Genome binning of viral entities from bulk metagenomics data

Autor: Joachim Johansen, Damian R. Plichta, Jakob Nybo Nissen, Marie Louise Jespersen, Shiraz A. Shah, Ling Deng, Jakob Stokholm, Hans Bisgaard, Dennis Sandris Nielsen, Søren J. Sørensen, Simon Rasmussen

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-12 (2022)

Here, Johansen et al. develop an approach, Phages from Metagenomics Binning (PHAMB), that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate t

Externí odkaz: https://doaj.org/article/2c44accba90c47bbab7eeacd53765ca3

Impact of the rumen microbiome on milk fatty acid composition of Holstein cattle

Autor: Bart Buitenhuis, Jan Lassen, Samantha Joan Noel, Damian R. Plichta, Peter Sørensen, Gareth F. Difford, Nina A. Poulsen

Publikováno v: Genetics Selection Evolution, Vol 51, Iss 1, Pp 1-8 (2019)

Abstract Background Fatty acids (FA) in bovine milk derive through body mobilization, de novo synthesis or from the feed via the blood stream. To be able to digest feedstuff, the cow depends on its rumen microbiome. The relative abundance of the micr

Externí odkaz: https://doaj.org/article/594c6c0abee844fc9aa8815db8f83721

Discovery of bioactive microbial gene products in inflammatory bowel disease

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

Publikováno v: Nature

Microbial communities and their associated bioactive compounds(1–3) are often disrupted in conditions such as the inflammatory bowel diseases (IBD)(4). However, even in well-characterized environments (for example, the human gastrointestinal tract)

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c023b8fe6a301666aaa08dbcf916265c
https://doi.org/10.1038/s41586-022-04648-7

Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1

Autor: Peter J. Oefner, Damian R. Plichta, Anders Ø. Petersen, Daniel C. Chung, Wolfram Gronwald, Ramnik J. Xavier, Annamari Ranki, Hera Vlamakis, Martta Jokinen, Gerhard Liebisch, Katja Dettmer

Publikováno v: J Allergy Clin Immunol
Petersen, A, Jokinen, M, Plichta, D R, Liebisch, G, Gronwald, W, Dettmer, K, Oefner, P J, Vlamakis, H, Chung, D C, Ranki, A & Xavier, R J 2021, ' Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1 ', Journal of Allergy and Clinical Immunology, vol. 148, no. 3, pp. 876-888 . https://doi.org/10.1016/j.jaci.2021.03.025

BACKGROUND: Gastrointestinal dysfunction is a frequent and disabling manifestation of autoimmune polyendocrine syndrome type 1 (APS-1), a rare monogenic multi-organ autoimmune disease caused by the loss of central AIRE-controlled immune tolerance. OB

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::808656f1200240d39f165329158bc32e
https://doi.org/10.1016/j.jaci.2021.03.025

Association of distinct microbial signatures with premalignant colorectal adenomas

Autor: Jonathan Wei Jie Lee, Damian R. Plichta, Shreya Asher, Marisa Delsignore, Tiffany Jeong, Jessica McGoldrick, Kyle Staller, Hamed Khalili, Ramnik J. Xavier, Daniel C. Chung

Publikováno v: Cell Host & Microbe. 31:827-838.e3

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::99b0eb85f61657677ad6e338d8b62844
https://doi.org/10.1016/j.chom.2023.04.007