Results 51 to 60 of about 246,967 (290)

High-throughput sequencing of 16S rRNA gene amplicons : effects of extraction procedure, primer length and annealing temperature [PDF]

, 2012
The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing.
Cogan, Tristan, Constantinidou, Chrystala, Pallen, Mark J., Penn, Charles W., Sergeant, Martin J.   +4 more
core   +3 more sources

SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis

ISME Communications, 2023
Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the ...
Jackie Zorz, Carmen Li, Anirban Chakraborty, Daniel A. Gittins, Taylor Surcon, Natasha Morrison, Robbie Bennett, Adam MacDonald, Casey R. J. Hubert   +8 more
doaj   +1 more source

Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils

mSystems, 2021
A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations.
Haitao Wang, Alexandre Bagnoud, Rafael I. Ponce-Toledo, Melina Kerou, Micha Weil, Christa Schleper, Tim Urich   +6 more
doaj   +1 more source

Accurate Profiling of Microbial Communities from Massively Parallel Sequencing using Convex Optimization [PDF]

, 2013
We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using short sequence
A. Amir, B.J. Paster, C. Lozupone, C.A. Lozupone, D. Hiller, D. Kessner, D.H. Haft, E.R. Mardis, I. Eskin, J.R. Cole, M. Grant, M. Hamady, N. Segata, P. Meinicke, P.B. Eckburg, S. Pavoine, T.J. Gentry, T.Z. DeSantis   +17 more
core   +2 more sources

Triplicate PCR Reactions for 16S rRNA Gene Amplicon Sequencing are Unnecessary [PDF]

BioTechniques, 2019
Conventional wisdom holds that PCR amplification for sequencing should employ pooled replicate reactions to reduce bias due to jackpot effects and chimera formation. However, modern amplicon data analysis employs methods that may be less sensitive to such artifacts.
Marotz, Clarisse, Sharma, Anukriti, Humphrey, Greg, Gottel, Neil, Daum, Christopher, Gilbert, Jack A, Eloe-Fadrosh, Emiley, Knight, Rob   +7 more
openaire   +5 more sources

Phylogenetic Position of Riemerella anatipestifer Based on 16S rRNA Gene Sequences [PDF]

International Journal of Systematic Bacteriology, 1997
Riemerella anatipestifer, the causative agent of septicemia anserum exsudativa (also called new duckling disease), belongs to the family Flavobacteriaceae of gram-negative bacteria. We determined the DNA sequences of the rrs genes encoding the 16S rRNAs of four R. anatipestifer strains by directly sequencing PCR-amplified rrs genes.
Subramaniam, S., Chua, K.-L., Tan, H.-M., Loh, H., Kuhnert, P., Frey, J.   +5 more
openaire   +2 more sources

Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?

Poultry Science
Bacteria are the major component of poultry gastrointestinal tract (GIT) microbiota and play an important role in host health, nutrition, physiology regulation, intestinal development, and growth.
Joshua M. Lyte, Mitiku M. Seyoum, Diana Ayala, Jannigje G. Kers, Valentina Caputi, Timothy Johnson, Li Zhang, Joshua Rehberger, Guolong Zhang, Sami Dridi, Brett Hale, Jean E. De Oliveira, Daniel Grum, Alexandra H. Smith, Michael Kogut, Steven C. Ricke, Anne Ballou, Bill Potter, Monika Proszkowiec-Weglarz   +18 more
doaj   +1 more source

Identification of bacterial pathogens in sudden unexpected death in infancy and childhood using 16S rRNA gene sequencing

Frontiers in Microbiology, 2023
BackgroundSudden unexpected death in infancy (SUDI) is the most common cause of post-neonatal death in the developed world. Following an extensive investigation, the cause of ~40% of deaths remains unknown.
Lily Gates, Talisa Mistry, Olumide Ogunbiyi, Kerry-Anne Kite, Nigel J. Klein, Neil J. Sebire, Dagmar G. Alber   +6 more
doaj   +1 more source

Bacteria isolated from Bengal cat (Felis catus × Prionailurus bengalensis) anal sac secretions produce volatile compounds potentially associated with animal signaling. [PDF]

, 2019
In social animals, scent secretions and marking behaviors play critical roles in communication, including intraspecific signals, such as identifying individuals and group membership, as well as interspecific signaling.
Cho, Adrienne W, Coil, David A, Davis, Cristina E, Eisen, Jonathan A, Ganz, Holly H, Jospin, Guillaume, McCartney, Mitchell M, Yamaguchi, Mei S, Zaw, Thant H   +8 more
core   +1 more source

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons. [PDF]

, 2019
While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface.
Arogyaswamy, Keshav, Aronson, Emma L, Billings, Sharon A, Botthoff, Jon K, Brewer, Tess E, Campbell, Ashley N, Dove, Nicholas C, Fairbanks, Dawson, Fierer, Noah, Gallery, Rachel E, Hart, Stephen C, Kaye, Jason, King, Gary, Logan, Geoffrey, Lohse, Kathleen A, Maltz, Mia R, Mayorga, Emilio, O'Neill, Caitlin, Owens, Sarah M, Packman, Aaron, Pett-Ridge, Jennifer, Plante, Alain F, Richter, Daniel D, Silver, Whendee L, Yang, Wendy H   +24 more
core   +2 more sources