Contamination in low microbial biomass microbiome studies: issues and recommendations

R Eisenhofer, JJ Minich, C Marotz, A Cooper… - Trends in …, 2019 - cell.com
Next-generation sequencing approaches in microbiome research have allowed surveys of
microbial communities, their genomes, and their functions with higher sensitivity than ever …

Where less may be more: how the rare biosphere pulls ecosystems strings

A Jousset, C Bienhold, A Chatzinotas… - The ISME …, 2017 - academic.oup.com
Rare species are increasingly recognized as crucial, yet vulnerable components of Earth's
ecosystems. This is also true for microbial communities, which are typically composed of a …

Beyond microbial diversity for predicting soil functions: A mini review

P Nannipieri, J Ascher-Jenull, MT Ceccherini… - Pedosphere, 2020 - Elsevier
Since the advent of sequencing technologies, the determination of microbial diversity to
predict microbial functions, which are the major determinants of soil functions, has become a …

Temporal patterns of rarity provide a more complete view of microbial diversity

A Shade, JA Gilbert - Trends in microbiology, 2015 - cell.com
Recently, conditionally rare taxa (CRTs)–those taxa that are typically in very low abundance
but occasionally achieve prevalence–were shown to contribute to patterns of microbial …

Exploring the secretomes of microbes and microbial communities using filamentous phage display

D Gagic, M Ciric, WX Wen, F Ng… - Frontiers in microbiology, 2016 - frontiersin.org
Microbial surface and secreted proteins (the secretome) contain a large number of proteins
that interact with other microbes, host and/or environment. These proteins are exported by …

Emerging methods to study bacteriophage infection at the single-cell level

VT Dang, MB Sullivan - Frontiers in Microbiology, 2014 - frontiersin.org
Bacteria and their viruses (phages) are abundant across diverse ecosystems and their
interactions influence global biogeochemical cycles and incidence of disease …

Preliminary evidences of the presence of extracellular DNA single stranded forms in soil

SI Pathan, P Arfaioli, MT Ceccherini, J Ascher-Jenull… - PLoS …, 2020 - journals.plos.org
The relevance of extracellular DNA (eDNA) in the soil ecosystem is becoming more and
more evident to the scientific community by the progressive discovery of functions …

The use of random forests modelling to detect yeast-mannan sensitive bacterial changes in the broiler cecum

A Corrigan, N Russell, M Welge, L Auvil, C Bushell… - Scientific reports, 2018 - nature.com
In this study, sequencing of the 16S rRNA gene targeting the V4-V6 regions was conducted
to assess the cecal microbial alterations in response to dietary supplementation with a yeast …

Genome-wide capture sequencing to detect hepatitis C virus at the end of antiviral therapy

P Peng, Y Xu, MW Fried, AM Di Bisceglie… - BMC Infectious …, 2020 - Springer
Background Viral relapse is a major concern in hepatitis C virus (HCV) antiviral therapy.
Currently, there are no satisfactory methods to predict viral relapse, especially in the era of …

Construction of an experimental study and addition of adapter sequences using HiDi DNA polymerase for improving DNA normalization methods relevant to novel …

Y Uenosono, R Kawakami, S Matsumoto… - Journal of …, 2023 - Elsevier
Microorganisms in the environment can be distinguished into dominant and rare microbial
species based on their genes. It is difficult to obtain genetic information derived from rare …