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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
exaly   +4 more sources

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   +2 more sources

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

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   +2 more sources

Use of Metatranscriptomics in Microbiome Research [PDF]

Bioinformatics and Biology Insights, 2016
The human intestinal microbiome is a microbial ecosystem that expresses as many as 100 times more genes than the human host, thereby constituting an important component of the human holobiome, which contributes to multiple health and disease processes.
Stavros Bashiardes, Gili Zilberman-Schapira, Eran Elinav   +2 more
openaire   +5 more sources

A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass

Gut Microbes
The high background of host RNA poses a major challenge to metatranscriptome analysis of human samples. Hence, metatranscriptomics has been mainly applied to microbe-rich samples, while its application in human tissues with low ratio of microbial to host
Joana Pereira-Marques, Rui M Ferreira, Ceu Figueiredo   +2 more
exaly   +3 more sources

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

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 ...
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

Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses

Pathogens, 2022
The genus Varicosavirus is one of six genera of plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped, flexuous, rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature of varicosaviruses, which is shared
Nicolas Bejerman, Ralf G. Dietzgen, Humberto Debat   +2 more
doaj   +1 more source

Molecular signature of postmortem lung tissue from COVID-19 patients suggests distinct trajectories driving mortality

Disease Models & Mechanisms, 2022
To elucidate the molecular mechanisms that manifest lung abnormalities during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, we performed whole-transcriptome sequencing of lung autopsies from 31 patients with severe COVID-19 and
Anshul Budhraja, Anubhav Basu, Atish Gheware, Dasari Abhilash, Seesandra Rajagopala, Suman Pakala, Madhuresh Sumit, Animesh Ray, Arulselvi Subramaniam, Purva Mathur, Aruna Nambirajan, Sachin Kumar, Ritu Gupta, Naveet Wig, Anjan Trikha, Randeep Guleria, Chitra Sarkar, Ishaan Gupta, Deepali Jain   +18 more
doaj   +1 more source

Genomic and Transcriptomic Evidence Supports Methane Metabolism in Archaeoglobi

mSystems, 2020
Euryarchaeal lineages have been believed to have a methanogenic last common ancestor. However, members of euryarchaeal Archaeoglobi have long been considered nonmethanogenic and their evolutionary history remains elusive.
Yi-Fan Liu, Jing Chen, Livia S. Zaramela, Li-Ying Wang, Serge Maurice Mbadinga, Zhao-Wei Hou, Xiao-Lin Wu, Ji-Dong Gu, Karsten Zengler, Bo-Zhong Mu   +9 more
doaj   +1 more source