Search

Your search keyword '"Carter, Matthew M"' showing total 24 results
Start Over Author "Carter, Matthew M"
24 results on '"Carter, Matthew M"'

2. Cell types of origin of the cell-free transcriptome

Author

Jones, Robert C, Karkanias, Jim, Krasnow, Mark, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D’Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Vorperian, Sevahn K, Wang, Wanxin, Weinstein, Hannah NW, Winkler, Juliane, Wu, Timothy TH, Xie, Jamie, and Yung, Andrea R

Subjects
Human Genome, Genetics, Cell-Free Nucleic Acids, Humans, Transcriptome, Tabula Sapiens Consortium
Abstract

Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the Tabula Sapiens transcriptomic cell atlas as well as individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset. We define cell type signature scores, which allow the inference of cell types that contribute to cell-free RNA for a variety of diseases.

Published
2022

3. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Author

Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Vorperian, Sevahn K, Wang, Wanxin, Weinstein, Hannah NW, Winkler, Juliane, Wu, Timothy TH, Xie, Jamie, Yung, Andrea R, Zhang, Yue, and Detweiler, Angela M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Atlases as Topic, B-Lymphocytes, Cells, Humans, Organ Specificity, RNA Splicing, Single-Cell Analysis, T-Lymphocytes, Transcriptome, Tabula Sapiens Consortium*, General Science & Technology
Abstract

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Published
2022

4. Assessing the effects of alternative plant-based meats v. animal meats on biomarkers of inflammation: a secondary analysis of the SWAP-MEAT randomized crossover trial

Author

Crimarco, Anthony, Landry, Matthew J, Carter, Matthew M, and Gardner, Christopher D

Subjects
Epidemiology, Biomedical and Clinical Sciences, Nutrition and Dietetics, Health Sciences, Clinical Trials and Supportive Activities, Clinical Research, Nutrition, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Animals, Cross-Over Studies, Meat, Biomarkers, Inflammation, Dietary intervention, Plant-based meat, Red meat, Nutrition and dietetics
Abstract

Alternative plant-based meats have grown in popularity with consumers recently and researchers are examining the potential health effects, or risks, from consuming these products. Because there have been no studies to date that have specifically assessed the health effects of plant-based meats on biomarkers of inflammation, the purpose of this work was to conduct a secondary analysis of the Study With Appetizing Plantfood - Meat Eating Alternatives Trial (SWAP-MEAT). SWAP-MEAT was a randomised crossover trial that involved generally healthy adults eating 2 or more servings of plant-based meats per day for 8 weeks (i.e. Plant phase) followed by 2 or more servings of animal meats per day for 8 weeks (i.e. Animal phase). Results of linear mixed-effects models indicated only 4 out of 92 biomarkers reached statistical significance. The results were contrary to our hypothesis, since we expected relative improvements in biomarkers of inflammation from the plant-based meats.

Published
2022

6. Author Correction: Mapping the genomic landscape of CRISPR–Cas9 cleavage

Author

Cameron, Peter, Fuller, Chris K., Donohoue, Paul D., Jones, Brittnee N., Thompson, Matthew S., Carter, Matthew M., Gradia, Scott, Vidal, Bastien, Garner, Elizabeth, Slorach, Euan M., Lau, Elaine, Banh, Lynda M., Lied, Alexandra M., Edwards, Leslie S., Settle, Alexander H., Capurso, Daniel, Llaca, Victor, Deschamps, Stéphane, Cigan, Mark, Young, Joshua K., and May, Andrew P.

Published
2023
Full Text
View/download PDF

8. Unveiling the epigenetic impact of vegan vs. omnivorous diets on aging: insights from the Twins Nutrition Study (TwiNS).

Author

Dwaraka, Varun B., Aronica, Lucia, Carreras-Gallo, Natalia, Robinson, Jennifer L., Hennings, Tayler, Carter, Matthew M., Corley, Michael J., Lin, Aaron, Turner, Logan, Smith, Ryan, Mendez, Tavis L., Went, Hannah, Ebel, Emily R., Sonnenburg, Erica D., Sonnenburg, Justin L., and Gardner, Christopher D.

Subjects
VEGANISM, EPIGENETICS, TWIN studies, DIET, DNA methylation
Abstract

Background : Geroscience focuses on interventions to mitigate molecular changes associated with aging. Lifestyle modifications, medications, and social factors influence the aging process, yet the complex molecular mechanisms require an in-depth exploration of the epigenetic landscape. The specific epigenetic clock and predictor effects of a vegan diet, compared to an omnivorous diet, remain underexplored despite potential impacts on aging-related outcomes. Methods: This study examined the impact of an entirely plant-based or healthy omnivorous diet over 8 weeks on blood DNA methylation in paired twins. Various measures of epigenetic age acceleration (PC GrimAge, PC PhenoAge, DunedinPACE) were assessed, along with system-specific effects (Inflammation, Heart, Hormone, Liver, and Metabolic). Methylation surrogates of clinical, metabolite, and protein markers were analyzed to observe diet-specific shifts. Results: Distinct responses were observed, with the vegan cohort exhibiting significant decreases in overall epigenetic age acceleration, aligning with anti-aging effects of plant-based diets. Diet-specific shifts were noted in the analysis of methylation surrogates, demonstrating the influence of diet on complex trait prediction through DNA methylation markers. An epigenome-wide analysis revealed differentially methylated loci specific to each diet, providing insights into the affected pathways. Conclusions: This study suggests that a short-term vegan diet is associated with epigenetic age benefits and reduced calorie intake. The use of epigenetic biomarker proxies (EBPs) highlights their potential for assessing dietary impacts and facilitating personalized nutrition strategies for healthy aging. Future research should explore the long-term effects of vegan diets on epigenetic health and overall well-being, considering the importance of proper nutrient supplementation. Trial registration: Clinicaltrials.gov identifier: NCT05297825 [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

9. Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition

Author

Gerrick, Elias R., primary, Zlitni, Soumaya, additional, West, Patrick T., additional, Carter, Matthew M., additional, Mechler, Claire M., additional, Olm, Matthew R., additional, Caffrey, Elisa B., additional, Li, Jessica A., additional, Higginbottom, Steven K., additional, Severyn, Christopher J., additional, Kracke, Frauke, additional, Spormann, Alfred M., additional, Sonnenburg, Justin L., additional, Bhatt, Ami S., additional, and Howitt, Michael R., additional

Published
2023
Full Text
View/download PDF

11. Butyrate Differentiates Permissiveness to Clostridioides difficile Infection and Influences Growth of Diverse C. difficile Isolates

Author

Pensinger, Daniel A., primary, Fisher, Andrea T., additional, Dobrila, Horia A., additional, Van Treuren, William, additional, Gardner, Jackson O., additional, Higginbottom, Steven K., additional, Carter, Matthew M., additional, Schumann, Benjamin, additional, Bertozzi, Carolyn R., additional, Anikst, Victoria, additional, Martin, Cody, additional, Robilotti, Elizabeth V., additional, Chow, Jo May, additional, Buck, Rachael H., additional, Tompkins, Lucy S., additional, Sonnenburg, Justin L., additional, and Hryckowian, Andrew J., additional

Published
2023
Full Text
View/download PDF

12. A microbiome‐targeting fibre‐enriched nutritional formula is well tolerated and improves quality of life and haemoglobin A1c in type 2 diabetes: A double‐blind , randomized, placebo‐controlled trial

Author

Frias, Juan P., primary, Lee, Martin L., additional, Carter, Matthew M., additional, Ebel, Emily R., additional, Lai, Ren‐Hau, additional, Rikse, Lars, additional, Washington, Marc E., additional, Sonnenburg, Justin L., additional, and Damman, Christopher J., additional

Published
2023
Full Text
View/download PDF

13. Mapping the genomic landscape of CRISPR–Cas9 cleavage

Author

Cameron, Peter, Fuller, Chris K, Donohoue, Paul D, Jones, Brittnee N, Thompson, Matthew S, Carter, Matthew M, Gradia, Scott, Vidal, Bastien, Garner, Elizabeth, Slorach, Euan M, Lau, Elaine, Banh, Lynda M, Lied, Alexandra M, Edwards, Leslie S, Settle, Alexander H, Capurso, Daniel, Llaca, Victor, Deschamps, Stéphane, Cigan, Mark, Young, Joshua K, and May, Andrew P

Published
2017
Full Text
View/download PDF

14. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Author

Tabula Sapiens Consortium, Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, and Vo, Kim Chi

Subjects
B-Lymphocytes, General Science & Technology, Cells, T-Lymphocytes, RNA Splicing, Human Genome, Tabula Sapiens Consortium, Atlases as Topic, Organ Specificity, Genetics, Humans, Generic health relevance, Single-Cell Analysis, Transcriptome, Biotechnology
Abstract

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Published
2022

15. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles

Author

Olm, Matthew R., primary, Dahan, Dylan, additional, Carter, Matthew M., additional, Merrill, Bryan D., additional, Yu, Feiqiao B., additional, Jain, Sunit, additional, Meng, Xiandong, additional, Tripathi, Surya, additional, Wastyk, Hannah, additional, Neff, Norma, additional, Holmes, Susan, additional, Sonnenburg, Erica D., additional, Jha, Aashish R., additional, and Sonnenburg, Justin L., additional

Published
2022
Full Text
View/download PDF

16. Butyrate differentiates permissiveness to Clostridioides difficile infection and influences growth of diverse C. difficile isolates

Author

Pensinger, Daniel A., primary, Fisher, Andrea T., additional, Dobrila, Horia A., additional, Van Treuren, William, additional, Gardner, Jackson O., additional, Higginbottom, Steven K., additional, Carter, Matthew M., additional, Schumann, Benjamin, additional, Bertozzi, Carolyn R., additional, Anikst, Victoria, additional, Martin, Cody, additional, Robilotti, Elizabeth V., additional, Chow, JoMay, additional, Buck, Rachael H., additional, Tompkins, Lucy S., additional, Sonnenburg, Justin L., additional, and Hryckowian, Andrew J., additional

Published
2022
Full Text
View/download PDF

18. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.

Author

Tabula Sapiens Consortium*, Tabula Sapiens Consortium*, Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Tabula Sapiens Consortium*, Tabula Sapiens Consortium*, Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, and Vo, Kim Chi

Abstract

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Published
2022

19. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes

Author

Merrill, Bryan D., primary, Carter, Matthew M., additional, Olm, Matthew R., additional, Dahan, Dylan, additional, Tripathi, Surya, additional, Spencer, Sean P., additional, Yu, Brian, additional, Jain, Sunit, additional, Neff, Norma, additional, Jha, Aashish R., additional, Sonnenburg, Erica D., additional, and Sonnenburg, Justin L., additional

Published
2022
Full Text
View/download PDF

22. A randomized crossover trial on the effect of plant-based compared with animal-based meat on trimethylamine-N-oxide and cardiovascular disease risk factors in generally healthy adults: Study With Appetizing Plantfood—Meat Eating Alternative Trial (SWAP-MEAT)

Author

Crimarco, Anthony, primary, Springfield, Sparkle, additional, Petlura, Christina, additional, Streaty, Taylor, additional, Cunanan, Kristen, additional, Lee, Justin, additional, Fielding-Singh, Priya, additional, Carter, Matthew M, additional, Topf, Madeline A, additional, Wastyk, Hannah C, additional, Sonnenburg, Erica D, additional, Sonnenburg, Justin L, additional, and Gardner, Christopher D, additional

Published
2020
Full Text
View/download PDF

23. DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

Author

van Overbeek, Megan, primary, Capurso, Daniel, additional, Carter, Matthew M., additional, Thompson, Matthew S., additional, Frias, Elizabeth, additional, Russ, Carsten, additional, Reece-Hoyes, John S., additional, Nye, Christopher, additional, Gradia, Scott, additional, Vidal, Bastien, additional, Zheng, Jiashun, additional, Hoffman, Gregory R., additional, Fuller, Christopher K., additional, and May, Andrew P., additional

Published
2016
Full Text
View/download PDF

24. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes.

Author

Merrill BD, Carter MM, Olm MR, Dahan D, Tripathi S, Spencer SP, Yu B, Jain S, Neff N, Jha AR, Sonnenburg ED, and Sonnenburg JL

Abstract

The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing and strain cultivation on 351 fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophages, and eukaryotes, 43% of which are absent from existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, high-resolution strain tracking, and 124 gut-resident species vanishing in industrialized populations reveals differentiating dynamics of the Hadza gut microbiome. Industrialized gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource that expands our understanding of microbes capable of colonizing the human gut and clarifies the extensive perturbation brought on by the industrialized lifestyle.

Published
2022
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results