A practical guide to amplicon and metagenomic analysis of microbiome data

YX Liu, Y Qin, T Chen, M Lu, X Qian, X Guo… - Protein & cell, 2021 - academic.oup.com
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the
field of microbiome research, and massive microbiome datasets are now being generated …

Rhizosphere microbiome assembly and its impact on plant growth

Q Qu, Z Zhang, W Peijnenburg, W Liu… - Journal of agricultural …, 2020 - ACS Publications
Microorganisms colonizing the plant rhizosphere provide a number of beneficial functions
for their host. Although an increasing number of investigations clarified the great functional …

ImageGP: An easy‐to‐use data visualization web server for scientific researchers

T Chen, YX Liu, L Huang - Imeta, 2022 - Wiley Online Library
Data visualization plays a crucial role in illustrating results and sharing knowledge among
researchers. Though many types of visualization tools are widely used, most of them require …

EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research

YX Liu, L Chen, T Ma, X Li, M Zheng, X Zhou, L Chen… - Imeta, 2023 - Wiley Online Library
It is difficult for beginners to learn and use amplicon analysis software because there are so
many software tools to choose from, and all of them need multiple steps of operation. Herein …

PICRUSt2: An improved and extensible approach for metagenome inference

GM Douglas, VJ Maffei, J Zaneveld, SN Yurgel… - BioRxiv, 2019 - biorxiv.org
One major limitation of microbial community marker gene sequencing is that it does not
provide direct information on the functional composition of sampled communities. Here, we …

Biodegradable microplastics enhance soil microbial network complexity and ecological stochasticity

Y Sun, X Li, N Cao, C Duan, C Ding, Y Huang… - Journal of Hazardous …, 2022 - Elsevier
Biodegradable plastics have emerged as an ecological alternative to conventional
petroleum-based plastics. Despite the recent advances in the effects of conventional …

From hairballs to hypotheses–biological insights from microbial networks

L Röttjers, K Faust - FEMS microbiology reviews, 2018 - academic.oup.com
Microbial networks are an increasingly popular tool to investigate microbial community
structure, as they integrate multiple types of information and may represent systems-level …

Comparative analyses of vertebrate gut microbiomes reveal convergence between birds and bats

SJ Song, JG Sanders, F Delsuc, J Metcalf, K Amato… - MBio, 2020 - journals.asm.org
Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome
in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages …

Salinity is a key determinant for soil microbial communities in a desert ecosystem

K Zhang, Y Shi, X Cui, P Yue, K Li, X Liu, BM Tripathi… - Msystems, 2019 - journals.asm.org
Soil salinization is a growing environmental problem caused by both natural and human
activities. Excessive salinity in soil suppresses growth, decreases species diversity, and …

Microplastics act as vectors for antibiotic resistance genes in landfill leachate: The enhanced roles of the long-term aging process

Y Su, Z Zhang, J Zhu, J Shi, H Wei, B **e, H Shi - Environmental Pollution, 2021 - Elsevier
Microplastics (MPs) are found to be ubiquitous and serve as vectors for other contaminants,
and the inevitable aging process changes MP properties and fates. However, whether the …