The multi-kingdom microbiome catalog of the chicken gastrointestinal tract

Y Wang, M Qu, Y Bi, WJ Liu, S Ma, B Wan, Y Hu… - Biosafety and …, 2024 - mednexus.org
Chicken is an important food animal worldwide and plays an important role in human life by
providing meat and eggs. Despite recent significant advances in gut microbiome studies, a …

Biogeographic patterns and drivers of soil viromes

B Ma, Y Wang, K Zhao, E Stirling, X Lv, Y Yu… - Nature Ecology & …, 2024 - nature.com
Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on
soil viromes have been limited in both spatial scale and biome coverage. Here we present a …

Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria

S Karimian, N Farahmandzad… - World Journal of …, 2024 - Springer
Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less
than the detectable level. The non-genetic approaches including biological interactions …

Acidophilic partial nitrification (pH< 6) facilitates ultra-efficient short-flow nitrogen transformation: experimental validation and genomic insights

F Zhang, Z Du, J Wang, Y Du, Y Peng - Water Research, 2024 - Elsevier
Partial nitrification (PN) represents an energy-efficient bioprocess; however, it often
confronts challenges such as unstable nitrite accumulation, nitrite oxidizing bacteria shocks …

Unlocking partial nitrification by acidophilic microorganisms in ultra-low strength wastewater: Long-term investigation and genomic insights

F Zhang, Z Du, J Wang, Y Peng - Chemical Engineering Journal, 2024 - Elsevier
Achieving partial nitrification (PN) in low-strength wastewater is still a worldwide issue. In
this study, conversion from nitrification to PN was successfully achieved with a self-sustained …

Molecular mechanism for target RNA recognition and cleavage of Cas13h

F Chen, C Zhang, J Xue, F Wang, Z Li - Nucleic Acids Research, 2024 - academic.oup.com
Abstract RNA-targeting type VI CRISPR-Cas effectors are widely used in RNA applications.
Cas13h is a recently identified subtype of Cas13 ribonuclease, with strong RNA cleavage …

[HTML][HTML] From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

WE Anthony, SD Allison, CM Broderick… - Environmental …, 2024 - Springer
Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic
analysis is generating vast amounts of data, creating immense challenges in sequence …

[HTML][HTML] Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic,(micro) eukaryotic, and viral multi …

JL Espinoza, A Phillips, MB Prentice, GS Tan… - bioRxiv, 2024 - ncbi.nlm.nih.gov
The microbiome is a complex community of microorganisms, encompassing prokaryotic
(bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a …

Microflora Danica: the atlas of Danish environmental microbiomes

CM Singleton, TBN Jensen, F Delogu, EA Sørensen… - bioRxiv, 2024 - biorxiv.org
The last 20 years have witnessed unprecedented advances in revealing the microbiomes
underpinning important processes in natural and human associated environments. Recent …

Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity

R Chikhi, B Raffestin, A Korobeynikov, RC Edgar… - bioRxiv, 2024 - biorxiv.org
The NCBI Sequence Read Archive (SRA) is the largest public repository of DNA sequencing
data, containing the most comprehensive snapshot of Earth's genetic diversity to date. As its …