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 …

Tara Oceans: towards global ocean ecosystems biology

S Sunagawa, SG Acinas, P Bork, C Bowler… - Nature Reviews …, 2020‏ - nature.com
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate
change, is crucial. Here, we review the work of Tara Oceans, an international …

Patterns in soil microbial diversity across Europe

M Labouyrie, C Ballabio, F Romero, P Panagos… - Nature …, 2023‏ - nature.com
Factors driving microbial community composition and diversity are well established but the
relationship with microbial functioning is poorly understood, especially at large scales. We …

Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally

Z Peng, X Qian, Y Liu, X Li, H Gao, Y An, J Qi… - Nature …, 2024‏ - nature.com
Agriculture contributes to a decline in local species diversity and to above-and below-
ground biotic homogenization. Here, we conduct a continental survey using 1185 soil …

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 …

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 …

Erosion reduces soil microbial diversity, network complexity and multifunctionality

L Qiu, Q Zhang, H Zhu, PB Reich, S Banerjee… - The ISME …, 2021‏ - academic.oup.com
While soil erosion drives land degradation, the impact of erosion on soil microbial
communities and multiple soil functions remains unclear. This hinders our ability to assess …

microeco: an R package for data mining in microbial community ecology

C Liu, Y Cui, X Li, M Yao - FEMS microbiology ecology, 2021‏ - academic.oup.com
ABSTRACT A large amount of sequencing data is produced in microbial community ecology
studies using the high-throughput sequencing technique, especially amplicon-sequencing …

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 …

Effects of microplastics and nitrogen deposition on soil multifunctionality, particularly C and N cycling

S Zhang, L Pei, Y Zhao, J Shan, X Zheng, G Xu… - Journal of Hazardous …, 2023‏ - Elsevier
Both nitrogen deposition (ND) and microplastics (MPs) pose global change challenges. The
effects of MPs co-existing with ND on ecosystem functions are still largely unknown. Herein …