Results 41 to 50 of about 173,789 (325)

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Nature Communications, 2019
Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome
R. Hendriksen, Patrick Munk, P. Njage, B. V. van Bunnik, L. McNally, O. Lukjancenko, Timo Röder, David F. Nieuwenhuijse, S. Pedersen, J. Kjeldgaard, R. Kaas, P. Clausen, J. Vogt, P. Leekitcharoenphon, M. G. van de Schans, T. Zuidema, A. M. de Roda Husman, Simon Rasmussen, Bent Petersen, C. Amid, G. Cochrane, Thomas Sicheritz-Pontén, H. Schmitt, Jorge Raul Matheu Alvarez, A. Aidara-Kane, S. J. Pamp, O. Lund, T. Hald, M. Woolhouse, M. Koopmans, H. Vigre, T. Petersen, F. Aarestrup   +32 more
semanticscholar   +1 more source

Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens

Microorganisms, 2021
Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegetables, with a corresponding increase in economic losses caused by the introduction of transboundary plant pathogens.
E. Piombo, A. Abdelfattah, S. Droby, M. Wisniewski, D. Spadaro, L. Schena   +5 more
semanticscholar   +1 more source

Biotechnological applications of functional metagenomics in the food and pharmaceutical industries [PDF]

, 2015
peer-reviewedMicroorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods.
Alvarez-Ordonez, Avelino, Cotter, Paul D., Coughlan, Laura M., Hill, Colin   +3 more
core   +1 more source

Giant virus diversity and host interactions through global metagenomics

Nature, 2020
Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae.
Frederik Schulz, S. Roux, David Páez-Espino, S. Jungbluth, D. Walsh, Vincent J. Denef, K. McMahon, K. Konstantinidis, E. Eloe-Fadrosh, N. Kyrpides, T. Woyke   +10 more
semanticscholar   +1 more source

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements

Microbiome, 2021
Background Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization.
Dieter M. Tourlousse, Koji Narita, Takamasa Miura, M. Sakamoto, Akiko Ohashi, Keita Shiina, Masami Matsuda, Daisuke Miura, Mamiko Shimamura, Yoshifumi Ohyama, A. Yamazoe, Yoshihito Uchino, K. Kameyama, S. Arioka, Jiro Kataoka, Takayoshi Hisada, K. Fujii, Shunsuke Takahashi, M. Kuroiwa, Masatomo Rokushima, Mitsue Nishiyama, Yoshiki Tanaka, Takuya Fuchikami, Hitomi Aoki, S. Kira, R. Koyanagi, T. Naito, M. Nishiwaki, H. Kumagai, M. Konda, Ken Kasahara, M. Ohkuma, H. Kawasaki, Y. Sekiguchi, J. Terauchi   +34 more
semanticscholar   +1 more source

Unraveling metagenomics through long-read sequencing: a comprehensive review

Journal of Translational Medicine
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics.
Chankyung Kim, M. Pongpanich, T. Porntaveetus   +2 more
semanticscholar   +1 more source

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi

mSphere, 2018
A wide diversity of fungi have been detected in the human gastrointestinal (GI) tract with the potential to provide or influence important functions. However, many of the fungi most commonly detected in stool samples are also present in food or the oral ...
Thomas A. Auchtung, Tatiana Y. Fofanova, Christopher J. Stewart, Andrea K. Nash, Matthew C. Wong, Jonathan R. Gesell, Jennifer M. Auchtung, Nadim J. Ajami, Joseph F. Petrosino   +8 more
doaj   +1 more source

Genome-resolved metagenomics: a game changer for microbiome medicine

Experimental and Molecular Medicine
Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome medicine. This emerging field aims to understand and leverage the human microbiota and derivative molecules for
Nayeon Kim, Junyeong Ma, Wonjong Kim, Jungyeon Kim, Peter A Belenky, Insuk Lee   +5 more
semanticscholar   +1 more source

Integrating Viral Metagenomics into an Ecological Framework.

Annual Review of Virology, 2021
Viral metagenomics has expanded our knowledge of the ecology of uncultured viruses, within both environmental (e.g., terrestrial and aquatic) and host-associated (e.g., plants and animals, including humans) contexts. Here, we emphasize the implementation
P. Sommers, Anushila Chatterjee, A. Varsani, G. Trubl   +3 more
semanticscholar   +1 more source

Accelerating exhaustive pairwise metagenomic comparisons [PDF]

, 2017
In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of
A Alyass, B Nichols, BD Ondov, CD Polychronopoulos, G Benoit, G Jing, H Li, JA Hanley, MLV Pitteway, O Gotoh, O Torreno, SF Altschul, Y Liu, Y Liu   +13 more
core   +2 more sources