results revealed significant variations in gut microbiota abundance and composition, as well as specific fecal metabolome profiling in CRC and inflammation. The identification of potential biomarkers for CRC and inflammation contributes to the diagnosis of these conditions. The integrated microbiome and metabolomic analysis suggests that microbes facilitate tumorigenesis of CRC through interfering with host metabolism.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Jhansi L. Leslie, Matthew L. Jenior, Kimberly C. Vendrov, Alexandra K. Standke, Madeline R. Barron, Tricia J. O'Brien, Lavinia Unverdorben, Pariyamon Thaprawat, Ingrid L. Bergin, Patrick D. Schloss, Vincent B. Young
Summary: Precolonization with a less virulent strain of C. difficile to reduce glycine levels can decrease germination of a second strain, potentially offering protection from reinfection. This finding highlights the importance of targeting nutrients utilized by all life stages for bacterial therapeutics aiming to restore colonization resistance in the gut.
Correction
Microbiology
Ada K. Hagan, Begum D. Topcuoglu, Mia E. Gregory, Hazel A. Barton, Patrick D. Schloss
Article
Microbiology
Nicholas A. Lesniak, Alyxandria M. Schubert, Hamide Sinani, Patrick D. Schloss
Summary: The gut bacterial community plays a crucial role in preventing pathogens like C. difficile from colonizing and causing infection. Different antibiotic treatments result in varying changes in the bacterial community, affecting the ability to clear C. difficile colonization. Understanding how different gut bacterial communities eliminate C. difficile colonization will help improve C. difficile infection treatments in the future.
Article
Ecology
Stefanie Widder, Jiangchao Zhao, Lisa A. Carmody, Qingyang Zhang, Linda M. Kalikin, Patrick D. Schloss, John J. LiPuma
Summary: In this study, bacterial communities in the airways of cystic fibrosis patients were analyzed, leading to the identification of different pulmotypes which show temporal sequence patterns and significant correlations with patient clinical status. By constructing pulmotype-specific metabolic activity profiles, it was found that microbial communities within pulmotypes drive distinct community functions.
Article
Microbiology
Courtney R. Armour, Begum D. Topcuoglu, Andrea Garretto, Patrick D. Schloss
Summary: Colorectal cancer, a common and deadly disease in the United States, can be effectively prevented with early detection and treatment. The gut microbiome has shown promise as a noninvasive method for detecting colorectal cancer. In this study, researchers investigated the optimal taxonomic resolution for microbiome-based classification of colorectal cancer and found that mid-range resolution (family, genus, and OTU) provides the best prediction performance.
Article
Microbiology
Kelly L. Sovacool, Sarah L. Westcott, M. Brodie Mumphrey, Gabrielle A. Dotson, Patrick D. Schloss
Summary: Advancements in DNA sequencing technology have allowed researchers to generate millions of sequence reads from microorganisms. Efficient software tools are needed to assign microbial sequences into taxonomic groups. Existing methods either produce inconsistent results or have reduced quality. To address this, we developed OptiFit, a new algorithm that allows for consistent and high-quality assignments, making it easier to compare different studies or add new data to existing studies.
Article
Oncology
Rosa Klotz, Magdalena Holze, Colette Doerr-Harim, Erich Grohmann, Barbara Nied, Burkhard Lebert, Susanne Weg-Remers, Claudia Lutz, Karin Meissler, Patrick Schloss, Charlotte Ullrich, Susanne Frankenhauser, Heidi Lutter, Diedrich Buehler, Azaz Ahmed, Toto Gronlund, Andre L. Mihaljevic
Summary: This study aimed to identify and prioritize unresolved research questions related to colorectal cancer through collaboration with relevant stakeholders. Through nationwide surveys and a consensus workshop, the top 10 research topics were determined to provide researchers and funding bodies with directions for patient-relevant research projects.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Microbiology
Madeline R. Barron, Kelly L. Sovacool, Lisa Abernathy-Close, Kimberly C. Vendrov, Alexandra K. Standke, Ingrid L. Bergin, Patrick D. Schloss, Vincent B. Young
Summary: Patients with inflammatory bowel disease (IBD) have an increased risk of developing C. difficile infection (CDI), even in the absence of antibiotic treatment. The mechanisms regulating C. difficile colonization in IBD patients remain unclear. In this study, a mouse model was used to demonstrate that intestinal inflammation alters microbiota composition, leading to susceptibility to C. difficile colonization. Treating inflammation with an anti-p40 monoclonal antibody restores colonization resistance. Microbiota transfer experiments confirm that the microbiota shaped in the setting of IBD is the primary driver of susceptibility to C. difficile colonization.
Article
Microbiology
Nicholas A. Lesniak, Alyxandria M. Schubert, Kaitlin J. Flynn, Jhansi L. Leslie, Hamide Sinani, Ingrid L. Bergin, Vincent B. Young, Patrick D. Schloss
Summary: Clostridioides difficile colonization can lead to a range of infection severities, from mild diarrhea to life-threatening conditions. While factors such as patient age, blood cell count, and C. difficile characteristics have been associated with disease severity, the role of specific gut bacteria in influencing severity is unclear. This study demonstrates that different gut bacterial communities can contribute to variations in Clostridioides difficile infection outcomes. Certain bacterial groups were associated with more severe outcomes, while others were associated with milder outcomes. Incorporating gut bacterial community data into severity models may aid in identifying at-risk patients and improving interventions.
Article
Microbiology
Nicholas A. Lesniak, Sarah Tomkovich, Andrew Henry, Ana Taylor, Joanna Colovas, Lucas Bishop, Kathryn McBride, Patrick D. Schloss
Summary: Antibiotic use is a major risk factor for Clostridioides difficile infection (CDI). Fecal microbiota transplant can restore gut bacterial community and eliminate the infection. This study explored the potential of using fecal community transplant to prevent CDI and found that it can prevent or clear C. difficile.
Article
Microbiology
Patrick D. Schloss
Summary: The Riffomonas YouTube channel is dedicated to teaching scientists and others how to conduct reproducible research using modern data science tools, bridging the gap between those familiar with laboratory research and the methods of data analysis.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Behavioral Sciences
Anne C. Sabol, William L. Close, Lauren Petrullo, Connor T. Lambert, Brian Keane, Nancy G. Solomon, Patrick D. Schloss, Ben Dantzer
Summary: The sociality of prairie voles does not affect the diversity of their oral microbiome, which contrasts with studies predominantly conducted on primates and gut microbiome. This highlights the importance of investigating other microbiome regions and relationships in different species.
Article
Oncology
S. B. Rifkin, M. A. Sze, K. Tuck, E. Koeppe, E. M. Stoffel, P. D. Schloss
Summary: This study investigated the association between microbiome and CRC risk in Lynch syndrome (LS). The results showed significant differences in microbiome composition between LS and non-LS, with specific taxa differences observed in LS-CRC patients. However, larger prospective studies are needed to determine if microbiome composition contributes to CRN development in LS patients.
JOURNAL OF GASTROINTESTINAL CANCER
(2023)
Editorial Material
Microbiology
Patrick D. Schloss, Christina A. Cuomo
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Patrick D. Schloss
Summary: Published in 2014, the study by McMurdie and Holmes examines how to control for the unavoidable uneven sequencing depths in 16S rRNA gene sequencing. Their findings have significantly impacted the methods used by microbiome researchers. However, there are several issues with the design and analysis of their simulations that compromise their results. When reproducing and expanding upon their analysis, it becomes clear that rarefaction is actually the most robust approach for controlling uneven sequencing effort across samples.