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Sequencing-based analysis of microbiomes
Microbiomes occupy a range of niches and, in addition to having diverse compositions, they have varied functional roles that have an impact on agriculture, environmental sciences, and human health and disease....
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Open AccessTemperature-dependent differences in mouse gut motility are mediated by stress
Researchers have advocated elevating mouse housing temperatures from the conventional ~22 °C to the mouse thermoneutral point of 30 °C to enhance translational research. However, the impact of environmental te...
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Phage-inclusive profiling of human gut microbiomes with Phanta
Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based...
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Quantifying bias introduced by sample collection in relative and absolute microbiome measurements
To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidenc...
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Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron
Serine hydrolases have important roles in signaling and human metabolism, yet little is known about their functions in gut commensal bacteria. Using bioinformatics and chemoproteomics, we identify serine hydro...
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Phage diversity in cell-free DNA identifies bacterial pathogens in human sepsis cases
Bacteriophages, viruses that infect bacteria, have great specificity for their bacterial hosts at the strain and species level. However, the relationship between the phageome and associated bacterial populatio...
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Open AccessAntimicrobial exposure is associated with decreased survival in triple-negative breast cancer
Antimicrobial exposure during curative-intent treatment of triple-negative breast cancer (TNBC) may lead to gut microbiome dysbiosis, decreased circulating and tumor-infiltrating lymphocytes, and inferior outc...
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Open AccessSystematic discovery of recombinases for efficient integration of large DNA sequences into the human genome
Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characte...
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Equitable partnerships and the path to inclusive, innovative and impactful human microbiome research
Practical recommendations on achieving equitability in biomedical research can advance essential efforts to balance research representation. In this Comment, we highlight how to generate interoperable and robu...
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Open AccessA compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients
Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled a large-scale longitudinal dataset of fecal microbiota and ...
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Open AccessShort- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa
Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extr...
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Open AccessRare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults
Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may ...
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Open AccessPublisher Correction: Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA
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Open AccessStandardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA
Patients with COVID-19 shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. This may be significant for patient health, epidemiology, and diagnosis. However, methods to p...
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Simultaneous ribosome profiling of hundreds of microbes from the human microbiome
Ribosome profiling enables sequencing of ribosome-bound fragments of RNA, revealing which transcripts are being translated as well as the position of ribosomes along mRNAs. Although ribosome profiling has been...
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Open AccessMetagenomic compendium of 189,680 DNA viruses from the human gut microbiome
Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that c...
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Open AccessComparative genomics identifies thousands of candidate structured RNAs in human microbiomes
Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic seque...
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Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome
Short-read metagenomic sequencing and de novo genome assembly of the human gut microbiome can yield draft bacterial genomes without isolation and culture. However, bacterial genomes assembled from short-read s...
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Open AccessMicrobes and microbiomes in 2020 and beyond
In the next decade, advances in our understanding of microbes and microbiomes will likely transform our way of life; providing novel therapeutics, alternate energy sources, and sha** fundamental doctrines of...
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Open AccessMetaRibo-Seq measures translation in microbiomes
No method exists to measure large-scale translation of genes in uncultured organisms in microbiomes. To overcome this limitation, we develop MetaRibo-Seq, a method for simultaneous ribosome profiling of tens t...
