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Articles by Ruth E. Ley
Extensive genomic diversity in Desulfovibrio reveals species-specific functional traits associated with disease
Abstract Desulfovibrio spp. are associated with inflammatory diseases and human health, yet limited representative genomes and isolates hinder our understanding of their role in disease. Here, we assembled a comprehensive database of 2658 Desulfovibrio genomes across 90 diseases and 32 countries, including 24 human isolates. Genomic analyses showed extensive species diversity and revealed disease-associated functional traits, including flagellin and adaptation-associated genes (i.e., ureases).
Bacterial lipid structural diversity mediates commensalism and pathogenesis
Abstract The human immune system must continuously distinguish between pathogenic bacteria and the numerous symbiotic bacteria that live in and on our bodies. In part, this distinction is driven by host sensing of specific lipid structures that comprise the bacterial membrane. Bacterial lipids from commensal and pathogenic bacteria alike are sensed via lipid recognition receptors, initiating downstream responses in the innate and adaptive immune systems.
Wheat fiber mitigates colitis via non-SCFA microbial metabolite-trained intestinal macrophages
Abstract The advent of highly refined wheat products has reduced fiber consumption, which is associated with increased risk for inflammatory bowel disease (IBD). We found that enriching diets with wheat fiber (WF) protected mice against colitis, especially relative to a low-fiber diet, as assessed by clinical, histopathologic, morphologic, and immunologic parameters.
Dietary fat disrupts a commensal-host lipid network that promotes metabolic health
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Keywords obesity Turicibacter sphingolipids ceramides microbiota metabolism high-fat diet lipids SPT spore-forming bacteria bacterial lipids Introduction Metabolic diseases, including type 2 diabetes (T2D), cardiovascular disease, and fatty liver disease, affect billions worldwide.1,2 Obesity and a Western diet high in fat and sugar place individuals at significant risk for these diseases.3,4,5,6 Diet influences many factors that contribute to obesity, including the composition of the...
By Kendra A. Klag, Trevor S. Tippetts, Sean M. Tatum, Kaylyn M. Bauer, Emmanuel Stephen-Victor, Allison Weis Verified, Rickesha Bell, James Weagley, J. Alan Maschek, Dai Long Vu, Stacey L. Heaver, Ruth E. Ley, Ryan M O’Connell, William L. Holland, Scott Summers, W. Zac Stephens, June Round, Darci Ott, Rebekah J. Nicolson
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Cell Metabolism
Verified
Carbohydrates and the oxidative branch of the pentose phosphate pathway modify Bacteroides thetaiotaomicron phage resistance by phase variable S-layers
Abstract The human gut microbiota consists of hundreds of bacterial species, some of which persist in the presence of lytic phage that infect them. Bacteroides employ numerous phase-variable strategies to survive in the presence of phage, including capsular polysaccharides (CPS) and S-layer lipoproteins. We previously reported that a Bacteroides thetaiotaomicron strain lacking CPS exhibits almost complete resistance to multiple phages when forced to express the S-layer protein BT1927.
Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution - Nature Biotechnology
Abstract Microbial species diversify into strains through single-nucleotide mutations and structural changes, such as recombination, insertions and deletions. Most strain-comparison methods quantify differences in single-nucleotide polymorphisms (SNPs) and are insensitive to structural changes. However, recombination is an important driver of phenotypic diversification in many species, including human pathogens.
Akibat evolusi, mikroba yang ada di usus manusia diwariskan dari generasi ke generasi
Ketika para manusia purba berpindah dari Afrika, mereka membawa serta mikroba usus mereka. Ternyata, mikroba ini juga ikut berevolusi bersama mereka. Mikrobioma yang berada pada usus manusia terdiri dari ratusan hingga ribuan spesies bakteri dan arkea). Dalam satu spesies mikroba tertentu, galur yang berbeda membawa gen yang berbeda yang dapat mempengaruhi kesehatan dan penyakit yang kita idap.
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies - Nature
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Abstract 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.
By Katherine Kennedy, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Peer Bork, Thorsten Braun, Frederic Bushman, Joël Doré, Ashlee M. Earl, Jonathan Eisen, Michal A. Elovitz, Stephanie Ganal-Vonarburg, Michael G Gänzle, Wendy S. Garrett, Lindsay Hall, Mathias Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Alice McHardy, Omry Koren, Trevor D. Lawley, Ruth E. Ley, Liam O’Mahony, Paul O’Toole, Eric G. Pamer, Julian Parkhill, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Harry Sokol, Tim Spector, Michael G. Surette, Alan Walker
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Nature
Verified
Interpreting tree ensemble machine learning models with endoR
endoR outperforms state-of-the-art methods for metagenome data analysis. We utilized 50 AP datasets to evaluate the performance of endoR relative to the state-of-the-art (Fig 4 and S2 Text; results for the 100 FSD are provided in S9 Fig). Our evaluations included non-parametric statistical Wilcoxon rank-sum and χ2 tests, sparse covariance matrices computed with the sparCC [47] and graphical lasso (gLASSOciteFriedman2008glasso) methods, the Gini importance [19, 25], and SHAP values [28].
Humans Evolved With Their Microbiomes - Like Genes, Your Gut Microbes Pass From One Generation to the Next
When the first humans moved out of Africa, they carried their gut microbes with them. Turns out, these microbes also evolved along with them. The human gut microbiome is made up of hundreds to thousands of species of bacteria and archaea. Within a given species of microbe, different strains carry different genes that can affect your health and the diseases you’re susceptible to.
Like genes, your gut microbes pass from one generation to the next
When the first humans moved out of Africa, they carried their gut microbes with them. Turns out, these microbes also evolved along with them. The human gut microbiome is made up of hundreds to thousands of species of bacteria and archaea. Within a given species of microbe, different strains carry different genes that can affect your health and the diseases you’re susceptible to.
Like genes, your gut microbes pass from one generation to the next
Understanding the origins of gut microbes could improve understanding of their role in human health By Taichi A. Suzuki - Ruth Ley Bacteria Lactobacillus in human intestine (Getty Images/nopparit) This article was originally published on The Conversation. When the first humans moved out of Africa, they carried their gut microbes with them.
Humans Evolved With Their Microbiomes: Here’s How
When the first humans moved out of Africa, they carried their gut microbes with them. Turns out, these microbes also evolved along with them. The human gut microbiome is made up of hundreds to thousands of species of bacteria and archaea. Within a given species of microbe, different strains carry different genes that can affect your health and the diseases you’re susceptible to.
Your gut microbes are thousands of generations old - new study
When the first humans moved out of Africa, they carried their gut microbes with them. Turns out, these microbes also evolved along with them. The human gut microbiome is made up of hundreds to thousands of species of bacteria and archaea. Within a given species of microbe, different strains carry different genes that can affect your health and the diseases you’re susceptible to.
Like genes, your gut microbes pass from one generation to the next
When the first humans moved out of Africa, they carried their gut microbes with them. Turns out, these microbes also evolved along with them. The human gut microbiome is made up of hundreds to thousands of species of bacteria and archaea. Within a given species of microbe, different strains carry different genes that can affect your health and the diseases you’re susceptible to.
Humans evolved with their microbiomes. Like genes, your gut microbes pass from one generation to the next
When the first humans moved out of Africa, they carried their gut microbes with them. Turns out, these microbes also evolved along with them. The human gut microbiome is made up of hundreds to thousands of species of bacteria and archaea. Within a given species of microbe, different strains carry different genes that can affect your health and the diseases you're susceptible to.
Humans evolved with their microbiomes
(The Conversation is an independent and nonprofit source of news, analysis and commentary from academic experts.) (THE CONVERSATION) When the first humans moved out of Africa, they carried their gut microbes with them. Turns out, these microbes also evolved along with them.
Humans evolved with their microbiomes - like genes, your gut microbes pass from one generation to the next
When the first humans moved out of Africa, they carried their gut microbes with them. Turns out, these microbes also evolved along with them. The human gut microbiome is made up of hundreds to thousands of species of bacteria and archaea. Within a given species of microbe, different strains carry different genes that can affect your health and the diseases you’re susceptible to.
ResMiCo: increasing the quality of metagenome-assembled genomes with deep learning
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Characterization of inositol lipid metabolism in gut-associated Bacteroidetes - Nature Microbiology
Abstract Inositol lipids are ubiquitous in eukaryotes and have finely tuned roles in cellular signalling and membrane homoeostasis. In Bacteria, however, inositol lipid production is relatively rare. Recently, the prominent human gut bacterium Bacteroides thetaiotaomicron (BT) was reported to produce inositol lipids and sphingolipids, but the pathways remain ambiguous and their prevalence unclear.
The human microbiome: there is much left to do
This week marks the tenth anniversary of the first big survey of microbial diversity in the human body, published in Nature by the Human Microbiome Project (HMP) Consortium, of which I was a member. Before then, microbiologists knew that the body played host to a large mass of microorganisms — a heady mix of bacteria, along with archaea, fungi and viruses, spread over the skin, in the mouth and in the gut — together dubbed the microbiome. But until 2012, we lacked an inventory of them.
Microbiome engineering: Taming the untractable
In this issue of Cell, Jin et al. describe several innovative tools for microbiome engineering to enable in situ editing of complex communities. However, challenges remain to overcome the widespread genetic intractability of microbiome constituents. To read this article in full you will need to make a payment Purchase one-time access: Academic and PersonalCorporate R&D Professionals Read-It-Now Purchase access to all full-text HTML articles for 6 or 36 hr at a low cost.
Interpreting tree ensemble machine learning models with endoR
Abstract Background: Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa or genomic content may be associated. Results: We developed endoR, a method to interpret a fitted tree ensemble model.
SynTracker: a synteny based tool for tracking microbial strains
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The role of the microbiota in human genetic adaptation
Getting to the guts of local evolution The microbiota of mammals is a product of coevolution. However, humans exhibit a range of adaptive peculiarities that can be quite geographically specific. The human microbiota also displays a variety of community compositions and a range of overlapping and redundant metabolic characteristics that can alter host physiology.
Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels
Abstract Gut microbes are linked to host metabolism, but specific mechanisms remain to be uncovered. Ceramides, a type of sphingolipid (SL), have been implicated in the development of a range of metabolic disorders from insulin resistance (IR) to hepatic steatosis. SLs are obtained from the diet and generated by de novo synthesis in mammalian tissues. Another potential, but unexplored, source of mammalian SLs is production by Bacteroidetes, the dominant phylum of the gut microbiome.
Iron Deficiency Causes Wrinkles in Host-Commensal Relationships
Iron is essential for both the host and its resident microbes, resulting in competition under iron-deficient conditions. However, the molecular details underlying this competition are not fully understood. In this issue, Das et al. (2019) Das N.K. Schwartz A.J. Barthel G. Inohara N. Liu Q. Sankar A. Hill D.R. Ma X. Lamberg O. Schnizlein M.K. et al. Microbial metabolite signaling is required for systemic iron homeostasis. Cell Metab.
Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases
Abstract Alterations in gut microbiota composition are associated with metabolic syndrome and chronic inflammatory diseases such as inflammatory bowel disease. One feature of inflammation-associated gut microbiotas is enrichment of motile bacteria, which can facilitate microbiota encroachment into the mucosa and activate pro-inflammatory gene expression.
The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health
Abstract The Christensenellaceae, a recently described family in the phylum Firmicutes, is emerging as an important player in human health. The relative abundance of Christensenellaceae in the human gut is inversely related to host body mass index (BMI) in different populations and multiple studies, making its relationship with BMI the most robust and reproducible link between the microbial ecology of the human gut and metabolic disease reported to date.
Expanding the scope and scale of microbiome research
Although the draft human genome was completed in 2001 [1, 2], only in 2006 [3] did we come to realize that the vast majority of the genes in our own species, or any species, remained uncharacterized in ‘genome projects’. Indeed, our understanding of the roles played by complex microbial communities, often termed ‘microbiomes’, in the human body and in the environment continues to expand dramatically.
The Relationship Between the Human Genome and Microbiome Comes into View
The body’s microbiome, composed of microbial cells that number in the trillions, is involved in human health and disease in ways that are just starting to emerge. The microbiome is assembled at birth, develops with its host, and is greatly influenced by environmental factors such as diet and other exposures. Recently, a role for human genetic variation has emerged as also influential in accounting for interpersonal differences in microbiomes.
Corralling Colonic Flagellated Microbiota
Keeping the gut microbiota physically separated from the epithelial cells of the host is critical to health. A breach of the epithelium can induce acute disease and allow systemic infection. Moreover, encroachment of bacteria on the epithelium promotes chronic inflammatory conditions, including inflammatory bowel disease and the metabolic syndrome.
An obesity-associated gut microbiome with increased capacity for energy harvest
The worldwide obesity epidemic is stimulating efforts to identify host and environmental factors that affect energy balance. Comparisons of the distal gut microbiota of genetically obese mice and their lean littermates, as well as those of obese and lean human volunteers have revealed that obesity is associated with changes in the relative abundance of the two dominant bacterial divisions, the Bacteroidetes and the Firmicutes.
Genes and Microbes Influence One Another, Scientists Find
The ecology of the gut microbiome may trigger or contribute to a variety of diseases, including autoimmune disorders and obesity, research suggests. Factors such as early environment, diet and antibiotic exposure have a lot to do with why people differ from one another in the composition of their microbiomes. But specific gene variants are also linked to greater risks of developing many of these diseases. Do your genes act on your microbiome, which in turn promotes disease?
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