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Article
Open AccessMAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies
Metagenomic sequencing has provided great advantages in the characterisation of microbiomes, but currently available analysis tools lack the ability to combine subspecies-level taxonomic resolution and accurat...
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Article
Open AccessCo-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition
In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes...
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Open AccessDifferential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults
Despite their crucial importance for human health, there is still relatively limited knowledge on how the gut resistome changes or responds to antibiotic treatment across ages, especially in the latter case. H...
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Article
Open AccessA community resource for paired genomic and metabolomic data mining
Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)gen...
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Article
Open AccessPrenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial
Maternal dietary interventions during pregnancy with fish oil and high dose vitamin D have been shown to reduce the incidence of asthma and wheeze in offspring, potentially through microbial effects in pregnan...
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Article
Open AccessInfant airway microbiota and topical immune perturbations in the origins of childhood asthma
Asthma is believed to arise through early life aberrant immune development in response to environmental exposures that may influence the airway microbiota. Here, we examine the airway microbiota during the fir...
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Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
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Article
Open AccessLong-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages
It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches ...
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Article
Soil bacteria show different tolerance ranges to an unprecedented disturbance
Soil microbial communities have remarkable capacities to cope with ceaseless environmental changes, but little is known about their adaptation potential when facing an unprecedented disturbance. We tested the ...
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Open AccessWarming, shading and a moth outbreak reduce tundra carbon sink strength dramatically by changing plant cover and soil microbial activity
Future increases in temperature and cloud cover will alter plant growth and decomposition of the large carbon pools stored in Arctic soils. A better understanding of interactions between above- and belowground...
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Open AccessLarge-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies
There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of ...
