Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies

S Busato, M Gordon, M Chaudhari, I Jensen… - Current opinion in plant …, 2023 - Elsevier
The plant-associated microbiome is a key component of plant systems, contributing to their
health, growth, and productivity. The application of machine learning (ML) in this field …

Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt

AT Nottingham, JJ Scott, K Saltonstall, K Broders… - Nature …, 2022 - nature.com
Perturbation of soil microbial communities by rising temperatures could have important
consequences for biodiversity and future climate, particularly in tropical forests where high …

[HTML][HTML] Effects of rare microbiome taxa filtering on statistical analysis

Q Cao, X Sun, K Rajesh, N Chalasani… - Frontiers in …, 2021 - frontiersin.org
Background: The accuracy of microbial community detection in 16S rRNA marker-gene and
metagenomic studies suffers from contamination and sequencing errors that lead to either …

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 …

[PDF][PDF] Fecal microbiome distinguishes alcohol consumption from alcoholic hepatitis but does not discriminate disease severity

E Smirnova, P Puri, MD Muthiah, K Daitya… - …, 2020 - Wiley Online Library
Background and Aims The role of the intestinal microbiome in alcoholic hepatitis is not
established. The aims of this study were to (1) characterize the fecal microbial ecology …

[HTML][HTML] Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies

Y Jia, S Zhao, W Guo, L Peng, F Zhao, L Wang… - Environmental …, 2022 - Springer
Background Increasing studies have demonstrated potential disproportionate functional and
ecological contributions of rare taxa in a microbial community. However, the study of the …

[HTML][HTML] The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer

BA Peters, HI Pass, RD Burk, X Xue, C Goparaju… - Genome medicine, 2022 - Springer
Background Cancer recurrence after tumor resection in early-stage non-small cell lung
cancer (NSCLC) is common, yet difficult to predict. The lung microbiota and systemic …

Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome

CJ Sweeney, R Kaushik… - Integrated Environmental …, 2024 - Wiley Online Library
There is increasing interest in further developing the plant protection product (PPP)
environmental risk assessment, particularly within the European Union, to include the …

Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis

K Gutiérrez-García, MRL Whitaker… - ISME …, 2023 - academic.oup.com
Ingestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is
harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich …

[HTML][HTML] Response of the human gut and saliva microbiome to urbanization in Cameroon

A Lokmer, S Aflalo, N Amougou, S Lafosse… - Scientific reports, 2020 - nature.com
Urban populations from highly industrialized countries are characterized by a lower gut
bacterial diversity as well as by changes in composition compared to rural populations from …