Benchmarking metagenomics tools for taxonomic classification

HY Simon, KJ Siddle, DJ Park, PC Sabeti - Cell, 2019 - cell.com
Metagenomic sequencing is revolutionizing the detection and characterization of microbial
species, and a wide variety of software tools are available to perform taxonomic …

Shotgun metagenomics, from sampling to analysis

C Quince, AW Walker, JT Simpson, NJ Loman… - Nature …, 2017 - nature.com
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …

microeco: an R package for data mining in microbial community ecology

C Liu, Y Cui, X Li, M Yao - FEMS microbiology ecology, 2021 - academic.oup.com
ABSTRACT A large amount of sequencing data is produced in microbial community ecology
studies using the high-throughput sequencing technique, especially amplicon-sequencing …

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 …

Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish

R Qiao, C Sheng, Y Lu, Y Zhang, H Ren… - Science of the Total …, 2019 - Elsevier
Microplastics (MPs) can be ingested by a variety of species and mainly accumulate in the
gut. However, the consequences of MPs exposure in the gut are largely unknown. Here we …

Gut microbiome alterations in Alzheimer's disease

NM Vogt, RL Kerby, KA Dill-McFarland, SJ Harding… - Scientific reports, 2017 - nature.com
Alzheimer's disease (AD) is the most common form of dementia. However, the
etiopathogenesis of this devastating disease is not fully understood. Recent studies in …

Gut commensal Parabacteroides goldsteinii plays a predominant role in the anti-obesity effects of polysaccharides isolated from Hirsutella sinensis

TR Wu, CS Lin, CJ Chang, TL Lin, J Martel, YF Ko… - Gut, 2019 - gut.bmj.com
Objective The medicinal fungus Ophiocordyceps sinensis and its anamorph Hirsutella
sinensis have a long history of use in traditional Chinese medicine for their …

[PDF][PDF] MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

A Dhariwal, J Chong, S Habib, IL King… - Nucleic acids …, 2017 - academic.oup.com
The widespread application of next-generation sequencing technologies has revolutionized
microbiome research by enabling high-throughput profiling of the genetic contents of …

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

RM Ferreira, J Pereira-Marques, I Pinto-Ribeiro… - Gut, 2018 - gut.bmj.com
Objective Gastric carcinoma development is triggered by Helicobacter pylori. Chronic H.
pylori infection leads to reduced acid secretion, which may allow the growth of a different …

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

R Seshadri, SC Leahy, GT Attwood, KH Teh… - Nature …, 2018 - nature.com
Productivity of ruminant livestock depends on the rumen microbiota, which ferment
indigestible plant polysaccharides into nutrients used for growth. Understanding the …