Implications of streamlining theory for microbial ecology
SJ Giovannoni, J Cameron Thrash… - The ISME …, 2014 - academic.oup.com
Whether a small cell, a small genome or a minimal set of chemical reactions with self-
replicating properties, simplicity is beguiling. As Leonardo da Vinci reportedly said,'simplicity …
replicating properties, simplicity is beguiling. As Leonardo da Vinci reportedly said,'simplicity …
SAR11 bacteria: the most abundant plankton in the oceans
SJ Giovannoni - Annual review of marine science, 2017 - annualreviews.org
SAR11 is a group of small, carbon-oxidizing bacteria that reach a global estimated
population size of 2.4× 1028 cells—approximately 25% of all plankton. They are found …
population size of 2.4× 1028 cells—approximately 25% of all plankton. They are found …
[PDF][PDF] Bracken: estimating species abundance in metagenomics data
Metagenomic experiments attempt to characterize microbial communities using high-
throughput DNA sequencing. Identification of the microorganisms in a sample provides …
throughput DNA sequencing. Identification of the microorganisms in a sample provides …
Lytic to temperate switching of viral communities
Microbial viruses can control host abundances via density-dependent lytic predator–prey
dynamics. Less clear is how temperate viruses, which coexist and replicate with their host …
dynamics. Less clear is how temperate viruses, which coexist and replicate with their host …
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
Background Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral
genomes, evaluate community diversity, and assess ecological hypotheses. While viromic …
genomes, evaluate community diversity, and assess ecological hypotheses. While viromic …
Viruses in the faecal microbiota of monozygotic twins and their mothers
Viral diversity and life cycles are poorly understood in the human gut and other body
habitats. Phages and their encoded functions may provide informative signatures of a …
habitats. Phages and their encoded functions may provide informative signatures of a …
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
S Nayfach, KS Pollard - Genome biology, 2015 - Springer
Average genome size is an important, yet often overlooked, property of microbial
communities. We developed MicrobeCensus to rapidly and accurately estimate average …
communities. We developed MicrobeCensus to rapidly and accurately estimate average …
A global network of coexisting microbes from environmental and whole-genome sequence data
Microbes are the most abundant and diverse organisms on Earth. In contrast to macroscopic
organisms, their environmental preferences and ecological interdependencies remain …
organisms, their environmental preferences and ecological interdependencies remain …
Microbiome, metagenomics, and high-dimensional compositional data analysis
H Li - Annual Review of Statistics and Its Application, 2015 - annualreviews.org
The human microbiome is the totality of all microbes in and on the human body, and its
importance in health and disease has been increasingly recognized. High-throughput …
importance in health and disease has been increasingly recognized. High-throughput …
The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics
TJ Williams, D Wilkins, E Long, F Evans… - Environmental …, 2013 - Wiley Online Library
Heterotrophic marine bacteria play key roles in remineralizing organic matter generated
from primary production. However, far more is known about which groups are dominant than …
from primary production. However, far more is known about which groups are dominant than …