Using clusterProfiler to characterize multiomics data

S Xu, E Hu, Y Cai, Z ** the gut microbiome in a Dutch population
R Gacesa, A Kurilshikov, A Vich Vila, T Sinha… - Nature, 2022 - nature.com
The gut microbiome is associated with diverse diseases,–, but a universal signature of a
healthy or unhealthy microbiome has not been identified, and there is a need to understand …

PICRUSt2 for prediction of metagenome functions

GM Douglas, VJ Maffei, JR Zaneveld, SN Yurgel… - Nature …, 2020 - nature.com
To the Editor—One limitation of microbial community marker-gene sequencing is that it does
not provide information about the functional composition of sampled communities …

Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients

EN Baruch, I Youngster, G Ben-Betzalel, R Ortenberg… - Science, 2021 - science.org
The gut microbiome has been shown to influence the response of tumors to anti–PD-1
(programmed cell death–1) immunotherapy in preclinical mouse models and observational …

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

E Bolyen, JR Rideout, MR Dillon, NA Bokulich… - Nature …, 2019 - nature.com
To the Editor—Rapid advances in DNA-sequencing and bioinformatics technologies in the
past two decades have substantially improved understanding of the microbial world. This …

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation

S Federici, S Kredo-Russo, R Valdés-Mas… - Cell, 2022 - cell.com
Human gut commensals are increasingly suggested to impact non-communicable diseases,
such as inflammatory bowel diseases (IBD), yet their targeted suppression remains a …

Multivariable association discovery in population-scale meta-omics studies

H Mallick, A Rahnavard, LJ McIver, S Ma… - PLoS computational …, 2021 - journals.plos.org
It is challenging to associate features such as human health outcomes, diet, environmental
conditions, or other metadata to microbial community measurements, due in part to their …

Gut microbiome structure and metabolic activity in inflammatory bowel disease

EA Franzosa, A Sirota-Madi, J Avila-Pacheco… - Nature …, 2019 - nature.com
The inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative
colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has …