[HTML][HTML] 25 years of serving the community with ribosomal RNA gene reference databases and tools

FO Glöckner, P Yilmaz, C Quast, J Gerken… - Journal of …, 2017 - Elsevier
SILVA (lat. forest) is a comprehensive web resource, providing services around up to date,
high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria …

[HTML][HTML] Akkermansia muciniphila in the human gastrointestinal tract: when, where, and how?

SY Geerlings, I Kostopoulos, WM De Vos, C Belzer - Microorganisms, 2018 - mdpi.com
Akkermansia muciniphila is a mucin-degrading bacterium of the phylum Verrucomicrobia. Its
abundance in the human intestinal tract is inversely correlated to several disease states. A …

Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major …

DW Waite, M Chuvochina, C Pelikan… - … of Systematic and …, 2020 - microbiologyresearch.org
The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of
bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although …

Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species

Z Zhou, C Zhang, P Liu, L Fu, R Laso-Pérez, L Yang… - Nature, 2022 - nature.com
The methanogenic degradation of oil hydrocarbons can proceed through syntrophic
partnerships of hydrocarbon-degrading bacteria and methanogenic archaea,–. However …

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

CM Singleton, F Petriglieri, JM Kristensen… - Nature …, 2021 - nature.com
Microorganisms play crucial roles in water recycling, pollution removal and resource
recovery in the wastewater industry. The structure of these microbial communities is …

Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid production

EC Deehan, C Yang, ME Perez-Muñoz, NK Nguyen… - Cell host & …, 2020 - cell.com
Dietary fibers (DFs) impact the gut microbiome in ways often considered beneficial.
However, it is unknown if precise and predictable manipulations of the gut microbiota, and …

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

DH Parks, M Chuvochina, DW Waite, C Rinke… - Nature …, 2018 - nature.com
Taxonomy is an organizing principle of biology and is ideally based on evolutionary
relationships among organisms. Development of a robust bacterial taxonomy has been …

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

DH Parks, C Rinke, M Chuvochina, PA Chaumeil… - Nature …, 2017 - nature.com
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently
available microbial genomes. This is being addressed by advances in sequencing …

[LIBRO][B] Environmental DNA: For biodiversity research and monitoring

P Taberlet, A Bonin, L Zinger, E Coissac - 2018 - books.google.com
Environmental DNA (eDNA) refers to DNA that can be extracted from environmental
samples (such as soil, water, feces, or air) without the prior isolation of any target organism …

Bacterial chemolithoautotrophy via manganese oxidation

H Yu, JR Leadbetter - Nature, 2020 - nature.com
Manganese is one of the most abundant elements on Earth. The oxidation of manganese
has long been theorized—yet has not been demonstrated,–—to fuel the growth of …