Reintroducing mothur: 10 years later

PD Schloss - Applied and environmental microbiology, 2020 - journals.asm.org
More than 10 years ago, we published the paper describing the mothur software package in
Applied and Environmental Microbiology. Our goal was to create a comprehensive package …

[HTML][HTML] Mining microbes for mental health: determining the role of microbial metabolic pathways in human brain health and disease

S Spichak, TFS Bastiaanssen, K Berding… - Neuroscience & …, 2021 - Elsevier
There is increasing knowledge regarding the role of the microbiome in modulating brain and
behaviour. Indeed, the actions of microbial metabolites are key for appropriate gut-brain …

Bacteroidota inhibit microglia clearance of amyloid-beta and promote plaque deposition in Alzheimer's disease mouse models

C Wasén, LC Beauchamp, J Vincentini, S Li… - Nature …, 2024 - nature.com
The gut microbiota and microglia play critical roles in Alzheimer's disease (AD), and
elevated Bacteroides is correlated with cerebrospinal fluid amyloid-β (Aβ) and tau levels in …

Parallelization of MAFFT for large-scale multiple sequence alignments

T Nakamura, KD Yamada, K Tomii, K Katoh - Bioinformatics, 2018 - academic.oup.com
We report an update for the MAFFT multiple sequence alignment program to enable parallel
calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently …

Development of gut microbiota during the first 2 years of life

ML Wernroth, S Peura, AM Hedman, S Hetty… - Scientific reports, 2022 - nature.com
Although development of microbiota in childhood has been linked to chronic immune-
related conditions, early childhood determinants of microbiota development have not been …

Environmentally dependent interactions shape patterns in gene content across natural microbiomes

K Crocker, KK Lee, M Chakraverti-Wuerthwein… - Nature …, 2024 - nature.com
Sequencing surveys of microbial communities in hosts, oceans and soils have revealed
ubiquitous patterns linking community composition to environmental conditions. While …

[HTML][HTML] MiDAS 3: an ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level …

M Nierychlo, KS Andersen, Y Xu, N Green, C Jiang… - Water Research, 2020 - Elsevier
The function of the microbiomes in wastewater treatment systems and anaerobic digesters is
dictated by the physiological activity of their members and complex interactions between …

Relaxed targeting rules help PIWI proteins silence transposons

I Gainetdinov, J Vega-Badillo, K Cecchini, A Bagci… - Nature, 2023 - nature.com
In eukaryotes, small RNA guides, such as small interfering RNAs and microRNAs, direct
AGO-clade Argonaute proteins to regulate gene expression and defend the genome against …

Lack of detection of a human placenta microbiome in samples from preterm and term deliveries

JS Leiby, K McCormick, S Sherrill-Mix, EL Clarke… - Microbiome, 2018 - Springer
Background Historically, the human womb has been thought to be sterile in healthy
pregnancies, but this idea has been challenged by recent studies using DNA sequence …

Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

JE Schmidt, AD Kent, VL Brisson, ACM Gaudin - Microbiome, 2019 - Springer
Background Rhizosphere microbial communities are key regulators of plant performance,
yet few studies have assessed the impact of different management approaches on the …