Community profiling of the urinary microbiota: considerations for low-biomass samples

L Karstens, M Asquith, V Caruso… - Nature Reviews …, 2018 - nature.com
Many studies have shown that the urinary tract harbours its own microbial community known
as the urinary microbiota, which have been implicated in urinary tract disorders. This …

[HTML][HTML] The microbiome and lung cancer

A Maddi, A Sabharwal, T Violante… - Journal of thoracic …, 2019 - ncbi.nlm.nih.gov
It has become increasingly clear that we live in a symbiotic relationship with microbes within
us. We are just beginning to unravel the nature and strength of this relationship and its …

Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity …

M Chiarello, M McCauley, S Villéger, CR Jackson - PloS one, 2022 - journals.plos.org
Advances in the analysis of amplicon sequence datasets have introduced a methodological
shift in how research teams investigate microbial biodiversity, away from sequence identity …

Irradiation at ultra-high (FLASH) dose rates reduces acute normal tissue toxicity in the mouse gastrointestinal system

JL Ruan, C Lee, S Wouters, IDC Tullis… - International Journal of …, 2021 - Elsevier
Purpose Preclinical studies using ultra-high dose rate (FLASH) irradiation have
demonstrated reduced normal tissue toxicity compared with conventional dose rate (CONV) …

Microbiota-based markers predictive of development of Clostridioides difficile infection

M Berkell, M Mysara, BB Xavier… - Nature …, 2021 - nature.com
Antibiotic-induced modulation of the intestinal microbiota can lead to Clostridioides difficile
infection (CDI), which is associated with considerable morbidity, mortality, and healthcare …

Soil microbial community structure and functionality changes in response to long‐term metal and radionuclide pollution

T Rogiers, J Claesen, A Van Gompel… - Environmental …, 2021 - Wiley Online Library
Microbial communities are essential for a healthy soil ecosystem. Metals and radionuclides
can exert a persistent pressure on the soil microbial community. However, little is known on …

Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology

C Weißbecker, B Schnabel, A Heintz-Buschart - GigaScience, 2020 - academic.oup.com
Background Amplicon sequencing of phylogenetic marker genes, eg, 16S, 18S, or ITS
ribosomal RNA sequences, is still the most commonly used method to determine the …

The influences of bioinformatics tools and reference databases in analyzing the human oral microbial community

MA Sierra, Q Li, S Pushalkar, B Paul, TA Sandoval… - Genes, 2020 - mdpi.com
There is currently no criterion to select appropriate bioinformatics tools and reference
databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study …

The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease

JP Segal, BH Mullish, MN Quraishi… - Therapeutic …, 2019 - journals.sagepub.com
The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex
interaction between a patient's genetic predisposition, environment, gut microbiota and …

Alterations of gut microbiota biodiversity and relative abundance in women with PCOS: A systematic review and meta-analysis

Y Zou, R Liao, R Cheng, H Chung, H Zhu… - Microbial Pathogenesis, 2023 - Elsevier
Background Numerous studies have implicated that the gut microbiota is associated with
polycystic ovary syndrome (PCOS). However, a comprehensive data-based summary shown …