Zobrazeno 1 - 10
of 8 171
pro vyhledávání: '"HUMAN GUT"'
pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes
Autor:
Nicola De Bernardini, Guido Zampieri, Stefano Campanaro, Johannes Zimmermann, Silvio Waschina, Laura Treu
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-25 (2024)
Abstract The accurate reconstruction of genome-scale metabolic models (GEMs) for unculturable species poses challenges due to the incomplete and fragmented genetic information typical of metagenome-assembled genomes (MAGs). While existing tools lever
Externí odkaz:
https://doaj.org/article/67809d26033d4aedab3f807a39e96978
Autor:
Eugeni Belda, Jacqueline Capeau, Jean-Daniel Zucker, Emmanuelle Le Chatelier, Nicolas Pons, Florian Plaza Oñate, Benoit Quinquis, Rohia Alili, Soraya Fellahi, Christine Katlama, Karine Clément, Bruno Fève, Stéphane Jaureguiberry, Cécile Goujard, Olivier Lambotte, Joël Doré, Edi Prifti, Jean-Philippe Bastard
Publikováno v:
BMC Medical Genomics, Vol 17, Iss 1, Pp 1-21 (2024)
Abstract Background Persons living with HIV (PWH) harbor an altered gut microbiome (higher abundance of Prevotella and lower abundance of Bacillota and Ruminococcus lineages) compared to non-infected individuals. Some of these alterations are linked
Externí odkaz:
https://doaj.org/article/7ee4c2305c564879b8a953569a27e899
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-24 (2024)
Abstract Identifying viruses from metagenomes is a common step to explore the virus composition in the human gut. Here, we introduce VirRep, a hybrid language representation learning framework, for identifying viruses from human gut metagenomes. VirR
Externí odkaz:
https://doaj.org/article/341bf682e3ab446b89d916387f132077
Autor:
Bo Zheng, Junming Xu, Yijie Zhang, Junjie Qin, Decai Yuan, Tingting Fan, Weibin Wu, Yan Chen, Yuyang Jiang
Publikováno v:
Heliyon, Vol 10, Iss 18, Pp e37422- (2024)
Metagenomic shotgun sequencing data can identify microbes and their proportions. But metagenomic shotgun data profiling results obtained from multiple projects using different reference databases are difficult to compare and apply meta-analysis. Our
Externí odkaz:
https://doaj.org/article/6d68b5392acf4c4b8490e1a6bf91898a
Autor:
Camille d’Humières, Margot Delavy, Laurie Alla, Farid Ichou, Emilie Gauliard, Amine Ghozlane, Florence Levenez, Nathalie Galleron, Benoit Quinquis, Nicolas Pons, Jimmy Mullaert, Antoine Bridier-Nahmias, Bénédicte Condamine, Marie Touchon, Dominique Rainteau, Antonin Lamazière, Philippe Lesnik, Maharajah Ponnaiah, Marie Lhomme, Natacha Sertour, Savannah Devente, Jean-Denis Docquier, Marie-Elisabeth Bougnoux, Olivier Tenaillon, Mélanie Magnan, Etienne Ruppé, Nathalie Grall, Xavier Duval, Dusko Ehrlich, France Mentré, Erick Denamur, Eduardo P. C. Rocha, Emmanuelle Le Chatelier, Charles Burdet, for the PrediRes study group
Publikováno v:
Microbiome, Vol 12, Iss 1, Pp 1-19 (2024)
Abstract Background Antibiotics notoriously perturb the gut microbiota. We treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days, and collected in each subject 12 faecal samples up to day 90. Using untargeted and targeted phenot
Externí odkaz:
https://doaj.org/article/868dc641a38f41ccb98c0e6e9993a156
Autor:
Sungho Lee, Insuk Lee
Publikováno v:
Gut Microbes, Vol 16, Iss 1 (2024)
The gut microbiome, linked significantly to host diseases, offers potential for disease diagnosis through machine learning (ML) pipelines. These pipelines, crucial in modeling diseases using high-dimensional microbiome data, involve selecting profile
Externí odkaz:
https://doaj.org/article/eaf044b4aeab455bafc8101c655ad768
Autor:
Wen‐Bing Jin, Chun‐Jun Guo
Publikováno v:
iMeta, Vol 3, Iss 4, Pp n/a-n/a (2024)
Abstract Hundreds of microbiota gene expressions are significantly different between healthy and diseased humans. The “bottleneck” preventing a mechanistic dissection of how they affect host biology/disease is that many genes are encoded by nonmo
Externí odkaz:
https://doaj.org/article/2e734eeae3f64cf68f87a604685f5601
Publikováno v:
Frontiers in Microbiology, Vol 15 (2024)
In this study, we present MetaBakery (http://metabakery.fe.uni-lj.si), an integrated application designed as a framework for synergistically executing the bioBakery workflow and associated utilities. MetaBakery streamlines the processing of any numbe
Externí odkaz:
https://doaj.org/article/a97bb990f53e4ea7b6b7e2dfdbaaa806
Publikováno v:
Frontiers in Microbiomes, Vol 3 (2024)
IntroductionThe human gut microbiome harbors millions of bacterial species, including opportunistic pathogens, and this microbial community is exposed to antimicrobial agents present in food, the external environment, or drugs. Thus, it increases the
Externí odkaz:
https://doaj.org/article/34039d505c9c477688500b99b9c44cc2
Publikováno v:
Frontiers in Microbiology, Vol 15 (2024)
The concept of “enterotypes” in microbiome research has attracted substantial interest, particularly focusing on the abundance of Prevotella spp. in the human gut. In this study, the intricate dynamics of Prevotella spp. in the human gut microbio
Externí odkaz:
https://doaj.org/article/e958125bb5104af4a9c78d02b6ffd4c0