Diversity within species: interpreting strains in microbiomes

T Van Rossum, P Ferretti, OM Maistrenko… - Nature Reviews …, 2020 - nature.com
Studying within-species variation has traditionally been limited to culturable bacterial
isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing …

Applications of machine learning in human microbiome studies: a review on feature selection, biomarker identification, disease prediction and treatment

LJ Marcos-Zambrano… - Frontiers in …, 2021 - frontiersin.org
The number of microbiome-related studies has notably increased the availability of data on
human microbiome composition and function. These studies provide the essential material …

[HTML][HTML] Bifidobacteria-mediated immune system imprinting early in life

BM Henrick, L Rodriguez, T Lakshmikanth, C Pou… - Cell, 2021 - cell.com
Immune-microbe interactions early in life influence the risk of allergies, asthma, and other
inflammatory diseases. Breastfeeding guides healthier immune-microbe relationships by …

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

F Asnicar, SE Berry, AM Valdes, LH Nguyen… - Nature medicine, 2021 - nature.com
The gut microbiome is shaped by diet and influences host metabolism; however, these links
are complex and can be unique to each individual. We performed deep metagenomic …

Species-level functional profiling of metagenomes and metatranscriptomes

EA Franzosa, LJ McIver, G Rahnavard, LR Thompson… - Nature …, 2018 - nature.com
Functional profiles of microbial communities are typically generated using comprehensive
metagenomic or metatranscriptomic sequence read searches, which are time-consuming …

Best practices for analysing microbiomes

R Knight, A Vrbanac, BC Taylor, A Aksenov… - Nature Reviews …, 2018 - nature.com
Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …

Microbiota in tumors: from understanding to application

Y ** infant gut microbiome
P Ferretti, E Pasolli, A Tett, F Asnicar, V Gorfer, S Fedi… - Cell host & …, 2018 - cell.com
The acquisition and development of the infant microbiome are key to establishing a healthy
host-microbiome symbiosis. The maternal microbial reservoir is thought to play a crucial role …

The progress of gut microbiome research related to brain disorders

S Zhu, Y Jiang, K Xu, M Cui, W Ye, G Zhao… - Journal of …, 2020 - Springer
There is increasing evidence showing that the dynamic changes in the gut microbiota can
alter brain physiology and behavior. Cognition was originally thought to be regulated only by …

Metagenome-wide association of gut microbiome features for schizophrenia

F Zhu, Y Ju, W Wang, Q Wang, R Guo, Q Ma… - Nature …, 2020 - nature.com
Evidence is mounting that the gut-brain axis plays an important role in mental diseases
fueling mechanistic investigations to provide a basis for future targeted interventions …