[HTML][HTML] The future of biotic indices in the ecogenomic era: Integrating (e) DNA metabarcoding in biological assessment of aquatic ecosystems

J Pawlowski, M Kelly-Quinn, F Altermatt… - Science of the Total …, 2018 - Elsevier
The bioassessment of aquatic ecosystems is currently based on various biotic indices that
use the occurrence and/or abundance of selected taxonomic groups to define ecological …

Taxonomy, ecology and biotechnological applications of thraustochytrids: A review

LF Marchan, KJL Chang, PD Nichols, WJ Mitchell… - Biotechnology …, 2018 - Elsevier
Thraustochytrids were first discovered in 1934, and since the 1960's they have been
increasingly studied for their beneficial and deleterious effects. This review aims to provide …

The gut mycobiome of the Human Microbiome Project healthy cohort

AK Nash, TA Auchtung, MC Wong, DP Smith, JR Gesell… - Microbiome, 2017 - Springer
Background Most studies describing the human gut microbiome in healthy and diseased
states have emphasized the bacterial component, but the fungal microbiome (ie, the …

Biodegradability of polyethylene by bacteria and fungi from Dandora dumpsite Nairobi-Kenya

CN Muhonja, H Makonde, G Magoma, M Imbuga - PloS one, 2018 - journals.plos.org
This study aimed at isolating and identifying bacteria and fungi with the capacity to degrade
low density polyethylene (LDPE). The level of biodegradation of LDPE sheets with bacterial …

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

EP Starr, EE Nuccio, J Pett-Ridge, JF Banfield… - Proceedings of the …, 2019 - pnas.org
Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health,
and biogeochemical processes. However, very little is known about RNA viruses in an …

Design and evaluation of Illumina MiSeq-compatible, 18S rRNA gene-specific primers for improved characterization of mixed phototrophic communities

IM Bradley, AJ Pinto, JS Guest - Applied and environmental …, 2016 - journals.asm.org
The use of high-throughput sequencing technologies with the 16S rRNA gene for
characterization of bacterial and archaeal communities has become routine. However, the …

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

G Lear, I Dickie, J Banks, S Boyer, HL Buckley… - New Zealand Journal of …, 2018 - JSTOR
Advances in the sequencing of DNA extracted from media such as soil and water offer huge
opportunities for biodiversity monitoring and assessment, particularly where the collection or …

Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities

J Urra, I Alkorta, I Mijangos, L Epelde… - Science of the Total …, 2019 - Elsevier
The application of sewage sludge as soil amendment is a common agricultural practice.
However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils …

Diversity of plant DNA in stool is linked to dietary quality, age, and household income

BL Petrone, A Aqeel, S Jiang, HK Durand… - Proceedings of the …, 2023 - pnas.org
Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to
quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast …

Supervised machine learning outperforms taxonomy‐based environmental DNA metabarcoding applied to biomonitoring

T Cordier, D Forster, Y Dufresne… - Molecular ecology …, 2018 - Wiley Online Library
Biodiversity monitoring is the standard for environmental impact assessment of
anthropogenic activities. Several recent studies showed that high‐throughput amplicon …