المؤلفون: Gentry, Emily C, Collins, Stephanie L, Panitchpakdi, Morgan, Belda-Ferre, Pedro, Stewart, Allison K, Carrillo Terrazas, Marvic, Lu, Hsueh-han, Zuffa, Simone, Yan, Tingting, Avila-Pacheco, Julian, Plichta, Damian R, Aron, Allegra T, Wang, Mingxun, Jarmusch, Alan K, Hao, Fuhua, Syrkin-Nikolau, Mashette, Vlamakis, Hera, Ananthakrishnan, Ashwin N, Boland, Brigid S, Hemperly, Amy, Vande Casteele, Niels, Gonzalez, Frank J, Clish, Clary B, Xavier, Ramnik J, Chu, Hiutung, Baker, Erin S, Patterson, Andrew D, Knight, Rob, Siegel, Dionicio, Dorrestein, Pieter C

المصدر: Nature. 626(7998)

مصطلحات موضوعية: Medical Biochemistry and Metabolomics, Analytical Chemistry, Biomedical and Clinical Sciences, Chemical Sciences, Inflammatory Bowel Disease, Digestive Diseases, Crohn's Disease, Prevention, Animals, Humans, Bifidobacterium, Bile Acids and Salts, CD4-Positive T-Lymphocytes, Clostridium, Cohort Studies, Crohn Disease, Enterococcus, Esters, Fatty Acids, Inflammatory Bowel Diseases, Metabolomics, Phenotype, Pregnane X Receptor, Reproducibility of Results, Tandem Mass Spectrometry, Amides, General Science & Technology

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/9tp855xwTest

المؤلفون: Vatanen, Tommi, Ang, Qi Yan, Siegwald, Léa, Sarker, Shafiqul Alam, Le Roy, Caroline I., Duboux, Stéphane, Delannoy-Bruno, Omar, Ngom-Bru, Catherine, Boulangé, Claire L., Stražar, Martin, Avila-Pacheco, Julian, Deik, Amy, Pierce, Kerry, Bullock, Kevin, Dennis, Courtney, Sultana, Shamima, Sayed, Sharika, Rahman, Mahbubar, Ahmed, Tahmeed, Modesto, Monica, Mattarelli, Paola, Clish, Clary B., Vlamakis, Hera, Plichta, Damian R., Sakwinska, Olga, Xavier, Ramnik J.

المساهمون: CAMM - Research Program for Clinical and Molecular Metabolism, University of Helsinki, Faculty Common Matters (Faculty of Medicine)

مصطلحات موضوعية: bifidobacteria, Bifidobacterium longum, breastfeeding, diarrhea, gut metabolome, infant growth, infant gut, microbiome, weaning, 3111 Biomedicine, 1182 Biochemistry, cell and molecular biology

وصف الملف: application/pdf

العلاقة: Finally, B. longum subsp. infantis and its associated metabolites, such as indolelactate, were positively correlated with two measures of growth (WFL and WFA) in our cohort, thus adding to a growing body of evidence supporting the importance of B. longum subsp. infantis and its metabolites for infant development (Barratt et al., 2022). We found N-acetylglutamate levels in the stool, as well as two microbial pathways involving N-acetylglutamate, to be positively associated with all tested growth measures including LFA. This observation is notable since bacterially produced N-acetyl amino acids enhanced growth in a Drosophila model (Gallo et al., 2021; Martino et al., 2018). A more recent study provided mechanistic insights on how a related compound, N-acetylglutamine, promoted growth in a Drosophila model via down-regulation of a peptidoglycan recognition protein and immune effectors against beneficial microbes, thus providing an intriguing example of host-microbe symbiosis wherein bacterial metabolic products mediate host immune regulation and growth (Gallo et al., 2021; Martino et al., 2018).We would like to thank participants and their families for their involvement in the study. We thank Tiffany Poon, Luke Besse, and Sara Garamszegi for project management of sample processing and data handling. We thank Florence Rochat, Nadine Porta, Anne Bruttin and Solenn Pruvost for technical assistance in obtaining and sequencing bacterial isolates. We also thank the Broad Institute Genomics Platform and Microbial ‘Omics Core for help with sequencing data generation and sample processing. We are grateful to Heather Kang for editorial assistance. Generation of metagenomics and metabolomics data was supported by a grant from Nestle to the Broad Institute (H.V.). Principal investigators, T.V. O.S. H.V. and R.J.X.; metagenomic data analysis, T.V. Q.Y.A. L.S. and D.R.P.; metabolomic data analysis, T.V. Q.Y.A. M.S. A.D. K.P. K.B. C.D. J.A.-P. and C.B.C.; bacterial isolation and genome sequencing and annotation, L.S. S.D. C.N.-B. and O.S.; phylogenetic and functional genomic analyses: T.V. L.S. S.D. C.N.-B. and O.D.-B.; study design, S.A.S. and T.A.; collection of samples and health information, S.A.S. S.Sayed, S.Sultana, and M.R.; manuscript drafting: T.V. Q.Y.A. L.S. C.I.L.R. C.L.B. D.R.P. S.D. O.D.-B. O.S. and R.J.X. All authors discussed the results, critically reviewed the text, and approved the final manuscript. L.S. C.L.B. C.I.L.R. S.D. O.D-B. C.N-B. and O.S. are employees of Société des Produits Nestlé (SPN). R.J.X. is a member of the Scientific Advisory Board at Nestlé, founder of Jnana and Celsius Therapeutics and board member of MoonLake Immunotherapeutics. We filed a patent related to findings described in this study. R.J.X. H.V. T.V. O.S. L.S. S.D. and C.N.-B. are listed as inventors (Bifidobacterium Longum Transitional Microorganisms, Compositions and Uses Thereof, PCT/US2022/035,310). We would like to thank participants and their families for their involvement in the study. We thank Tiffany Poon, Luke Besse, and Sara Garamszegi for project management of sample processing and data handling. We thank Florence Rochat, Nadine Porta, Anne Bruttin and Solenn Pruvost for technical assistance in obtaining and sequencing bacterial isolates. We also thank the Broad Institute Genomics Platform and Microbial ‘Omics Core for help with sequencing data generation and sample processing. We are grateful to Heather Kang for editorial assistance. Generation of metagenomics and metabolomics data was supported by a grant from Nestle to the Broad Institute (H.V.).; Vatanen , T , Ang , Q Y , Siegwald , L , Sarker , S A , Le Roy , C I , Duboux , S , Delannoy-Bruno , O , Ngom-Bru , C , Boulangé , C L , Stražar , M , Avila-Pacheco , J , Deik , A , Pierce , K , Bullock , K , Dennis , C , Sultana , S , Sayed , S , Rahman , M , Ahmed , T , Modesto , M , Mattarelli , P , Clish , C B , Vlamakis , H , Plichta , D R , Sakwinska , O & Xavier , R J 2022 , ' A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning ' , Cell , vol. 185 , no. 23 , pp. 4280-4297.e12 . https://doi.org/10.1016/j.cell.2022.10.011Test; ORCID: /0000-0003-0949-1291/work/128033163; http://hdl.handle.net/10138/573344Test; 51bb33c1-fd6c-48ca-bf9d-c4596edd9d6e; 85141522383; 000908351600006

الإتاحة: http://hdl.handle.net/10138/573344Test

المؤلفون: Vatanen, Tommi, Jabbar, Karolina S., Ruohtula, Terhi, Honkanen, Jarno, Avila-Pacheco, Julian, Siljander, Heli, Stražar, Martin, Oikarinen, Sami, Hyöty, Heikki, Ilonen, Jorma, Mitchell, Caroline M., Yassour, Moran, Virtanen, Suvi M., Clish, Clary B., Plichta, Damian R., Vlamakis, Hera, Knip, Mikael, Xavier, Ramnik J.

المساهمون: CAMM - Research Program for Clinical and Molecular Metabolism, Faculty Common Matters (Faculty of Medicine), University of Helsinki, Children's Hospital, Helsinki University Hospital Area, HUS Children and Adolescents, Clinicum

مصطلحات موضوعية: gut metabolome, horizontal gene transfer, infant gut microbiome, mother-to-infant microbiome transmission, 3111 Biomedicine, 1182 Biochemistry, cell and molecular biology

وصف الملف: application/pdf

العلاقة: We thank Tiffany Poon, Luke Besse, and Timothy Arthur for sample and data management and Theresa Reimels for editorial assistance and figure preparation. This work was funded by the National Institutes of Health ( P30 DK043351 to R.J.X.), Juvenile Diabetes Research Foundation ( 2-SRA-2016-247-S-B ), Center for Microbiome Informatics and Therapeutics, and Wallenberg Foundations (to K.S.J.). M.Y. is the Rosalind, Paul and Robin Berlin Faculty Development Chair in Perinatal Research. We thank Tiffany Poon, Luke Besse, and Timothy Arthur for sample and data management and Theresa Reimels for editorial assistance and figure preparation. This work was funded by the National Institutes of Health (P30 DK043351 to R.J.X.), Juvenile Diabetes Research Foundation (2-SRA-2016-247-S-B), Center for Microbiome Informatics and Therapeutics, and Wallenberg Foundations (to K.S.J.). M.Y. is the Rosalind, Paul and Robin Berlin Faculty Development Chair in Perinatal Research. T.V. H.V. M.K. and R.J.X. served as principal investigators. T.V. and K.S.J. analyzed metagenomic data. T.V. K.S.J. J.A.-P. M.S. C.B.C. and D.R.P. analyzed metabolomic data. T.R. analyzed intestinal biomarkers. J.H. analyzed cytokines. T.R. J.H. H.S. S.O. H.H. J.I. S.M.V. and M.K. contributed to collection of stool and blood samples and patient information. M.Y. and C.M.M. collected breast milk samples. T.V. K.S.J. D.R.P. H.V. and R.J.X. drafted the manuscript. All authors discussed the results, critically reviewed the text, and approved the final manuscript. R.J.X. is co-founder of Jnana Therapeutics and Celsius Therapeutics, board director at MoonLake Immunotherapeutics, and consultant to Nestlé; these organizations had no role in the study.; Vatanen , T , Jabbar , K S , Ruohtula , T , Honkanen , J , Avila-Pacheco , J , Siljander , H , Stražar , M , Oikarinen , S , Hyöty , H , Ilonen , J , Mitchell , C M , Yassour , M , Virtanen , S M , Clish , C B , Plichta , D R , Vlamakis , H , Knip , M & Xavier , R J 2022 , ' Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism ' , Cell , vol. 185 , no. 26 , pp. 4921-4936.e15 . https://doi.org/10.1016/j.cell.2022.11.023Test , https://doi.org/10.1016/j.cell.2022.11.023Test; ORCID: /0000-0002-2779-3384/work/128032679; ORCID: /0000-0003-0949-1291/work/128033162; 85144246023; b361273f-28e6-4eab-a116-e5c6f415caea; http://hdl.handle.net/10138/569828Test; 000910695500001

الإتاحة: http://hdl.handle.net/10138/569828Test

المؤلفون: Li, Chenhao, Stražar, Martin, Mohamed, Ahmed M.T., Pacheco, Julian A., Walker, Rebecca L., Lebar, Tina, Zhao, Shijie, Lockart, Julia, Dame, Andrea, Thurimella, Kumar, Jeanfavre, Sarah, Brown, Eric M., Ang, Qi Yan, Berdy, Brittany, Sergio, Dallis, Invernizzi, Rachele, Tinoco, Antonio, Pishchany, Gleb, Vasan, Ramachandran S., Balskus, Emily, Huttenhower, Curtis, Vlamakis, Hera, Clish, Clary, Shaw, Stanley Y., Plichta, Damian R., Xavier, Ramnik J.

المساهمون: National Institutes of Health

المصدر: Cell ; volume 187, issue 8, page 1834-1852.e19 ; ISSN 0092-8674

مصطلحات موضوعية: General Biochemistry, Genetics and Molecular Biology

الإتاحة: https://doi.org/10.1016/j.cell.2024.03.014Test
https://api.elsevier.com/content/article/PII:S0092867424003052?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S0092867424003052?httpAccept=text/plainTest

المؤلفون: Kenny, Douglas J., Plichta, Damian R., Shungin, Dmitry, Koppel, Nitzan, Hall, A. Brantley, Fu, Beverly, Vasan, Ramachandran S., Shaw, Stanley Y., Vlamakis, Hera, Balskus, Emily P., Xavier, Ramnik J.

المصدر: Cell Host and Microbe. 28(2):245-257

وصف الملف: electronic

الوصول الحر: https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-174956Test
https://doi.org/10.1016/j.chom.2020.05.013Test
https://umu.diva-portal.org/smash/get/diva2:1469559/FULLTEXT01.pdfTest

المؤلفون: Ansaldo, Eduard, Slayden, Leianna C, Ching, Krystal L, Koch, Meghan A, Wolf, Natalie K, Plichta, Damian R, Brown, Eric M, Graham, Daniel B, Xavier, Ramnik J, Moon, James J, Barton, Gregory M

المصدر: Science. 364(6446)

مصطلحات موضوعية: Biodefense, Emerging Infectious Diseases, Digestive Diseases, Vaccine Related, Prevention, Underpinning research, 1.1 Normal biological development and functioning, Inflammatory and immune system, Adaptive Immunity, Animals, Cell Movement, Female, Gastrointestinal Microbiome, Germ-Free Life, Homeostasis, Immunity, Mucosal, Immunoglobulin G, Intestinal Mucosa, Intestines, Male, Mice, Mice, Inbred C57BL, T-Lymphocytes, Helper-Inducer, Verrucomicrobia, General Science & Technology

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/2th6084xTest

المؤلفون: Lloyd-Price, Jason, Arze, Cesar, Ananthakrishnan, Ashwin N, Schirmer, Melanie, Avila-Pacheco, Julian, Poon, Tiffany W, Andrews, Elizabeth, Ajami, Nadim J, Bonham, Kevin S, Brislawn, Colin J, Casero, David, Courtney, Holly, Gonzalez, Antonio, Graeber, Thomas G, Hall, A Brantley, Lake, Kathleen, Landers, Carol J, Mallick, Himel, Plichta, Damian R, Prasad, Mahadev, Rahnavard, Gholamali, Sauk, Jenny, Shungin, Dmitry, Vázquez-Baeza, Yoshiki, White, Richard A, IBDMDB Investigators, Braun, Jonathan, Denson, Lee A, Jansson, Janet K, Knight, Rob, Kugathasan, Subra, McGovern, Dermot PB, Petrosino, Joseph F, Stappenbeck, Thaddeus S, Winter, Harland S, Clish, Clary B, Franzosa, Eric A, Vlamakis, Hera, Xavier, Ramnik J, Huttenhower, Curtis

المصدر: Nature. 569(7758)

مصطلحات موضوعية: IBDMDB Investigators, Animals, Humans, Viruses, Fungi, Inflammatory Bowel Diseases, Phylogeny, Species Specificity, Health, Transcriptome, Gastrointestinal Microbiome, General Science & Technology

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/0cr648dzTest

المؤلفون: Gentry, Emily C., Collins, Stephanie L., Panitchpakdi, Morgan, Belda-Ferre, Pedro, Stewart, Allison K., Carrillo Terrazas, Marvic, Lu, Hsueh-han, Zuffa, Simone, Yan, Tingting, Avila-Pacheco, Julian, Plichta, Damian R., Aron, Allegra T., Wang, Mingxun, Jarmusch, Alan K., Hao, Fuhua, Syrkin-Nikolau, Mashette, Vlamakis, Hera, Ananthakrishnan, Ashwin N., Boland, Brigid S., Hemperly, Amy, Vande Casteele, Niels, Gonzalez, Frank J., Clish, Clary B., Xavier, Ramnik J., Chu, Hiutung, Baker, Erin S., Patterson, Andrew D., Knight, Rob, Siegel, Dionicio, Dorrestein, Pieter C.

المصدر: Nature ; volume 626, issue 7998, page 419-426 ; ISSN 0028-0836 1476-4687

مصطلحات موضوعية: Multidisciplinary

الإتاحة: https://doi.org/10.1038/s41586-023-06906-8Test
https://www.nature.com/articles/s41586-023-06906-8.pdfTest
https://www.nature.com/articles/s41586-023-06906-8Test

المؤلفون: Scheid, Johannes F., Eraslan, Basak, Hudak, Andrew, Brown, Eric M., Sergio, Dallis, Delorey, Toni M., Phillips, Devan, Lefkovith, Ariel, Jess, Alison T., Duck, Lennard W., Elson, Charles O., Vlamakis, Hera, Plichta, Damian R., Deguine, Jacques, Ananthakrishnan, Ashwin N., Graham, Daniel B., Regev, Aviv, Xavier, Ramnik J.

المساهمون: National Institutes of Health, Crohn's and Colitis Foundation, Klarman Cell Observatory

المصدر: Journal of Experimental Medicine ; volume 220, issue 4 ; ISSN 0022-1007 1540-9538

الإتاحة: https://doi.org/10.1084/jem.20220538Test

المؤلفون: Stražar, Martin, Park, Jihye, Abelin, Jennifer G., Taylor, Hannah B., Pedersen, Thomas K., Plichta, Damian R., Brown, Eric M., Eraslan, Basak, Hung, Yuan-Mao, Ortiz, Kayla, Clauser, Karl R., Carr, Steven A., Xavier, Ramnik J., Graham, Daniel B.

المصدر: Immunity ; volume 56, issue 7, page 1681-1698.e13 ; ISSN 1074-7613

مصطلحات موضوعية: Infectious Diseases, Immunology, Immunology and Allergy

الإتاحة: https://doi.org/10.1016/j.immuni.2023.05.009Test
https://api.elsevier.com/content/article/PII:S1074761323002261?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S1074761323002261?httpAccept=text/plainTest