Bryan D. Merrill
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View article: A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions
A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions Open
Viruses are key modulators of human gut microbiome composition and function. While metagenomic sequencing has enabled culture-independent discovery of gut bacteriophage diversity, existing genomic catalogues suffer from limited geographic …
View article: Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes
Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes Open
View article: Data supporting publication: Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
Data supporting publication: Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes Open
Genomes, mapping databases, and data supporting the publication "Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes". Please see the README on GitHub for descriptions of files and tutorials on how to us…
View article: Data supporting publication: Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
Data supporting publication: Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes Open
Genomes, mapping databases, and data supporting the publication "Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes". Please see the README on GitHub for descriptions of files and tutorials on how to us…
View article: Data supporting publication: Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
Data supporting publication: Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes Open
Genomes, mapping databases, and data supporting the publication "Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes". Please see the README on GitHub for descriptions of files and tutorials on how to us…
View article: Robust variation in infant gut microbiome assembly across a spectrum of lifestyles
Robust variation in infant gut microbiome assembly across a spectrum of lifestyles Open
Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers…
View article: Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles
Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles Open
Infant microbiome assembly is intensely studied in infants from industrialized nations, but little is known about this process in populations living non-industrialized lifestyles. In this study we deeply sequenced infant stool samples from…
View article: Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes Open
Summary The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. H…
View article: The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut
The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut Open
Attempts to explore the role of the microbiota in animal physiology have resulted in large-scale efforts to cultivate the thousands of microbes that are associated with humans. In contrast, relatively few lab mouse-associated bacteria have…
View article: Molecular hallmarks of heterochronic parabiosis at single-cell resolution
Molecular hallmarks of heterochronic parabiosis at single-cell resolution Open
View article: Independent host- and bacterium-based determinants protect a model symbiosis from phage predation
Independent host- and bacterium-based determinants protect a model symbiosis from phage predation Open
View article: A metabolomics pipeline for the mechanistic interrogation of the gut microbiome
A metabolomics pipeline for the mechanistic interrogation of the gut microbiome Open
View article: Gut-microbiota-targeted diets modulate human immune status
Gut-microbiota-targeted diets modulate human immune status Open
View article: Independent host- and bacterium-based determinants protect a model symbiosis from phage predation
Independent host- and bacterium-based determinants protect a model symbiosis from phage predation Open
Summary/Abstract Bacteriophages (phages) are diverse and abundant constituents of microbial communities worldwide, and are capable of modulating bacterial populations in diverse ways. Here we describe a novel phage, ϕHNL01, which infects t…
View article: Community-led, integrated, reproducible multi-omics with anvi’o
Community-led, integrated, reproducible multi-omics with anvi’o Open
View article: Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs
Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs Open
View article: Gut Microbiota-Targeted Diets Modulate Human Immune Status
Gut Microbiota-Targeted Diets Modulate Human Immune Status Open
Diet modulates the gut microbiome, and gut microbes, in turn, can impact the immune system. Here, we used two gut microbiota-targeted dietary interventions, plant-based fiber or fermented foods, to determine how each influences the human m…
View article: Ageing hallmarks exhibit organ-specific temporal signatures
Ageing hallmarks exhibit organ-specific temporal signatures Open
View article: A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse Open
View article: Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions
Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions Open
View article: Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron
Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron Open
View article: <i>Bacteroides thetaiotaomicron</i>-infecting bacteriophage isolates inform sequence-based host range predictions
<i>Bacteroides thetaiotaomicron</i>-infecting bacteriophage isolates inform sequence-based host range predictions Open
Summary Our emerging view of the gut microbiome largely focuses on bacteria and less is known about other microbial components such as of bacteriophages (phages). Though phages are abundant in the gut, very few phages have been isolated fr…
View article: Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs
Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs Open
View article: Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs
Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs Open
Summary That antibiotics alter microbiota composition and increase infection susceptibility is well known, but their generalizable effects on the gut commensal community and dependence on environmental variables remain open questions. Here…
View article: Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in <i>Bacteroides thetaiotaomicron</i>
Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in <i>Bacteroides thetaiotaomicron</i> Open
A variety of cell surface structures, including capsular polysaccharides (CPS), dictate interactions between bacteria and their environment including their viruses (bacteriophages). Members of the prominent human gut Bacteroidetes characte…
View article: Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet and Environmental Reservoirs
Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet and Environmental Reservoirs Open
View article: Bystander Phage Therapy: Inducing Host-Associated Bacteria to Produce Antimicrobial Toxins against the Pathogen Using Phages
Bystander Phage Therapy: Inducing Host-Associated Bacteria to Produce Antimicrobial Toxins against the Pathogen Using Phages Open
Brevibacillus laterosporus is often present in beehives, including presence in hives infected with the causative agent of American Foulbrood (AFB), Paenibacillus larvae. In this work, 12 B. laterosporus bacteriophages induced bactericidal …
View article: Complete Genome Sequences of 18 Paenibacillus larvae Phages from the Western United States
Complete Genome Sequences of 18 Paenibacillus larvae Phages from the Western United States Open
We present here the complete genomes of 18 phages that infect Paenibacillus larvae , the causative agent of American foulbrood in honeybees. The phages were isolated between 2014 and 2016 as part of an undergraduate phage discovery course …
View article: A PCR-Based Method for Distinguishing between Two Common Beehive Bacteria, Paenibacillus larvae and Brevibacillus laterosporus
A PCR-Based Method for Distinguishing between Two Common Beehive Bacteria, Paenibacillus larvae and Brevibacillus laterosporus Open
16S rRNA gene sequencing in bacteria has long been held as the gold standard for typing bacteria and, for the most part, is an excellent method of taxonomically identifying different bacterial species. However, the high level of 16S rRNA s…
View article: Complete Genome Sequences of Paenibacillus larvae Phages BN12, Dragolir, Kiel007, Leyra, Likha, Pagassa, PBL1c, and Tadhana
Complete Genome Sequences of Paenibacillus larvae Phages BN12, Dragolir, Kiel007, Leyra, Likha, Pagassa, PBL1c, and Tadhana Open
We present here the complete genomes of eight phages that infect Paenibacillus larvae , the causative agent of American foulbrood in honeybees. Phage PBL1c was originally isolated in 1984 from a P. larvae lysogen, while the remaining phage…