Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic

M Klapper, A Hübner, A Ibrahim, I Wasmuth, M Borry… - Science, 2023 - science.org
Major advances over the past decade in the field of ancient DNA are providing access to
past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this …

[HTML][HTML] aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow

Z Pochon, N Bergfeldt, E Kırdök, M Vicente, T Naidoo… - Genome Biology, 2023 - Springer
Abstract Analysis of microbial data from archaeological samples is a growing field with great
potential for understanding ancient environments, lifestyles, and diseases. However, high …

[HTML][HTML] Sustained bacterial N2O reduction at acidic pH

G He, G Chen, Y Xie, CM Swift, D Ramirez… - Nature …, 2024 - nature.com
Nitrous oxide (N2O) is a climate-active gas with emissions predicted to increase due to
agricultural intensification. Microbial reduction of N2O to dinitrogen (N2) is the major …

metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data

H Zafeiropoulos, M Beracochea, S Ninidakis… - …, 2023 - academic.oup.com
Abstract Background Genomic Observatories (GOs) are sites of long-term scientific study
that undertake regular assessments of the genomic biodiversity. The European Marine …

Improving viral annotation with artificial intelligence

ZN Flamholz, C Li, L Kelly - Mbio, 2024 - journals.asm.org
ABSTRACT Viruses of bacteria,“phages,” are fundamental, poorly understood components
of microbial community structure and function. Additionally, their dependence on hosts for …

Microbial Bioremediation and Multiomics Technologies for Sustainable Development: Recent Trends

F Ameen, SA Bhat, V Kumar - 2024 - books.google.com
The steadily increasing presence of both natural and anthropogenic pollutants in our
environment poses a considerable challenge, given the recalcitrance of many of these …

[HTML][HTML] Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden

G Westmeijer, F van Dam, R Kietäväinen… - Communications …, 2024 - nature.com
The continental bedrock contains groundwater-bearing fractures that are home to microbial
populations that are vital in mediating the Earth's biogeochemical cycles. However, their …

Presence of Fe(II) and nitrate shapes aquifer-originating communities leading to an autotrophic enrichment dominated by an Fe(II)-oxidizing Gallionellaceae sp

N Jakus, N Blackwell, D Straub… - FEMS Microbiology …, 2021 - academic.oup.com
Autotrophic nitrate reduction coupled to Fe (II) oxidation is an important nitrate removal
process in anoxic aquifers. However, it remains unknown how changes of O2 and carbon …

Metaphor—a workflow for streamlined assembly and binning of metagenomes

VW Salazar, B Shaban, MM Quiroga, R Turnbull… - …, 2023 - academic.oup.com
Recent advances in bioinformatics and high-throughput sequencing have enabled the large-
scale recovery of genomes from metagenomes. This has the potential to bring important …

Optimized method for bacterial nucleic acid extraction from positive blood culture broth for whole-genome sequencing, resistance phenotype prediction, and …

MJ Bauer, AM Peri, L Lüftinger, S Beisken… - Journal of Clinical …, 2022 - Am Soc Microbiol
The application of direct metagenomic sequencing from positive blood culture broth may
solve the challenges of sequencing from low-bacterial-load blood samples in patients with …