Optimizing methods and dodging pitfalls in microbiome research

D Kim, CE Hofstaedter, C Zhao, L Mattei, C Tanes… - Microbiome, 2017 - Springer
Research on the human microbiome has yielded numerous insights into health and disease,
but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for …

[PDF][PDF] Practical considerations for large-scale gut microbiome studies

D Vandeputte, RY Tito, R Vanleeuwen… - FEMS microbiology …, 2017 - academic.oup.com
First insights on the human gut microbiome have been gained from medium-sized, cross-
sectional studies. However, given the modest portion of explained variance of currently …

Gut microbiome heritability is nearly universal but environmentally contingent

L Grieneisen, M Dasari, TJ Gould, JR Björk, JC Grenier… - Science, 2021 - science.org
Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this
similarity results from shared genotypes versus shared environments has been …

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas

A Baniel, KR Amato, JC Beehner, TJ Bergman… - Microbiome, 2021 - Springer
Background Adaptive shifts in gut microbiome composition are one route by which animals
adapt to seasonal changes in food availability and diet. However, outside of dietary shifts …

Climate change drives loss of bacterial gut mutualists at the expense of host survival in wild meerkats

A Risely, N Müller‐Klein, DW Schmid… - Global Change …, 2023 - Wiley Online Library
Climate change and climate‐driven increases in infectious disease threaten wildlife
populations globally. Gut microbial responses are predicted to either buffer or exacerbate …

Impact of preservation method and 16S rRNA hypervariable region on gut microbiota profiling

Z Chen, PC Hui, M Hui, YK Yeoh, PY Wong… - Msystems, 2019 - Am Soc Microbiol
Proper preservation of stool samples to minimize microbial community shifts and inactivate
infectious agents is important for self-collected specimens requiring shipment to laboratories …

Generating amplicon reads for microbial community assessment with next‐generation sequencing

M Gołębiewski, A Tretyn - Journal of Applied Microbiology, 2020 - academic.oup.com
Marker gene amplicon sequencing is often preferred over whole genome sequencing for
microbial community characterization, due to its lower cost while still enabling assessment of …

Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population

SF Worsley, CS Davies, CZ Lee… - Molecular …, 2024 - Wiley Online Library
In humans, gut microbiome (GM) differences are often correlated with, and sometimes
causally implicated in, ageing. However, it is unclear how these findings translate in wild …

Altitudinal variation of the gut microbiota in wild house mice

TA Suzuki, FM Martins, MW Nachman - Molecular ecology, 2019 - Wiley Online Library
The maintenance of oxygen homeostasis in the gut is critical for the maintenance of a
healthy gut microbiota. However, few studies have explored how the concentration of …

Standard sample storage conditions have an impact on inferred microbiome composition and antimicrobial resistance patterns

CS Poulsen, RS Kaas, FM Aarestrup… - Microbiology …, 2021 - Am Soc Microbiol
Storage of biological specimens is crucial in the life and medical sciences. Storage
conditions for samples can be different for a number of reasons, and it is unclear what effect …