Next-generation sequencing: insights to advance clinical investigations of the microbiome
CR Wensel, JL Pluznick, SL Salzberg… - The Journal of clinical …, 2022 - Am Soc Clin Investig
Next-generation sequencing (NGS) technology has advanced our understanding of the
human microbiome by allowing for the discovery and characterization of unculturable …
human microbiome by allowing for the discovery and characterization of unculturable …
The gut microbiota and its biogeography
G McCallum, C Tropini - Nature Reviews Microbiology, 2024 - nature.com
Biogeography is the study of species distribution and diversity within an ecosystem and is at
the core of how we understand ecosystem dynamics and interactions at the macroscale. In …
the core of how we understand ecosystem dynamics and interactions at the macroscale. In …
MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data
Microbiome studies have become routine in biomedical, agricultural and environmental
sciences with diverse aims, including diversity profiling, functional characterization, and …
sciences with diverse aims, including diversity profiling, functional characterization, and …
Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms
Parkinson's disease (PD) may start in the gut and spread to the brain. To investigate the role
of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using …
of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using …
The gut microbiome and hypertension
A large body of evidence has emerged in the past decade supporting a role for the gut
microbiome in the regulation of blood pressure. The field has moved from association to …
microbiome in the regulation of blood pressure. The field has moved from association to …
Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment
KM Schneider, A Mohs, W Gui, EJC Galvez… - Nature …, 2022 - nature.com
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide,
and therapeutic options for advanced HCC are limited. Here, we observe that intestinal …
and therapeutic options for advanced HCC are limited. Here, we observe that intestinal …
Phyllosphere microbiome induces host metabolic defence against rice false-smut disease
X Liu, H Matsumoto, T Lv, C Zhan, H Fang, Q Pan… - Nature …, 2023 - nature.com
Mutualistic interactions between host plants and their microbiota have the potential to
provide disease resistance. Most research has focused on the rhizosphere, but it is unclear …
provide disease resistance. Most research has focused on the rhizosphere, but it is unclear …
Machine learning and deep learning applications in microbiome research
R Hernández Medina, S Kutuzova… - ISME …, 2022 - academic.oup.com
The many microbial communities around us form interactive and dynamic ecosystems called
microbiomes. Though concealed from the naked eye, microbiomes govern and influence …
microbiomes. Though concealed from the naked eye, microbiomes govern and influence …
ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization
Microbiome research is now moving beyond the compositional analysis of microbial taxa in
a sample. Increasing evidence from large human microbiome studies suggests that …
a sample. Increasing evidence from large human microbiome studies suggests that …
The best practice for microbiome analysis using R
With the gradual maturity of sequencing technology, many microbiome studies have
published, driving the emergence and advance of related analysis tools. R language is the …
published, driving the emergence and advance of related analysis tools. R language is the …