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Article
Open AccessImplementation of pooled saliva tests for universal screening of cCMV infection
Congenital cytomegalovirus (cCMV) is the most common intrauterine infection, leading to neurodevelopmental disabilities. Universal newborn infant screening of cCMV has been increasingly advocated. In the absen...
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Article
Open AccessLongitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition
Breast milk contains human milk oligosaccharides (HMOs) that cannot be digested by infants, yet nourish their develo** gut microbiome. While Bifidobacterium are the best-known utilizers of individual HMOs, a lo...
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Article
Open AccessCRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei
The infant gut microbiome is impacted by early-life feeding, as human milk oligosaccharides (HMOs) found in breastmilk cannot be digested by infants and serve as nutrients for their gut bacteria. While the vas...
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Article
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluat...
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Open AccessLongitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis
Complex interactions between the gut microbiome and immune cells in infancy are thought to be part of the pathogenesis for the marked rise in pediatric allergic diseases, particularly food allergies. Food prot...
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Article
The evolution, evolvability and engineering of gene regulatory DNA
Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal phenotype and fitness1–3. Constructing complete fitness landscapes, in which DNA sequences are mapped to fitness, is a long-s...
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Article
Open AccessLessons learned from the prenatal microbiome controversy
For more than a century, the prenatal environment was considered sterile. Over the last few years, findings obtained with next-generation sequencing approaches from samples of the placenta, the amniotic fluid,...
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Publisher Correction: Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life
In the version of this Article originally published, in the first sentence of the second paragraph of the Discussion section, the word “operingrationally” should have read “operationally”. This has now been am...
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Article
Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life
The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on g...
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Article
Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes
Identifying immunodominant T cell epitopes remains a significant challenge in the context of infectious disease, autoimmunity, and immuno-oncology. To address the challenge of antigen discovery, we developed a...
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Article
Open AccessA novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functi...
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Article
Open AccessSub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes
Obesity and type 2 diabetes (T2D) are linked both with host genetics and with environmental factors, including dysbioses of the gut microbiota. However, it is unclear whether these microbial changes precede di...
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Article
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ec...
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Article
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Reconstructing full-length transcripts from high-throughput RNA sequencing data is difficult without a reference genome sequence. Grabherr et al. describe Trinity, an algorithm for assembling full-length transcri...
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Development and evaluation of RNA-seq methods
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Comprehensive comparative analysis of strand-specific RNA sequencing methods
The authors compare quality metrics of libraries from seven strand-specific RNA-seq methods in terms of complexity, strand specificity, evenness and continuity of coverage, and expression profiling. They provi...
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Article
Open AccessStrand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
Recent studies in budding yeast have shown that antisense transcription occurs at many loci. However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been sugg...
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Article
Open AccessRNA polymerase map** during stress responses reveals widespread nonproductive transcription in yeast
The use of genome-wide RNA abundance profiling by microarrays and deep sequencing has spurred a revolution in our understanding of transcriptional control. However, changes in mRNA abundance reflect the combin...
