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6. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Author

Kennedy, Katherine M., de Goffau, Marcus C., Perez-Muñoz, Maria Elisa, Arrieta, Marie-Claire, Bäckhed, Fredrik, Bork, Peer, Braun, Thorsten, Bushman, Frederic D., Dore, Joel, de Vos, Willem M., Earl, Ashlee M., Eisen, Jonathan A., Elovitz, Michal A., Ganal-Vonarburg, Stephanie C., Gänzle, Michael G., Garrett, Wendy S., Hall, Lindsay J., Hornef, Mathias W., Huttenhower, Curtis, Konnikova, Liza, Lebeer, Sarah, Macpherson, Andrew J., Massey, Ruth C., McHardy, Alice Carolyn, Koren, Omry, Lawley, Trevor D., Ley, Ruth E., O’Mahony, Liam, O’Toole, Paul W., Pamer, Eric G., Parkhill, Julian, Raes, Jeroen, Rattei, Thomas, Salonen, Anne, Segal, Eran, Segata, Nicola, Shanahan, Fergus, Sloboda, Deborah M., Smith, Gordon C. S., Sokol, Harry, Spector, Tim D., Surette, Michael G., Tannock, Gerald W., Walker, Alan W., Yassour, Moran, and Walter, Jens

Published
2023
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7. Challenges in IBD Research 2024: Preclinical Human IBD Mechanisms

Author

Ciorba, Matthew A, primary, Konnikova, Liza, additional, Hirota, Simon A, additional, Lucchetta, Elena M, additional, Turner, Jerrold R, additional, Slavin, Anthony, additional, Johnson, Kristen, additional, Condray, Cass D, additional, Hong, Sungmo, additional, Cressall, Brandon K, additional, Pizarro, Theresa T, additional, Hurtado-Lorenzo, Andrés, additional, Heller, Caren A, additional, Moss, Alan C, additional, Swantek, Jennifer L, additional, and Garrett, Wendy S, additional

Published
2024
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8. Discovery of bioactive microbial gene products in inflammatory bowel disease

Author

Zhang, Yancong, Bhosle, Amrisha, Bae, Sena, McIver, Lauren J., Pishchany, Gleb, Accorsi, Emma K., Thompson, Kelsey N., Arze, Cesar, Wang, Ya, Subramanian, Ayshwarya, Kearney, Sean M., Pawluk, April, Plichta, Damian R., Rahnavard, Ali, Shafquat, Afrah, Xavier, Ramnik J., Vlamakis, Hera, Garrett, Wendy S., Krueger, Andy, Huttenhower, Curtis, and Franzosa, Eric A.

Published
2022
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9. A single-cell survey of the small intestinal epithelium

Author

Haber, Adam L, Biton, Moshe, Rogel, Noga, Herbst, Rebecca H, Shekhar, Karthik, Smillie, Christopher, Burgin, Grace, Delorey, Toni M, Howitt, Michael R, Katz, Yarden, Tirosh, Itay, Beyaz, Semir, Dionne, Danielle, Zhang, Mei, Raychowdhury, Raktima, Garrett, Wendy S, Rozenblatt-Rosen, Orit, Shi, Hai Ning, Yilmaz, Omer, Xavier, Ramnik J, and Regev, Aviv

Subjects
Emerging Infectious Diseases, Digestive Diseases, Infectious Diseases, Vaccine Related, Aetiology, 2.1 Biological and endogenous factors, Animals, Cell Differentiation, Cytokines, Enterocytes, Epithelial Cells, Epithelium, Female, Gene Expression Profiling, Homeostasis, Intestine, Small, Leukocyte Common Antigens, Male, Mice, Organoids, Paneth Cells, Single-Cell Analysis, Transcription, Genetic, Thymic Stromal Lymphopoietin, General Science & Technology
Abstract

Intestinal epithelial cells absorb nutrients, respond to microbes, function as a barrier and help to coordinate immune responses. Here we report profiling of 53,193 individual epithelial cells from the small intestine and organoids of mice, which enabled the identification and characterization of previously unknown subtypes of intestinal epithelial cell and their gene signatures. We found unexpected diversity in hormone-secreting enteroendocrine cells and constructed the taxonomy of newly identified subtypes, and distinguished between two subtypes of tuft cell, one of which expresses the epithelial cytokine Tslp and the pan-immune marker CD45, which was not previously associated with non-haematopoietic cells. We also characterized the ways in which cell-intrinsic states and the proportions of different cell types respond to bacterial and helminth infections: Salmonella infection caused an increase in the abundance of Paneth cells and enterocytes, and broad activation of an antimicrobial program; Heligmosomoides polygyrus caused an increase in the abundance of goblet and tuft cells. Our survey highlights previously unidentified markers and programs, associates sensory molecules with cell types, and uncovers principles of gut homeostasis and response to pathogens.

Published
2017

10. Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies

Author

Everett, Christine, Li, Chengchen, Wilkinson, Jeremy E., Nguyen, Long H., McIver, Lauren J., Ivey, Kerry, Izard, Jacques, Palacios, Natalia, Eliassen, A. Heather, Willett, Walter C., Ascherio, Alberto, Sun, Qi, Tworoger, Shelley S., Chan, Andrew T., Garrett, Wendy S., Huttenhower, Curtis, Rimm, Eric B., and Song, Mingyang

Published
2021
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13. Randomised, placebo-controlled, phase 3 trial of the effect of the omega-3 polyunsaturated fatty acid eicosapentaenoic acid (EPA) on colorectal cancer recurrence and survival after surgery for resectable liver metastases: EPA for Metastasis Trial 2 (EMT2) study protocol

Author

Hull, Mark A, primary, Ow, Pei Loo, additional, Ruddock, Sharon, additional, Brend, Tim, additional, Smith, Alexandra F, additional, Marshall, Helen, additional, Song, Mingyang, additional, Chan, Andrew T, additional, Garrett, Wendy S, additional, Yilmaz, Omer, additional, Drew, David A, additional, Collinson, Fiona, additional, Cockbain, Andrew J, additional, Jones, Robert, additional, Loadman, Paul M, additional, Hall, Peter S, additional, Moriarty, Catherine, additional, Cairns, David A, additional, and Toogood, Giles J, additional

Published
2023
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14. The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome

Author

Kosumi, Keisuke, Hamada, Tsuyoshi, Koh, Hideo, Borowsky, Jennifer, Bullman, Susan, Twombly, Tyler S., Nevo, Daniel, Masugi, Yohei, Liu, Li, da Silva, Annacarolina, Chen, Yang, Du, Chunxia, Gu, Mancang, Li, Chenxi, Li, Wanwan, Liu, Hongli, Shi, Yan, Mima, Kosuke, Song, Mingyang, Nosho, Katsuhiko, Nowak, Jonathan A., Nishihara, Reiko, Baba, Hideo, Zhang, Xuehong, Wu, Kana, Wang, Molin, Huttenhower, Curtis, Garrett, Wendy S., Meyerson, Matthew L., Lennerz, Jochen K., Giannakis, Marios, Chan, Andrew T., Meyerhardt, Jeffrey A., Fuchs, Charles S., and Ogino, Shuji

Published
2018
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15. The Role of the Microbiome in the Etiopathogenesis of Colon Cancer.

Author

El Tekle, Geniver, Andreeva, Natalia, and Garrett, Wendy S.

Abstract

Studies in preclinical models support that the gut microbiota play a critical role in the development and progression of colorectal cancer (CRC). Specific microbial species and their corresponding virulence factors or associated small molecules can contribute to CRC development and progression either via direct effects on the neoplastic transformation of epithelial cells or through interactions with the host immune system. Induction of DNA damage, activation of Wnt/β-catenin and NF-κB proinflammatory pathways, and alteration of the nutrient's availability and the metabolic activity of cancer cells are the main mechanisms by which the microbiota contribute to CRC. Within the tumor microenvironment, the gut microbiota alter the recruitment, activation, and function of various immune cells, such as T cells, macrophages, and dendritic cells. Additionally, the microbiota shape the function and composition of cancer-associated fibroblasts and extracellular matrix components, fashioning an immunosuppressive and pro-tumorigenic niche for CRC. Understanding the complex interplay between gut microbiota and tumorigenesis can provide therapeutic opportunities for the prevention and treatment of CRC. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Colorectal cancer: the facts in the case of the microbiota

Author

Clay, Slater L., Fonseca-Pereira, Diogo, and Garrett, Wendy S.

Subjects
Microbiota (Symbiotic organisms) -- Health aspects, Colorectal cancer -- Risk factors -- Development and progression, Host-bacteria relationships -- Health aspects, Health care industry
Abstract

The importance of the microbiota in the development of colorectal cancer (CRC) is increasingly evident, but identifying specific microbial features that influence CRC initiation and progression remains a central task for investigators. Studies determining the microbial mechanisms that directly contribute to CRC development or progression are revealing bacterial factors such as toxins that contribute to colorectal carcinogenesis. However, even when investigators have identified bacteria that express toxins, questions remain about the host determinants of a toxin's cancer-potentiating effects. For other cancer-correlating bacteria that lack toxins, the challenge is to define cancer-relevant virulence factors. Herein, we evaluate three CRC-correlating bacteria, colibactin-producing Escherichia coli, enterotoxigenic Bacteroides fragilis, and Fusobacterium nucleatum, for their virulence features relevant to CRC. We also consider the beneficial bioactivity of gut microbes by highlighting a microbial metabolite that may enhance CRC antitumor immunity. In doing so, we aim to elucidate unique and shared mechanisms underlying the microbiota's contributions to CRC and to accelerate investigation from target validation to CRC therapeutic discovery., The microbiome's relevance to the initiation and progression of colorectal cancer (CRC) is increasingly appreciated, but defining how microorganisms influence susceptibility to and progression of cancer remains a challenge. Data [...]

Published
2022
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17. Diets That Promote Colon Inflammation Associate With Risk of Colorectal Carcinomas That Contain Fusobacterium nucleatum

Author

Liu, Li, Tabung, Fred K., Zhang, Xuehong, Nowak, Jonathan A., Qian, Zhi Rong, Hamada, Tsuyoshi, Nevo, Daniel, Bullman, Susan, Mima, Kosuke, Kosumi, Keisuke, da Silva, Annacarolina, Song, Mingyang, Cao, Yin, Twombly, Tyler S., Shi, Yan, Liu, Hongli, Gu, Mancang, Koh, Hideo, Li, Wanwan, Du, Chunxia, Chen, Yang, Li, Chenxi, Li, Wenbin, Mehta, Raaj S., Wu, Kana, Wang, Molin, Kostic, Aleksander D., Giannakis, Marios, Garrett, Wendy S., Hutthenhower, Curtis, Chan, Andrew T., Fuchs, Charles S., Nishihara, Reiko, Ogino, Shuji, and Giovannucci, Edward L.

Published
2018
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20. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine

Author

Geller, Leore T., Barzily-Rokni, Michal, Danino, Tal, Jonas, Oliver H., Shental, Noam, Nejman, Deborah, Gavert, Nancy, Zwang, Yaara, Cooper, Zachary A., Shee, Kevin, Thaiss, Christoph A., Reuben, Alexandre, Livny, Jonathan, Avraham, Roi, Frederick, Dennie T., Ligorio, Matteo, Chatman, Kelly, Johnston, Stephen E., Mosher, Carrie M., Brandis, Alexander, Fuks, Garold, Gurbatri, Candice, Gopalakrishnan, Vancheswaran, Kim, Michael, Hurd, Mark W., Katz, Matthew, Fleming, Jason, Maitra, Anirban, Smith, David A., Skalak, Matt, Bu, Jeffrey, Michaud, Monia, Trauger, Sunia A., Barshack, Iris, Golan, Talia, Sandbank, Judith, Flaherty, Keith T., Mandinova, Anna, Garrett, Wendy S., Thayer, Sarah P., Ferrone, Cristina R., Huttenhower, Curtis, Bhatia, Sangeeta N., Gevers, Dirk, Wargo, Jennifer A., Golub, Todd R., and Straussman, Ravid

Published
2017

21. QseC inhibition as an antivirulence approach for colitis-associated bacteria

Author

Rooks, Michelle G., Veiga, Patrick, Reeves, Analise Z., Lavoie, Sydney, Yasuda, Koji, Asano, Yasunari, Yoshihara, Kazufumi, Michaud, Monia, Wardwell-Scott, Leslie, Gallini, Carey Ann, Glickman, Jonathan N., Sudo, Nobuyuki, Huttenhower, Curtis, Lesser, Cammie F., and Garrett, Wendy S.

Published
2017

25. Publisher Correction: Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies

Author

Everett, Christine, Li, Chengchen, Wilkinson, Jeremy E., Nguyen, Long H., McIver, Lauren J., Ivey, Kerry, Izard, Jacques, Palacios, Natalia, Eliassen, A. Heather, Willett, Walter C., Ascherio, Alberto, Sun, Qi, Tworoger, Shelley S., Chan, Andrew T., Garrett, Wendy S., Huttenhower, Curtis, Rimm, Eric B., and Song, Mingyang

Published
2021
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27. Data from Calcium Intake and Risk of Colorectal Cancer According to Tumor-infiltrating T Cells

Author

Yang, Wanshui, primary, Liu, Li, primary, Keum, NaNa, primary, Qian, Zhi Rong, primary, Nowak, Jonathan A., primary, Hamada, Tsuyoshi, primary, Song, Mingyang, primary, Cao, Yin, primary, Nosho, Katsuhiko, primary, Smith-Warner, Stephanie A., primary, Zhang, Sui, primary, Masugi, Yohei, primary, Ng, Kimmie, primary, Kosumi, Keisuke, primary, Ma, Yanan, primary, Garrett, Wendy S., primary, Wang, Molin, primary, Nan, Hongmei, primary, Giannakis, Marios, primary, Meyerhardt, Jeffrey A., primary, Chan, Andrew T., primary, Fuchs, Charles S., primary, Nishihara, Reiko, primary, Wu, Kana, primary, Giovannucci, Edward L., primary, Ogino, Shuji, primary, and Zhang, Xuehong, primary

Published
2023
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28. Data from Fusobacterium nucleatum in Colorectal Cancer Relates to Immune Response Differentially by Tumor Microsatellite Instability Status

Author

Hamada, Tsuyoshi, primary, Zhang, Xuehong, primary, Mima, Kosuke, primary, Bullman, Susan, primary, Sukawa, Yasutaka, primary, Nowak, Jonathan A., primary, Kosumi, Keisuke, primary, Masugi, Yohei, primary, Twombly, Tyler S., primary, Cao, Yin, primary, Song, Mingyang, primary, Liu, Li, primary, da Silva, Annacarolina, primary, Shi, Yan, primary, Gu, Mancang, primary, Li, Wanwan, primary, Koh, Hideo, primary, Nosho, Katsuhiko, primary, Inamura, Kentaro, primary, Keum, NaNa, primary, Wu, Kana, primary, Meyerhardt, Jeffrey A., primary, Kostic, Aleksandar D., primary, Huttenhower, Curtis, primary, Garrett, Wendy S., primary, Meyerson, Matthew, primary, Giovannucci, Edward L., primary, Chan, Andrew T., primary, Fuchs, Charles S., primary, Nishihara, Reiko, primary, Giannakis, Marios, primary, and Ogino, Shuji, primary

Published
2023
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29. Figure S1, Table S1-7 from Calcium Intake and Risk of Colorectal Cancer According to Tumor-infiltrating T Cells

Author

Yang, Wanshui, primary, Liu, Li, primary, Keum, NaNa, primary, Qian, Zhi Rong, primary, Nowak, Jonathan A., primary, Hamada, Tsuyoshi, primary, Song, Mingyang, primary, Cao, Yin, primary, Nosho, Katsuhiko, primary, Smith-Warner, Stephanie A., primary, Zhang, Sui, primary, Masugi, Yohei, primary, Ng, Kimmie, primary, Kosumi, Keisuke, primary, Ma, Yanan, primary, Garrett, Wendy S., primary, Wang, Molin, primary, Nan, Hongmei, primary, Giannakis, Marios, primary, Meyerhardt, Jeffrey A., primary, Chan, Andrew T., primary, Fuchs, Charles S., primary, Nishihara, Reiko, primary, Wu, Kana, primary, Giovannucci, Edward L., primary, Ogino, Shuji, primary, and Zhang, Xuehong, primary

Published
2023
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30. Supplementary Data from Fusobacterium nucleatum in Colorectal Cancer Relates to Immune Response Differentially by Tumor Microsatellite Instability Status

Author

Hamada, Tsuyoshi, primary, Zhang, Xuehong, primary, Mima, Kosuke, primary, Bullman, Susan, primary, Sukawa, Yasutaka, primary, Nowak, Jonathan A., primary, Kosumi, Keisuke, primary, Masugi, Yohei, primary, Twombly, Tyler S., primary, Cao, Yin, primary, Song, Mingyang, primary, Liu, Li, primary, da Silva, Annacarolina, primary, Shi, Yan, primary, Gu, Mancang, primary, Li, Wanwan, primary, Koh, Hideo, primary, Nosho, Katsuhiko, primary, Inamura, Kentaro, primary, Keum, NaNa, primary, Wu, Kana, primary, Meyerhardt, Jeffrey A., primary, Kostic, Aleksandar D., primary, Huttenhower, Curtis, primary, Garrett, Wendy S., primary, Meyerson, Matthew, primary, Giovannucci, Edward L., primary, Chan, Andrew T., primary, Fuchs, Charles S., primary, Nishihara, Reiko, primary, Giannakis, Marios, primary, and Ogino, Shuji, primary

Published
2023
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31. Engineered Escherichia coli for the in situ secretion of therapeutic nanobodies in the gut

Author

Lynch, Jason P., primary, González-Prieto, Coral, additional, Reeves, Analise Z., additional, Bae, Sena, additional, Powale, Urmila, additional, Godbole, Neha P., additional, Tremblay, Jacqueline M., additional, Schmidt, Florian I., additional, Ploegh, Hidde L., additional, Kansra, Vikram, additional, Glickman, Jonathan N., additional, Leong, John M., additional, Shoemaker, Charles B., additional, Garrett, Wendy S., additional, and Lesser, Cammie F., additional

Published
2023
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34. Inverse relationship between Fusobacterium nucleatum amount and tumor CD274 (PD‐L1) expression in colorectal carcinoma.

Author

Ugai, Tomotaka, Shimizu, Takashi, Kawamura, Hidetaka, Ugai, Satoko, Takashima, Yasutoshi, Usui, Genki, Väyrynen, Juha P, Okadome, Kazuo, Haruki, Koichiro, Akimoto, Naohiko, Masugi, Yohei, da Silva, Annacarolina, Mima, Kosuke, Zhang, Xuehong, Chan, Andrew T, Wang, Molin, Garrett, Wendy S, Freeman, Gordon J, Meyerhardt, Jeffrey A, and Nowak, Jonathan A

Abstract

Objectives: The CD274 (programmed cell death 1 ligand 1, PD‐L1)/PDCD1 (programmed cell death 1, PD‐1) immune checkpoint axis is known to regulate the antitumor immune response. Evidence also supports an immunosuppressive effect of Fusobacterium nucleatum. We hypothesised that tumor CD274 overexpression might be inversely associated with abundance of F. nucleatum in colorectal carcinoma. Methods: We assessed tumor CD274 expression by immunohistochemistry and F. nucleatum DNA within tumor tissue by quantitative PCR in 812 cases among 4465 incident rectal and colon cancer cases that had occurred in two prospective cohort studies. Multivariable logistic regression analyses with inverse probability weighting were used to adjust for selection bias because of tissue data availability and potential confounders including microsatellite instability status, CpG island methylator phenotype, LINE‐1 methylation level and KRAS, BRAF and PIK3CA mutations. Results: Fusobacterium nucleatum DNA was detected in tumor tissue in 109 (13%) cases. Tumor CD274 expression level was inversely associated with the amount of F. nucleatum in colorectal cancer tissue (P = 0.0077). For one category‐unit increase in three ordinal F. nucleatum categories (negative vs. low vs. high), multivariable‐adjusted odds ratios (with 95% confidence interval) of the low, intermediate and high CD274 categories (vs. negative) were 0.78 (0.41–1.51), 0.64 (0.32–1.28) and 0.50 (0.25–0.99), respectively (Ptrend = 0.032). Conclusions: Tumor CD274 expression level was inversely associated with the amount of F. nucleatum in colorectal cancer tissue, suggesting that different immunosuppressive mechanisms (i.e. PDCD1 immune checkpoint activation and tumor F. nucleatum enrichment) tend to be used by different tumor subgroups. [ABSTRACT FROM AUTHOR]

Published
2023
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35. Abstract B002: History of appendectomy and colorectal cancer oncidence, overall and by intratumoral fusobacterium nucleatum status

Author

Ugai, Tomotaka, primary, Kawamura, Hidetaka, additional, Takashima, Yasutoshi, additional, Okadome, Kazuo, additional, Shimizu, Takashi, additional, Mima, Kosuke, additional, Kahaki, Seyed Mostafa Mousavi, additional, Zhao, Melissa, additional, Väyrynen, Juha P., additional, Zhang, Xuehong, additional, Ng, Kimmie, additional, Nowak, Jonathan A., additional, Meyerhardt, Jeffrey A., additional, Giovannucci, Edward L., additional, Giannakis, Marios, additional, Chan, Andrew T., additional, Huttenhower, Curtis, additional, Garrett, Wendy S., additional, Song, Mingyang, additional, and Ogino, Shuji, additional

Published
2022
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36. Additional file 1 of The gut microbiome modifies the associations of short- and long-term physical activity with body weight changes

Author

Wang, Kai, Mehta, Raaj S., Ma, Wenjie, Nguyen, Long H., Wang, Dong D., Ghazi, Andrew R., Yan, Yan, Al-Shaar, Laila, Wang, Yiqing, Hang, Dong, Fu, Benjamin C., Ogino, Shuji, Rimm, Eric B., Hu, Frank B., Carmody, Rachel N., Garrett, Wendy S., Sun, Qi, Chan, Andrew T., Huttenhower, Curtis, and Song, Mingyang

Abstract

Additional file 1: Supplementary Table 1. Characteristics of participants in the Men’s Lifestyle Validation Study according to quartiles of recent physical activity level. Supplementary Table 2. Spearman correlations between the variables of physical activity, body weight, body weight change, and plasma biomarkers. Supplementary Fig. 1. Spearman correlation between long-term total physical activity level and calorie-adjusted dietary intakes of major nutrients at p < 0.05. Supplementary Fig. 2. Principal coordinate analysis of all samples using species-level Bray–Curtis dissimilarity according to recent physical activity level measured by accelerometer. Supplementary Fig. 3. Gut microbial diversity using species taxonomic data according to recent total physical activity measured by accelerometer. Supplementary Fig. 4. Significant associations of physical activity, body weight measures, and plasma biomarkers of hemoglobin A1c (HbA1c) and high-sensitivity C-reactive protein (CRP) with microbial species (q ≤ 0.25). Supplementary Fig. 5. Significant associations of physical activity, body weight measures, and plasma biomarkers of hemoglobin A1c (HbA1c) and high-sensitivity C-reactive protein (CRP) with metagenomic pathways (MetaCyc) (q ≤ 0.25). Supplementary Fig. 6. Significant associations of physical activity, body weight measures, and plasma biomarkers of hemoglobin A1c (HbA1c) and high-sensitivity C-reactive protein (CRP) with metagenomic enzymes (Enzyme Commission, EC) (q ≤ 0.25). Supplementary Fig. 7. Interaction between physical activity measures and the first two principal coordinates axis (PCo1 or PCo2) in relation to body mass index at stool collection, fat mass percentage at stool collection, short-term (6 months) weight change, long-term weight change from age 21 to stool collection, plasma hemoglobin A1c (HbA1c) and high-sensitivity C-reactive protein (CRP). Supplementary Fig. 8. Interaction between physical activity and abundances of the top 10 most abundant species in relation to body mass index at stool collection, fat mass percentage at stool collection, short-term (6 months) weight change, long-term weight change from age 21 to stool collection, plasma hemoglobin A1c (HbA1c) and high-sensitivity C-reactive protein (CRP). Supplementary Fig. 9. Associations between intensity-specific physical activity and body weight measures according to Alistipes putredinis abundance. Supplementary Fig. 10. Relative abundance, prevalence, and interactions of all the species in the genus of Alistipes with physical activity in relation to body mass index at stool collection, fat mass percentage at stool collection, short-term (6 months) weight change, long-term weight change from age 21 to stool collection, plasma hemoglobin A1c (HbA1c) and high-sensitivity C-reactive protein (CRP).

Published
2023
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38. Western-Style Diet, pks Island-Carrying Escherichia coli, and Colorectal Cancer: Analyses From Two Large Prospective Cohort Studies

Author

Arima, Kota, primary, Zhong, Rong, additional, Ugai, Tomotaka, additional, Zhao, Melissa, additional, Haruki, Koichiro, additional, Akimoto, Naohiko, additional, Lau, Mai Chan, additional, Okadome, Kazuo, additional, Mehta, Raaj S., additional, Väyrynen, Juha P., additional, Kishikawa, Junko, additional, Twombly, Tyler S., additional, Shi, Shanshan, additional, Fujiyoshi, Kenji, additional, Kosumi, Keisuke, additional, Ogata, Yoko, additional, Baba, Hideo, additional, Wang, Fenglei, additional, Wu, Kana, additional, Song, Mingyang, additional, Zhang, Xuehong, additional, Fuchs, Charles S., additional, Sears, Cynthia L., additional, Willett, Walter C., additional, Giovannucci, Edward L., additional, Meyerhardt, Jeffrey A., additional, Garrett, Wendy S., additional, Huttenhower, Curtis, additional, Chan, Andrew T., additional, Nowak, Jonathan A., additional, Giannakis, Marios, additional, and Ogino, Shuji, additional

Published
2022
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40. Relating the metatranscriptome and metagenome of the human gut

Author

Franzosa, Eric A., Morgan, Xochitl C., Segata, Nicola, Waldron, Levi, Reyes, Joshua, Earl, Ashlee M., Giannoukos, Georgia, Boylan, Matthew R., Ciulla, Dawn, Gevers, Dirk, Izard, Jacques, Garrett, Wendy S., Chan, Andrew T., and Huttenhower, Curtis

Published
2014

43. Antibody to a conserved antigenic target is protective against diverse prokaryotic and eukaryotic pathogens

Author

Cywes-Bentley, Colette, Skurnik, David, Zaidi, Tanweer, Roux, Damien, Deoliveira, Rosane B., Garrett, Wendy S., Lu, Xi, O'Malley, Jennifer, Kinzel, Kathryn, Zaidi, Tauqeer, Rey, Astrid, Perrin, Christophe, Fichorova, Raina N., Kayatani, Alexander K. K., Maira-Litràn, Tomas, Gening, Marina L., Tsvetkov, Yury E., Nifantiev, Nikolay E., Bakaletz, Lauren O., Pelton, Stephen I., Golenbock, Douglas T., and Pier, Gerald B.

Published
2013

45. Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location

Author

Mima, Kosuke, Cao, Yin, Chan, Andrew T, Qian, Zhi Rong, Nowak, Jonathan A, Masugi, Yohei, Shi, Yan, Song, Mingyang, da Silva, Annacarolina, Gu, Mancang, Li, Wanwan, Hamada, Tsuyoshi, Kosumi, Keisuke, Hanyuda, Akiko, Liu, Li, Kostic, Aleksandar D, Giannakis, Marios, Bullman, Susan, Brennan, Caitlin A, Milner, Danny A, Baba, Hideo, Garraway, Levi A, Meyerhardt, Jeffrey A, Garrett, Wendy S, Huttenhower, Curtis, Meyerson, Matthew, Giovannucci, Edward L, Fuchs, Charles S, Nishihara, Reiko, and Ogino, Shuji

Published
2016
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48. Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response

Author

Spencer, Christine N., primary, McQuade, Jennifer L., additional, Gopalakrishnan, Vancheswaran, additional, McCulloch, John A., additional, Vetizou, Marie, additional, Cogdill, Alexandria P., additional, Khan, Md A. Wadud, additional, Zhang, Xiaotao, additional, White, Michael G., additional, Peterson, Christine B., additional, Wong, Matthew C., additional, Morad, Golnaz, additional, Rodgers, Theresa, additional, Badger, Jonathan H., additional, Helmink, Beth A., additional, Andrews, Miles C., additional, Rodrigues, Richard R., additional, Morgun, Andrey, additional, Kim, Young S., additional, Roszik, Jason, additional, Hoffman, Kristi L., additional, Zheng, Jiali, additional, Zhou, Yifan, additional, Medik, Yusra B., additional, Kahn, Laura M., additional, Johnson, Sarah, additional, Hudgens, Courtney W., additional, Wani, Khalida, additional, Gaudreau, Pierre-Olivier, additional, Harris, Angela L., additional, Jamal, Mohamed A., additional, Baruch, Erez N., additional, Perez-Guijarro, Eva, additional, Day, Chi-Ping, additional, Merlino, Glenn, additional, Pazdrak, Barbara, additional, Lochmann, Brooke S., additional, Szczepaniak-Sloane, Robert A., additional, Arora, Reetakshi, additional, Anderson, Jaime, additional, Zobniw, Chrystia M., additional, Posada, Eliza, additional, Sirmans, Elizabeth, additional, Simon, Julie, additional, Haydu, Lauren E., additional, Burton, Elizabeth M., additional, Wang, Linghua, additional, Dang, Minghao, additional, Clise-Dwyer, Karen, additional, Schneider, Sarah, additional, Chapman, Thomas, additional, Anang, Nana-Ama A. S., additional, Duncan, Sheila, additional, Toker, Joseph, additional, Malke, Jared C., additional, Glitza, Isabella C., additional, Amaria, Rodabe N., additional, Tawbi, Hussein A., additional, Diab, Adi, additional, Wong, Michael K., additional, Patel, Sapna P., additional, Woodman, Scott E., additional, Davies, Michael A., additional, Ross, Merrick I., additional, Gershenwald, Jeffrey E., additional, Lee, Jeffrey E., additional, Hwu, Patrick, additional, Jensen, Vanessa, additional, Samuels, Yardena, additional, Straussman, Ravid, additional, Ajami, Nadim J., additional, Nelson, Kelly C., additional, Nezi, Luigi, additional, Petrosino, Joseph F., additional, Futreal, P. Andrew, additional, Lazar, Alexander J., additional, Hu, Jianhua, additional, Jenq, Robert R., additional, Tetzlaff, Michael T., additional, Yan, Yan, additional, Garrett, Wendy S., additional, Huttenhower, Curtis, additional, Sharma, Padmanee, additional, Watowich, Stephanie S., additional, Allison, James P., additional, Cohen, Lorenzo, additional, Trinchieri, Giorgio, additional, Daniel, Carrie R., additional, and Wargo, Jennifer A., additional

Published
2021
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49. The Sulfur Microbial Diet Is Associated With Increased Risk of Early-Onset Colorectal Cancer Precursors

Author

Nguyen, Long H., primary, Cao, Yin, additional, Hur, Jinhee, additional, Mehta, Raaj S., additional, Sikavi, Daniel R., additional, Wang, Yiqing, additional, Ma, Wenjie, additional, Wu, Kana, additional, Song, Mingyang, additional, Giovannucci, Edward L., additional, Rimm, Eric B., additional, Willett, Walter C., additional, Garrett, Wendy S., additional, Izard, Jacques, additional, Huttenhower, Curtis, additional, and Chan, Andrew T., additional

Published
2021
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