Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity

JP Shaffer, LF Nothias, LR Thompson, JG Sanders… - Nature …, 2022 - nature.com
Despite advances in sequencing, lack of standardization makes comparisons across studies
challenging and hampers insights into the structure and function of microbial communities …

Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data

GI Austin, H Park, Y Meydan, D Seeram, T Sezin… - Nature …, 2023 - nature.com
Sequencing-based approaches for the analysis of microbial communities are susceptible to
contamination, which could mask biological signals or generate artifactual ones. Methods for …

A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities

JP Shaffer, CS Carpenter, C Martino, RA Salido… - …, 2022 - Taylor & Francis
Microbial communities contain a broad phylogenetic diversity of organisms; however, the
majority of methods center on describing bacteria and archaea. Fungi are important …

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

C Marotz, P Belda-Ferre, F Ali, P Das, S Huang… - Microbiome, 2021 - Springer
Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019
(COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies …

Multi-omics analysis of nitrifying sludge under carbon disulfide stress: Nitrification performance and molecular mechanisms

Q Liu, J Chen, Q Zhou, Y Hou, Z Li, W Li, S Lv, N Ren… - Water Research, 2024 - Elsevier
Carbon disulfide (CS 2) is a widely used enzyme inhibitor with cytotoxic properties,
commonly employed in viscose fibers and cellophane production due to its non-polar …

Evaluation of 96‐well high‐throughput DNA extraction methods for 16S rRNA gene metabarcoding

MP Chapuis, L Benoit, M Galan - Molecular Ecology Resources, 2023 - Wiley Online Library
Gaining meaningful insights into bacterial communities associated with animal hosts
requires the provision of high‐quality nucleic acids. Although many studies have compared …

Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus)

C Tang-Wing, I Mohanty, MK Bryant, K Makowski… - Msystems, 2024 - journals.asm.org
Gastrointestinal diseases are the most frequently reported clinical problems in captive
common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal …

Selective extracellular DNA (exDNA) extraction method reveals underestimated associations between extracellular antibiotic resistance genes and bacteria in diverse …

Q Yuan, S Wang, Y Chen, X Li, Y Xu, R Li… - Journal of …, 2023 - Elsevier
Extracellular antibiotic resistance genes (exARGs) constitute a significant type of antibiotic
resistance genes. However, current exARGs studies are restricted due to the lack of efficient …

Gut-associated microbes are present and active in the pig nasal cavity

P Obregon-Gutierrez, L Bonillo-Lopez, F Correa-Fiz… - Scientific reports, 2024 - nature.com
The nasal microbiota is a key contributor to animal health, and characterizing the nasal
microbiota composition is an important step towards elucidating the role of its different …

Effects of variation in urine sample storage conditions on 16S urogenital microbiome analyses

T Kumar, MK Bryant, K Cantrell, SJ Song, D McDonald… - Msystems, 2023 - Am Soc Microbiol
Replicability is a well-established challenge in microbiome research with a variety of
contributing factors at all stages, from sample collection to code execution. Here, we focus …