Defining and quantifying the core microbiome: challenges and prospects

AT Neu, EE Allen, K Roy - Proceedings of the National …, 2021 - National Acad Sciences
The term “core microbiome” has become widely used in microbial ecology over the last
decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and …

Current findings in endometrial microbiome: impact on uterine diseases

D Medina-Bastidas, I Camacho-Arroyo… - …, 2022 - rep.bioscientifica.com
Microbiome or microbiota is essential to regulate many mammalian physiological processes,
including reproduction. Like other organs or tissues, the upper female reproductive tract …

Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration

S Priya, MB Burns, T Ward, RAT Mars… - Nature …, 2022 - nature.com
While gut microbiome and host gene regulation independently contribute to gastrointestinal
disorders, it is unclear how the two may interact to influence host pathophysiology. Here we …

[HTML][HTML] Fecal microbiota transplantation ameliorates bone loss in mice with ovariectomy-induced osteoporosis via modulating gut microbiota and metabolic function

YW Zhang, MM Cao, YJ Li, PP Lu, GC Dai… - Journal of orthopaedic …, 2022 - Elsevier
Background Osteoporosis (OP) is a systemic metabolic bone disease characterized by
decreased bone mass and destruction of bone microstructure, which tends to result in …

The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production

J Firrman, LS Liu, K Mahalak, C Tanes… - FEMS Microbiology …, 2022 - academic.oup.com
Environmental pH is a critical parameter for maintenance of the gut microbiota. Here, the
impact of pH on the gut microbiota luminal and mucosal community structure and short chain …

Underpinning the ecological response of mixed chlorinated volatile organic compounds (CVOCs) associated with contaminated and bioremediated groundwaters: a …

B Hussain, JS Chen, SW Huang, IS Tsai, J Rathod… - Environmental …, 2023 - Elsevier
Understanding the structure, dynamics, and functionality of microbial communities is
essential for developing sustainable and effective bioremediation strategies, particularly for …

Gut-microbiota in children and adolescents with obesity: inferred functional analysis and machine-learning algorithms to classify microorganisms

M Squillario, C Bonaretti, A La Valle, E Di Marco… - Scientific reports, 2023 - nature.com
The fecal microbiome of 55 obese children and adolescents (BMI-SDS 3.2±0.7) and of 25
normal-weight subjects, matched both for age and sex (BMI-SDS− 0.3±1.1) was analysed …

Microbiome analysis via OTU and ASV-based pipelines—A comparative interpretation of ecological data in WWTP systems

JT Jeske, C Gallert - Bioengineering, 2022 - mdpi.com
Linking community composition and ecosystem function via the cultivation-independent
analysis of marker genes, eg, the 16S rRNA gene, is a staple of microbial ecology and …

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

A Regueira‐Iglesias, C Balsa‐Castro… - Molecular Oral …, 2023 - Wiley Online Library
The multi‐batch reanalysis approach of jointly reevaluating gene/genome sequences from
different works has gained particular relevance in the literature in recent years. The large …

RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing

JR Petrone, P Rios Glusberger, CD George… - Frontiers in …, 2023 - frontiersin.org
Despite the advent of third-generation sequencing technologies, modern bacterial ecology
studies still use Illumina to sequence small (~ 400 bp) hypervariable regions of the 16S …