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 …

Function and functional redundancy in microbial systems

S Louca, MF Polz, F Mazel, MBN Albright… - Nature ecology & …, 2018 - nature.com
Microbial communities often exhibit incredible taxonomic diversity, raising questions
regarding the mechanisms enabling species coexistence and the role of this diversity in …

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 …

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 …

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 …

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 …

DRAM for distilling microbial metabolism to automate the curation of microbiome function

M Shaffer, MA Borton, BB McGivern… - Nucleic acids …, 2020 - academic.oup.com
Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the
specific reactions catalyzed by these biological engines are hard to decode due to the …

Host selection shapes crop microbiome assembly and network complexity

C **ong, YG Zhu, JT Wang, B Singh, LL Han… - New …, 2021 - Wiley Online Library
Plant microbiomes are essential to host health and productivity but the ecological processes
that govern crop microbiome assembly are not fully known. Here we examined bacterial …

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 …

The ecology of the plastisphere: microbial composition, function, assembly, and network in the freshwater and seawater ecosystems

C Li, L Wang, S Ji, M Chang, L Wang, Y Gan, J Liu - Water Research, 2021 - Elsevier
Microplastics provide a unique habitat for microorganisms, forming the plastisphere. Yet the
ecology of the plastisphere, including the microbial composition, functions, assembly …