Results 11 to 20 of about 13,896 (217)

Comparison between metatranscriptomics and viral metagenomics, 16S, and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response [PDF]

Frontiers in Microbiology
IntroductionOmics-based studies focusing on a single kingdom, such as bacterial 16S gene sequencing, viral metagenomics, and human mRNA sequencing, are commonly used to explore the microbiome and its association with host responses.
Gregory Destras, Gregory Destras, Marina Sabatier, Marina Sabatier, Antonin Bal, Antonin Bal, Bruno Simon, Bruno Simon, Quentin Semanas, Hadrien Regue, Theophile Boyer, Dominique Ploin, Yves Gillet, Bruno Lina, Bruno Lina, Hussein Anani, Laurence Josset, Laurence Josset   +17 more
doaj   +2 more sources

Metatranscriptomics for Understanding the Microbiome in Food and Nutrition Science [PDF]

Metabolites
Microbiome science has greatly expanded our understanding of the diverse composition and function of gut microorganisms over the past decades. With its rich microbial composition, the microbiome hosts numerous functionalities essential for metabolizing ...
Christina F. Butowski, Yash Dixit, Marlon M. Reis, Chunlong Mu   +3 more
doaj   +2 more sources

Fungal ecology in the age of 'omics. [PDF]

New Phytol
Summary The advancement of technology in recent decades has given us an unprecedented ability to observe the natural world. With modern sequencing and bioinformatics technologies, we can obtain more information about the microscopic world, and its interactions with the macroscopic world, than ever before.
Shelton BR, Larrere J, Yusta Belsham D, Omacini M, Argüelles-Moyao A, Buscardo E, Alves da Silva DK, Zhao X, Nakamura N, Ángeles-Argáiz R, Paz C, Matías-Ferrer N, Hart MM.   +12 more
europepmc   +2 more sources

Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples [PDF]

Genome Medicine
Background Current surveillance of diarrhoeal disease is hindered by limitations of traditional diagnostic approaches, which often fail to identify the causative organism, particularly for novel or hard-to-culture bacterial pathogens.
Edward Cunningham-Oakes, Blanca M. Perez-Sepulveda, Yan Li, Jay C. D. Hinton, Charlotte A. Nelson, K. Marie McIntyre, Maya Wardeh, Sam Haldenby, Richard Gregory, Miren Iturriza-Gómara, Christiane Hertz-Fowler, Sarah J. O’Brien, Nigel A. Cunliffe, Alistair C. Darby, on behalf of the INTEGRATE consortium   +14 more
doaj   +2 more sources

SAMSA: a comprehensive metatranscriptome analysis pipeline [PDF]

BMC Bioinformatics, 2016
BackgroundAlthough metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data.
Danielle G. Lemay, David A. Mills, Ian Korf, Samuel T. Westreich   +3 more
core   +6 more sources

Understanding human health through metatranscriptomics

Trends in Molecular Medicine, 2023
Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises,
Teija Ojala, Esko Kankuri, Matti Kankainen   +2 more
openaire   +4 more sources

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework [version 2; peer review: 2 approved]

F1000Research, 2021
The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) and microbial diversity patterns across the habitats of our planet.
Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap   +13 more
doaj   +1 more source

Investigating microbiome and transcriptome data to uncover the key microbial community involved in lignocellulose degradation within the Deulajhari hot spring consortium

Data in Brief, 2023
Geothermally heated spring water contaminated with decomposed leaf biomass creates unique hot spring ecosystems that support the recycling of diverse nutrients and harbor microbial consortia capable of degrading lignocellulose.
Sangita Dixit, Kalpana Sahoo, Mahendra Gaur, Enketeswara Subudhi   +3 more
doaj   +1 more source

Metagenomics Versus Metatranscriptomics of the Murine Gut Microbiome for Assessing Microbial Metabolism During Inflammation

Frontiers in Microbiology, 2022
Shotgun metagenomics studies have improved our understanding of microbial population dynamics and have revealed significant contributions of microbes to gut homeostasis. They also allow in silico inference of the metagenome.
Juan Jovel, Juan Jovel, Aissata Nimaga, Tracy Jordan, Sandra O’Keefe, Jordan Patterson, Aducio Thiesen, Naomi Hotte, Michael Bording-Jorgensen, Sudip Subedi, Jessica Hamilton, Eric J. Carpenter, Béatrice Lauga, Shokrollah Elahi, Karen L. Madsen, Gane Ka-Shu Wong, Gane Ka-Shu Wong, Gane Ka-Shu Wong, Andrew L. Mason   +18 more
doaj   +1 more source

Sizing up metatranscriptomics [PDF]

The ISME Journal, 2012
Abstract A typical marine bacterial cell in coastal seawater contains only ∼200 molecules of mRNA, each of which lasts only a few minutes before being degraded. Such a surprisingly small and dynamic cellular mRNA reservoir has important implications for understanding the bacterium’s responses to environmental signals, as well as for our ...
Mary Ann, Moran, Brandon, Satinsky, Scott M, Gifford, Haiwei, Luo, Adam, Rivers, Leong-Keat, Chan, Jun, Meng, Bryndan P, Durham, Chen, Shen, Vanessa A, Varaljay, Christa B, Smith, Patricia L, Yager, Brian M, Hopkinson   +12 more
openaire   +2 more sources