Identifying biases and their potential solutions in human microbiome studies
Advances in DNA sequencing technology have vastly improved the ability of researchers to
explore the microbial inhabitants of the human body. Unfortunately, while these studies have …
explore the microbial inhabitants of the human body. Unfortunately, while these studies have …
The madness of microbiome: attempting to find consensus “best practice” for 16S microbiome studies
The development and continuous improvement of high-throughput sequencing platforms
have stimulated interest in the study of complex microbial communities. Currently, the most …
have stimulated interest in the study of complex microbial communities. Currently, the most …
Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?
Advances in DNA sequencing technology have revolutionized the field of molecular analysis
of trophic interactions, and it is now possible to recover counts of food DNA sequences from …
of trophic interactions, and it is now possible to recover counts of food DNA sequences from …
Genome-centric view of carbon processing in thawing permafrost
As global temperatures rise, large amounts of carbon sequestered in permafrost are
becoming available for microbial degradation. Accurate prediction of carbon gas emissions …
becoming available for microbial degradation. Accurate prediction of carbon gas emissions …
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
AE Pérez-Cobas, L Gomez-Valero… - Microbial …, 2020 - microbiologyresearch.org
Metagenomics and marker gene approaches, coupled with high-throughput sequencing
technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture …
technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture …
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
SF Stoddard, BJ Smith, R Hein, BRK Roller… - Nucleic acids …, 2015 - academic.oup.com
Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys of
microbial communities. rRNA genes are often co-located as part of an rrn operon, and …
microbial communities. rRNA genes are often co-located as part of an rrn operon, and …
Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology.
Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions …
Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions …
Accurate estimation of fungal diversity and abundance through improved lineage-specific primers optimized for Illumina amplicon sequencing
While high-throughput sequencing methods are revolutionizing fungal ecology, recovering
accurate estimates of species richness and abundance has proven elusive. We sought to …
accurate estimates of species richness and abundance has proven elusive. We sought to …
Exploiting rRNA operon copy number to investigate bacterial reproductive strategies
BRK Roller, SF Stoddard, TM Schmidt - Nature microbiology, 2016 - nature.com
The potential for rapid reproduction is a hallmark of microbial life, but microbes in nature
must also survive and compete when growth is constrained by resource availability …
must also survive and compete when growth is constrained by resource availability …
Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence
Culture-independent molecular surveys of plant root microbiomes indicate that soil type
generally has a stronger influence on microbial communities than host phylogeny. However …
generally has a stronger influence on microbial communities than host phylogeny. However …