Buck S Samuel

Buck S Samuel
Baylor College of Medicine | BCM · Department of Molecular Virology & Microbiology

PhD

About

28
Publications
8,256
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Introduction
Microbes are exquisite architects of both host physiology and the world around us. Research in my lab aims to comprehensively identify the molecular pathways that govern host-microbial interactions to influence host health. To this end, we have developed the high-throughput amenable and robust model C. elegans as a both a natural and translational system for microbiome research. We have leveraged this system to identify conserved genetic circuits that can be used to manage microbiome influence.
Additional affiliations
January 2008 - December 2014
Massachusetts General Hospital / Harvard Medical School
Position
  • PostDoc Position
September 2002 - December 2007
Washington University in St. Louis
Position
  • PhD Student
Education
September 2002 - December 2007
Washington University in St. Louis
Field of study
  • Molecular Microbiology and Genomics

Publications

Publications (28)
Article
Full-text available
The nematode Caenorhabditis elegans is used as a central model system across biological disciplines. Surprisingly, almost all research with this worm is performed in the absence of its native microbiome, possibly affecting generality of the obtained results. In fact, the C. elegans microbiome had been unknown until recently. This review brings toge...
Article
Full-text available
Most Caenorhabditis elegans studies have used laboratory Escherichia coli as diet and microbial environment. Here we characterize bacteria of C. elegans' natural habitats of rotting fruits and vegetation to provide greater context for its physiological responses. By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety...
Article
Full-text available
Mitochondrial function is challenged by toxic by-products of metabolism as well as by pathogen attack. Caenorhabditis elegans normally responds to mitochondrial dysfunction with activation of mitochondrial-repair, drug-detoxification and pathogen-response pathways. Here, from a genome-wide RNA interference (RNAi) screen, we identified 45 C. elegans...
Article
Full-text available
The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome (“microbiome”) contains at least 100 times as many genes as our own genome. We analyzed ∼78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction–amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy...
Article
Full-text available
Background: The initial acquisition and early development of the intestinal microbiome during infancy are important to human health across the lifespan. Mode of birth, antibiotic administration, environment of care, and nutrition have all been shown to play a role in the assembly of the intestinal microbiome during early life. For preterm infants,...
Article
Full-text available
The gut microbiota is essential for maintenance and repair of the intestinal epithelial barrier. As shifts in both intestinal epithelial barrier function and microbiota composition are found in inflammatory bowel disease patients, it is critical to understand the role of distinct bacteria in regulating barrier repair. We identified a mouse commensa...
Article
Full-text available
Hydrogen peroxide (H 2 O 2 ) is the most common chemical threat that organisms face. Here, we show that H 2 O 2 alters the bacterial food preference of Caenorhabditis elegans , enabling the nematodes to find a safe environment with food. H 2 O 2 induces the nematodes to leave food patches of laboratory and microbiome bacteria when those bacterial c...
Article
Full-text available
Background Skin-penetrating nematodes of the genus Strongyloides infect over 600 million people, posing a major global health burden. Their life cycle includes both a parasitic and free-living generation. During the parasitic generation, infective third-stage larvae (iL3s) actively engage in host seeking. During the free-living generation, the nema...
Preprint
Full-text available
Hydrogen peroxide (H 2 O 2 ) is the most common chemical threat that organisms face. Here, we show that H 2 O 2 alters the bacterial food preference of Caenorhabditis elegans , enabling the nematodes to find a safe environment with food. H 2 O 2 induces the nematodes to leave food patches of laboratory and microbiome bacteria when those bacterial c...
Article
Full-text available
Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to the establishment of distinct physiological environments. However, the genetic determinants contributing to the stability and variation of these microbiome types remain largely undefined. Here, we use the free-living nematode Caenorhabditis elegans to identif...
Article
Full-text available
The free-living nematode C.elegans remains one of the most robust and flexible genetic systems for interrogating the complexities of animal biology. Targeted genetic manipulations, such as RNA interference (RNAi), CRISPR/Cas9- or array-based transgenesis, all depend on initial delivery of nucleic acids. Delivery of dsRNA by feeding can be effective...
Preprint
Full-text available
Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to the establishment of distinct physiological environments. However, the genetic determinants contributing to the stability and variation of these microbiome types remain largely undefined. Here, we use the free-living nematode Caenorhabditis elegans to identif...
Preprint
Full-text available
The free-living nematode C. elegans remains one of the most robust and flexible genetic systems for interrogating the complexities of animal biology. Targeted genetic manipulations, such as RNA interference (RNAi), CRISPR/Cas9- or array-based transgenesis, all depend on initial delivery of nucleic acids. Delivery of dsRNA by feeding can be effectiv...
Article
Full-text available
The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic c...
Chapter
The gut microbiome is an important driver of host physiology and development. Altered abundance or membership of this microbe community can influence host health and disease progression, including the determination of host lifespan and healthspan. Here, we describe a robust pipeline to measure microbiome abundance and composition in the C. elegans...
Preprint
Full-text available
The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic c...
Article
The work of Zeevi et al. (2019) in a recent issue of Nature shows that variations in gene content and organization between different strains of the same microbial species are widespread in the human gut microbiota and could be linked to many measures of health.
Article
Full-text available
Escherichia coli encodes two DNA ligases, ligase A, which is essential under normal laboratory growth conditions, and ligase B, which is not. Here we report potential functions of ligase B. We found that across the entire Enterobacteriaceae family, ligase B is highly conserved in both amino acid identity and synteny with genes associated with oxida...
Data
Three-dimensional visualization of the results of the Principle Coordinate Analysis. Figure 2A of the main text shows part of the same results. Both are based on the same analysis. The color code is similar to that of Figure 2A: red, rotting stem substrates; dark red, compost substrates; orange, vector substrates; light blue, rotting fruit substrat...
Data
Heatmap of the relative abundance of 14 bacterial families that are present in 100% of the natural worm microbiomes. See legend on the right for abundance levels. Taxa and boxes in red highlight those that are abundant also in lab-enriched and microcosm microbiotas. The heatmap for the worm samples is also shown in Figure 3C of the main text, but h...
Data
Overview of included data sets, sequence accession numbers, and considered meta-data.
Data
Overview of identified operational taxonomic units (OTUs). Sheet I shows the identified OTUs and their abundances in the C. elegans samples, while sheet II those for substrate samples. Sheet III presents a list of all OTUs with their taxonomic classification. Sheet IV gives the 260 OTUs commonly found among the nematode samples, including the corre...
Article
Full-text available
Host-associated microbiomes influence host health. However, it is unclear whether genotypic variations in host organisms influence the microbiome in ways that have adaptive consequences for the host. Here, we show that wild accessions of Arabidopsis thaliana differ in their ability to associate with the root-associated bacterium Pseudomonas fluores...
Article
Full-text available
The distal human intestine harbors trillions of microbes that allow us to extract calories from otherwise indigestible dietary polysaccharides. The products of polysaccharide fermentation include short-chain fatty acids that are ligands for Gpr41, a G protein-coupled receptor expressed by a subset of enteroendocrine cells in the gut epithelium. To...
Article
Full-text available
The human gut is home to trillions of microbes, thousands of bacterial phylotypes, as well as hydrogen-consuming methanogenic archaea. Studies in gnotobiotic mice indicate that Methanobrevibacter smithii, the dominant archaeon in the human gut ecosystem, affects the specificity and efficiency of bacterial digestion of dietary polysaccharides, there...
Article
Full-text available
Our colons harbor trillions of microbes including a prominent archaeon, Methanobrevibacter smithii. To examine the contributions of Archaea to digestive health, we colonized germ-free mice with Bacteroides thetaiotaomicron, an adaptive bacterial forager of the polysaccharides that we consume, with or without M. smithii or the sulfate-reducing bacte...
Article
Full-text available
Animals have developed the means for supporting complex and dynamic consortia of microorganisms during their life cycle. A transcendent view of vertebrate biology therefore requires an understanding of the contributions of these indigenous microbial communities to host development and adult physiology. These contributions are most obvious in the gu...

Projects

Projects (2)
Project
Intestinal helminth infections plague much of the world’s population [>1-2 billion people] and inflict a wide spectrum of morbidity and mortality upon their hosts. This burden falls more heavily on impoverished nations and contributes to humanity’s five-million-year loss of ‘healthy’ lifespan. Though anti-helminth drugs do exist and can be effective, resistance to these drugs is precipitously on the rise. Thus, there is a need to advance our molecular understanding of the biology of these parasites to identify new ways to control helminth infections. Helminth parasites inhabit the intestine during their life cycle along with a complex community of microbes termed the microbiome. Disruption of the microbiome, an essential component of our health, can itself cause significant alterations in our health and physiology. What is often overlooked is the impact of our microbiome on the parasites themselves. Indeed, several parasites recruit members of this microbial community—e.g., Strongyloides, Trichuris spp. and others. These parasite microbiomes can positively influence the survival and physiology of the host parasite.
Project
We are interested in dissecting the molecular foundations of microbial influences on host health using C. elegans and its natural microbiome.