Next generation sequencing approaches to evaluate water and wastewater quality

E Garner, BC Davis, E Milligan, MF Blair, I Keenum… - Water Research, 2021 - Elsevier
The emergence of next generation sequencing (NGS) is revolutionizing the potential to
address complex microbiological challenges in the water industry. NGS technologies can …

Environmental biofilms as reservoirs for antimicrobial resistance

G Flores-Vargas, J Bergsveinson… - Frontiers in …, 2021 - frontiersin.org
Characterizing the response of microbial communities to a range of antibiotic concentrations
is one of the strategies used to understand the impact of antibiotic resistance. Many studies …

Coming-of-age characterization of soil viruses: a user's guide to virus isolation, detection within metagenomes, and viromics

G Trubl, P Hyman, S Roux, ST Abedon - Soil Systems, 2020 - mdpi.com
The study of soil viruses, though not new, has languished relative to the study of marine
viruses. This is particularly due to challenges associated with separating virions from …

Analysis of different size fractions provides a more complete perspective of viral diversity in a freshwater embayment

CN Palermo, DW Shea, SM Short - Applied and Environmental …, 2021 - Am Soc Microbiol
Inspired by recent discoveries of the prevalence of large viruses in the environment, we
reassessed the longstanding approach of filtering water through small-pore-size filters to …

Potential applications of human viral metagenomics and reference materials: considerations for current and future viruses

TM Santiago-Rodriguez… - Applied and Environmental …, 2020 - Am Soc Microbiol
Viruses are ubiquitous particles comprising genetic material that can infect bacteria,
archaea, and fungi, as well as human and other animal cells. Given that determining virus …

Viral diversity is linked to bacterial community composition in alpine stream biofilms

M Bekliz, P Pramateftaki, TJ Battin… - ISME …, 2022 - academic.oup.com
Biofilms play pivotal roles in fluvial ecosystems, yet virtually nothing is known about viruses
in these communities. Leveraging an optimized sample-to-sequence pipeline, we studied …

A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples

F Pinto, M Zolfo, F Beghini, F Armanini, F Asnicar… - BioRxiv, 2020 - biorxiv.org
Cultivation-free metagenomic analysis afforded unprecedented details on the diversity,
structure and potential functions of microbial communities in different environments. When …

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

M Bourquin - 2024 - infoscience.epfl.ch
Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by
glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant …

Diversity, Relative Abundance, and Functional Potential of Viral and Bacterial Communities

CN Palermo - 2022 - search.proquest.com
Viral and bacterial communities in Hamilton Harbour were explored to discern seasonal and
spatial changes in diversity, relative abundance, and functional potentials. The following …

Comparing the diversity and relative abundance of free and particle-associated aquatic viruses

CN Palermo, DW Shea, SM Short - bioRxiv, 2020 - biorxiv.org
Metagenomics has enabled rapid increases in virus discovery, in turn permitting revisions of
viral taxonomy and our understanding of the ecology of viruses and their hosts. Inspired by …