Forest microbiome and global change
Forests influence climate and mitigate global change through the storage of carbon in soils.
In turn, these complex ecosystems face important challenges, including increases in carbon …
In turn, these complex ecosystems face important challenges, including increases in carbon …
Microbiota succession throughout life from the cradle to the grave
Associations between age and the human microbiota are robust and reproducible. The
microbial composition at several body sites can predict human chronological age relatively …
microbial composition at several body sites can predict human chronological age relatively …
Enumerating soil biodiversity
MA Anthony, SF Bender… - Proceedings of the …, 2023 - National Acad Sciences
Soil is an immense habitat for diverse organisms across the tree of life, but just how many
organisms live in soil is surprisingly unknown. Previous efforts to enumerate soil biodiversity …
organisms live in soil is surprisingly unknown. Previous efforts to enumerate soil biodiversity …
[HTML][HTML] Greengenes2 unifies microbial data in a single reference tree
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually
attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that …
attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that …
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity
Ulcerative colitis (UC) is driven by disruptions in host–microbiota homoeostasis, but current
treatments exclusively target host inflammatory pathways. To understand how host …
treatments exclusively target host inflammatory pathways. To understand how host …
[HTML][HTML] Deciphering cell–cell interactions and communication from gene expression
E Armingol, A Officer, O Harismendy… - Nature Reviews …, 2021 - nature.com
Cell–cell interactions orchestrate organismal development, homeostasis and single-cell
functions. When cells do not properly interact or improperly decode molecular messages …
functions. When cells do not properly interact or improperly decode molecular messages …
[HTML][HTML] RESCRIPt: Reproducible sequence taxonomy reference database management
Nucleotide sequence and taxonomy reference databases are critical resources for
widespread applications including marker-gene and metagenome sequencing for …
widespread applications including marker-gene and metagenome sequencing for …
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 …
specific reactions catalyzed by these biological engines are hard to decode due to the …
[HTML][HTML] MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants
Microbial communities are responsible for biological wastewater treatment, but our
knowledge of their diversity and function is still poor. Here, we sequence more than 5 million …
knowledge of their diversity and function is still poor. Here, we sequence more than 5 million …
[HTML][HTML] Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities
Nutrient scarcity is pervasive for natural microbial communities, affecting species
reproduction and co-existence. However, it remains unclear whether there are general rules …
reproduction and co-existence. However, it remains unclear whether there are general rules …