Innovations to culturing the uncultured microbial majority

WH Lewis, G Tahon, P Geesink, DZ Sousa… - Nature Reviews …, 2021‏ - nature.com
Despite the surge of microbial genome data, experimental testing is important to confirm
inferences about the cell biology, ecological roles and evolution of microorganisms. As the …

The human gut microbiome: from association to modulation

TSB Schmidt, J Raes, P Bork - Cell, 2018‏ - cell.com
Our understanding of the human gut microbiome continues to evolve at a rapid pace, but
practical application of thisknowledge is still in its infancy. This review discusses the type of …

Establishing microbial composition measurement standards with reference frames

JT Morton, C Marotz, A Washburne, J Silverman… - Nature …, 2019‏ - nature.com
Differential abundance analysis is controversial throughout microbiome research. Gold
standard approaches require laborious measurements of total microbial load, or absolute …

Quantitative microbiome profiling links gut community variation to microbial load

D Vandeputte, G Kathagen, K D'hoe, S Vieira-Silva… - Nature, 2017‏ - nature.com
Current sequencing-based analyses of faecal microbiota quantify microbial taxa and
metabolic pathways as fractions of the sample sequence library generated by each …

The madness of microbiome: attempting to find consensus “best practice” for 16S microbiome studies

J Pollock, L Glendinning, T Wisedchanwet… - Applied and …, 2018‏ - journals.asm.org
The development and continuous improvement of high-throughput sequencing platforms
have stimulated interest in the study of complex microbial communities. Currently, the most …

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling

C Jian, P Luukkonen, H Yki-Järvinen, A Salonen… - PloS one, 2020‏ - journals.plos.org
The use of relative abundance data from next generation sequencing (NGS) can lead to
misinterpretations of microbial community structures, as the increase of one taxon leads to …

Diet tracing in ecology: Method comparison and selection

JM Nielsen, EL Clare, B Hayden… - Methods in Ecology …, 2018‏ - Wiley Online Library
Determining diet is a key prerequisite for understanding species interactions, food web
structure and ecological dynamics. In recent years, there has been considerable …

Not all animals need a microbiome

TJ Hammer, JG Sanders, N Fierer - FEMS microbiology letters, 2019‏ - academic.oup.com
It is often taken for granted that all animals host and depend upon a microbiome, yet this has
only been shown for a small proportion of species. We propose that animals span a …

Community assembly processes of the microbial rare biosphere

X Jia, F Dini-Andreote, JF Salles - Trends in microbiology, 2018‏ - cell.com
Our planet teems with microorganisms that often present a skewed abundance distribution
in a local community, with relatively few dominant species coexisting alongside a high …

Microbiology of the built environment

JA Gilbert, B Stephens - Nature Reviews Microbiology, 2018‏ - nature.com
The built environment comprises all structures built by humans, including our homes,
workplaces, schools and vehicles. As in any ecosystem on Earth, microorganisms have …