Scholars@Duke
Lawrence Anthony David

Lawrence Anthony David

Associate Professor of Molecular Genetics and Microbiology
Molecular Genetics and Microbiology
lawrence.david@duke.edu
4116 MSRB3 Building, Box 103053, Durham, NC 27710
Box 103053, Durham, NC 27710

Selected Publications

A pilot study of metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans.

Journal Article Food Funct · December 12, 2024 Objective biomarkers of food intake are a sought-after goal in nutrition research. Most biomarker development to date has focused on metabolites detected in blood, urine, skin, or hair, but detection of consumed foods in stool has also been shown to be pos ... Full text Link to item Cite

Weight, habitual fibre intake, and microbiome composition predict tolerance to fructan supplementation.

Journal Article Int J Food Sci Nutr · September 2024 Fructans are commonly used as dietary fibre supplements for their ability to promote the growth of beneficial gut microbes. However, fructan consumption has been associated with various dosage-dependent side effects. We characterised side effects in an exp ... Full text Link to item Cite

Interplay between particle size and microbial ecology in the gut microbiome.

Journal Article bioRxiv · April 27, 2024 Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is ... Full text Link to item Cite

The Binding Properties of Antibodies to Z-DNA in the Sera of Normal Healthy Subjects.

Journal Article Int J Mol Sci · February 22, 2024 Antibodies to DNA are a diverse set of antibodies that bind sites on DNA, a polymeric macromolecule that displays various conformations. In a previous study, we showed that sera of normal healthy subjects (NHS) contain IgG antibodies to Z-DNA, a left-hande ... Full text Link to item Cite

Ultra-processed food intake, gut microbiome, and glucose homeostasis in mid-life adults: Background, design, and methods of a controlled feeding trial.

Journal Article Contemp Clin Trials · February 2024 BACKGROUND: Aging is associated with gut dysbiosis, low-grade inflammation, and increased risk of type 2 diabetes (T2D). Prediabetes, which increases T2D and cardiovascular disease risk, is present in 45-50% of mid-life adults. The gut microbiota may link ... Full text Link to item Cite

Interplay between particle size and microbial ecology in the gut microbiome.

Journal Article ISME J · January 8, 2024 Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is ... Full text Link to item Cite

A pilot study of fecal pH and redox as functional markers in the premature infant gut microbiome.

Journal Article PLoS One · 2024 The infant gut microbiome is a crucial factor in health and development. In preterm infants, altered gut microbiome composition and function have been linked to serious neonatal complications such as necrotizing enterocolitis and sepsis, which can lead to ... Full text Link to item Cite

A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression.

Journal Article Nat Microbiol · August 2023 Akkermansia muciniphila, a mucophilic member of the gut microbiota, protects its host against metabolic disorders. Because it is genetically intractable, the mechanisms underlying mucin metabolism, gut colonization and its impact on host physiology are not ... Full text Link to item Cite

Diversity of plant DNA in stool is linked to dietary quality, age, and household income.

Journal Article Proc Natl Acad Sci U S A · July 4, 2023 Eating a varied diet is a central tenet of good nutrition. Here, we develop a molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL-P6 marker to 1,029 fecal samples from 324 participants across two ... Full text Link to item Cite

Prebiotic galactooligosaccharides interact with mouse gut microbiota to attenuate acute graft-versus-host disease.

Journal Article Blood · November 24, 2022 Previous studies suggest that gut microbiome disruption induced by chemotherapy, dietary deficiencies, and/or antibiotics are associated with increased incidence of acute graft-versus-host disease (aGVHD) following hematopoietic stem cell transplantation ( ... Full text Link to item Cite

Ecological memory of prior nutrient exposure in the human gut microbiome.

Journal Article ISME J · November 2022 Many ecosystems have been shown to retain a memory of past conditions, which in turn affects how they respond to future stimuli. In microbial ecosystems, community disturbance has been associated with lasting impacts on microbiome structure. However, wheth ... Full text Open Access Link to item Cite

Horizontal gene transfer enables programmable gene stability in synthetic microbiota.

Journal Article Nat Chem Biol · November 2022 The functions of many microbial communities exhibit remarkable stability despite fluctuations in the compositions of these communities. To date, a mechanistic understanding of this function-composition decoupling is lacking. Statistical mechanisms have bee ... Full text Link to item Cite

Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake.

Journal Article Microbiome · July 29, 2022 BACKGROUND: Short-chain fatty acids (SCFAs) derived from gut bacteria are associated with protective roles in diseases ranging from obesity to colorectal cancers. Intake of microbially accessible dietary fibers (prebiotics) lead to varying effects on SCFA ... Full text Link to item Cite

Modulation of microbial community dynamics by spatial partitioning.

Journal Article Nat Chem Biol · April 2022 Microbial communities inhabit spatial architectures that divide a global environment into isolated or semi-isolated local environments, which leads to the partitioning of a microbial community into a collection of local communities. Despite its ubiquity an ... Full text Open Access Link to item Cite

Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes.

Journal Article mSystems · February 22, 2022 Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields ... Full text Link to item Cite

Bayesian Multinomial Logistic Normal Models through Marginally Latent Matrix-T Processes

Journal Article Journal of Machine Learning Research · January 1, 2022 Bayesian multinomial logistic-normal (MLN) models are popular for the analysis of sequence count data (e.g., microbiome or gene expression data) due to their ability to model multivariate count data with complex covariance structure. However, existing impl ... Cite

Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity.

Journal Article Front Microbiol · 2022 Cross feeding between microbes is ubiquitous, but its impact on the diversity and productivity of microbial communities is incompletely understood. A reductionist approach using simple microbial communities has the potential to detect cross feeding interac ... Full text Link to item Cite

Measuring and mitigating PCR bias in microbiota datasets.

Journal Article PLoS Comput Biol · July 2021 PCR amplification plays an integral role in the measurement of mixed microbial communities via high-throughput DNA sequencing of the 16S ribosomal RNA (rRNA) gene. Yet PCR is also known to introduce multiple forms of bias in 16S rRNA studies. Here we prese ... Full text Link to item Cite

Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila.

Journal Article mBio · May 2021 The mucophilic anaerobic bacterium Akkermansia muciniphila is a prominent member of the gastrointestinal (GI) microbiota and the only known species of the Verrucomicrobia phylum in the mammalian gut. A high prevalence of A. muciniphila ... Full text Cite

The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights.

Journal Article Obesity (Silver Spring) · March 2021 OBJECTIVE: The purpose of this study was to establish a biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification. METHODS: A total of 223 adolescents aged 10 to 18 years with BMI ≥9 ... Full text Open Access Link to item Cite

Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study.

Journal Article J Infect Dis · February 3, 2021 BACKGROUND: Susceptibility to Vibrio cholerae infection is affected by blood group, age, and preexisting immunity, but these factors only partially explain who becomes infected. A recent study used 16S ribosomal RNA amplicon sequencing to quantify the comp ... Full text Link to item Cite

Individual Variation in Prebiotic Response.

Conference IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL · 2021 Cite

Ecological memory of prior nutrient exposure in the human gut microbiome

Journal Article · 2021 Many ecosystems retain an ecological memory of past conditions that affects responses to future stimuli. However, it remains unknown what mechanisms and dynamics may govern such a memory in microbial communities. Here, in both a human dietary intervention ... Full text Cite

Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake

Journal Article · 2021 Background Short-chain fatty acids (SCFAs) derived from gut bacteria are associated with protective roles in diseases ranging from obesity to colorectal cancers. Intake of microbially accessible dietary fibers (prebiotics) lead to varying effects ... Full text Cite

Conserved anti-inflammatory effects and sensing of butyrate in zebrafish.

Journal Article Gut Microbes · November 9, 2020 Short-chain fatty acids (SCFAs) are produced by microbial fermentation of dietary fiber in the gut. Butyrate is a particularly important SCFA with anti-inflammatory properties and is generally present at lower levels in inflammatory diseases associated wit ... Full text Link to item Cite

Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition.

Journal Article mBio · August 11, 2020 Pediatric obesity remains a public health burden and continues to increase in prevalence. The gut microbiota plays a causal role in obesity and is a promising therapeutic target. Specifically, the microbial production of short-chain fatty acids (SCFA) from ... Full text Link to item Cite

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture.

Journal Article mSystems · June 30, 2020 Culture and screening of gut bacteria enable testing of microbial function and therapeutic potential. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. Here, we c ... Full text Link to item Cite

Nasal microbiota exhibit neither reproducible nor orderly dynamics following rhinoviral infection

Journal Article · April 17, 2020 ABSTRACTBackgroundHow human-associated microbial communities resist and respond to perturbations remains incompletely understood. Viral challenge provides one opportunity to test how human ... Full text Cite

The emergence of microbiome centres.

Journal Article Nat Microbiol · January 2020 Full text Link to item Cite

PredictingVibrio choleraeinfection and disease severity using metagenomics in a prospective cohort study

Journal Article · 2020 ABSTRACTBackground Susceptibility to Vibrio cholerae infection is impacted by blood group, age, and pre-existing immunity, but these factors only partially explain who becomes infected. A recent study used 16S rRNA amplicon sequencing to ... Full text Cite

Naught all zeros in sequence count data are the same.

Journal Article Comput Struct Biotechnol J · 2020 Genomic studies feature multivariate count data from high-throughput DNA sequencing experiments, which often contain many zero values. These zeros can cause artifacts for statistical analyses and multiple modeling approaches have been developed in response ... Full text Link to item Cite

Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept.

Journal Article mSystems · October 8, 2019 Dietary intake is difficult to measure reliably in humans because approaches typically rely on self-reporting, which can be incomplete and biased. In field studies of animals, DNA sequencing-based approaches such as metabarcoding have been developed to cha ... Full text Link to item Cite

Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales of ecological data

Journal Article Ecological Monographs · May 1, 2019 The problem of pattern and scale is a central challenge in ecology. In community ecology, an important scale is that at which we aggregate species to define our units of study, such as aggregation of “nitrogen fixing trees” to understand patterns in carbon ... Full text Cite

Personalizing Food to the Gut Microbiome

Conference FASEB JOURNAL · 2019 Cite

Microbial nitrogen limitation in the mammalian large intestine.

Journal Article Nat Microbiol · December 2018 Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that ... Full text Link to item Cite

Correction to: Dynamic linear models guide design and analysis of microbiota studies within artificial human guts.

Journal Article Microbiome · November 27, 2018 AbstractFollowing publication of the original article [1], the authors noticed an error in the presentation of equations in the PDF version. ... Full text Link to item Cite

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts.

Journal Article Microbiome · November 12, 2018 BACKGROUND: Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answeri ... Full text Link to item Cite

Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection.

Journal Article J Infect Dis · July 13, 2018 BACKGROUND: Cholera is a public health problem worldwide, and the risk factors for infection are only partially understood. METHODS: We prospectively studied household contacts of patients with cholera to compare those who were infected to those who were n ... Full text Link to item Cite

Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut.

Journal Article Elife · June 19, 2018 How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact ... Full text Open Access Link to item Cite

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms.

Journal Article Ecol Evol · January 2018 Soils harbor large, diverse microbial communities critical for local and global ecosystem functioning that are controlled by multiple and poorly understood processes. In particular, while there is observational evidence of relationships between both biotic ... Full text Link to item Cite

Toward Personalized Control of Human Gut Bacterial Communities.

Journal Article mSystems · 2018 A key challenge in microbiology will be developing tools for manipulating human gut bacterial communities. Our ability to predict and control the dynamics of these communities is now in its infancy. To manage human gut microbiota, I am developing methods i ... Full text Link to item Cite

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts

Journal Article · 2018 ABSTRACT Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models’ fundamental biology include the timescales on which microbiota vary and the factors that drive such change. A ... Full text Cite

A phylogenetic transform enhances analysis of compositional microbiota data.

Journal Article Elife · February 15, 2017 Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abunda ... Full text Open Access Link to item Cite

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets.

Journal Article PeerJ · 2017 Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunitie ... Full text Link to item Cite

Dynamic poisson factor analysis

Conference Proceedings - IEEE International Conference on Data Mining, ICDM · July 2, 2016 We introduce a novel dynamic model for discrete time-series data, in which the temporal sampling may be nonuniform. The model is specified by constructing a hierarchy of Poisson factor analysis blocks, one for the transitions between latent states and the ... Full text Cite

The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota.

Journal Article Hepatology · March 2016 UNLABELLED: Several animal studies have emphasized the role of gut microbiota in nonalcoholic fatty liver disease (NAFLD). However, data about gut dysbiosis in human NAFLD remain scarce in the literature, especially studies including the whole spectrum of ... Full text Link to item Cite

A phylogenetic transform enhances analysis of compositional microbiota data

Journal Article · 2016 ABSTRACT High-throughput DNA sequencing technologies have revolutionized the study of microbial communities (microbiota) and have revealed their importance in both human health and disease. However, due to technical limitations, data from microbio ... Full text Cite

Phylogenetic factorization of compositional data

Journal Article · 2016 Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunitie ... Full text Cite

Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut.

Journal Article mBio · September 29, 2015 UNLABELLED: Gut microbiota influence the development and physiology of their animal hosts, and these effects are determined in part by the composition of these microbial communities. Gut microbiota composition can be affected by introduction of microbes fr ... Full text Link to item Cite

Gut microbial succession follows acute secretory diarrhea in humans.

Journal Article mBio · May 19, 2015 UNLABELLED: Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hyp ... Full text Link to item Cite

Diet rapidly and reproducibly alters the human gut microbiome.

Journal Article Nature · January 23, 2014 Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we s ... Full text Link to item Cite

Host lifestyle affects human microbiota on daily timescales.

Journal Article Genome Biol · 2014 BACKGROUND: Disturbance to human microbiota may underlie several pathologies. Yet, we lack a comprehensive understanding of how lifestyle affects the dynamics of human-associated microbial communities. RESULTS: Here, we link over 10,000 longitudinal measur ... Full text Link to item Cite

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton.

Journal Article ISME J · March 2013 How reproducibly microbial populations assemble in the wild remains poorly understood. Here, we assess evidence for ecological specialization and predictability of fine-scale population structure and habitat association in coastal ocean Vibrionaceae across ... Full text Link to item Cite

Ecology drives a global network of gene exchange connecting the human microbiome.

Journal Article Nature · October 30, 2011 Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic ... Full text Link to item Cite

Rapid evolutionary innovation during an Archaean genetic expansion.

Journal Article Nature · January 6, 2011 The natural history of Precambrian life is still unknown because of the rarity of microbial fossils and biomarkers. However, the composition of modern-day genomes may bear imprints of ancient biogeochemical events. Here we use an explicit model of macroevo ... Full text Link to item Cite

Metapopulation structure of Vibrionaceae among coastal marine invertebrates.

Journal Article Environ Microbiol · January 2011 Although animal-associated microbial communities (microbiomes) are increasingly recognized to influence health, the extent to which animals represent highly selective habitats for microbes leading to predominance of high host specificity remains poorly und ... Full text Link to item Cite

Looking for Darwin's footprints in the microbial world.

Journal Article Trends Microbiol · May 2009 As we observe the 200th anniversary of Charles Darwin's birth, microbiologists interested in the application of Darwin's ideas to the microscopic world have a lot to celebrate: an emerging picture of the (mostly microbial) Tree of Life at ever-increasing r ... Full text Link to item Cite

Resource partitioning and sympatric differentiation among closely related bacterioplankton.

Journal Article Science · May 23, 2008 Identifying ecologically differentiated populations within complex microbial communities remains challenging, yet is critical for interpreting the evolution and ecology of microbes in the wild. Here we describe spatial and temporal resource partitioning am ... Full text Link to item Cite

Quantification of cell edge velocities and traction forces reveals distinct motility modules during cell spreading.

Journal Article PLoS One · 2008 Actin-based cell motility and force generation are central to immune response, tissue development, and cancer metastasis, and understanding actin cytoskeleton regulation is a major goal of cell biologists. Cell spreading is a commonly used model system for ... Full text Link to item Cite

Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data.

Journal Article Ann N Y Acad Sci · December 2007 We seek to quantify the failure and success of dynamic Bayesian networks (DBNs), a popular tool for reverse-engineering networks from time-series data. In particular, we focus on data generated by continuous time processes (e.g., genetic expression) and sa ... Full text Link to item Cite

Behavioral deficits during early stages of aging in Caenorhabditis elegans result from locomotory deficits possibly linked to muscle frailty.

Journal Article J Gerontol A Biol Sci Med Sci · December 2004 Many behavioral responses require the coordination of sensory inputs with motor outputs. Aging is associated with progressive declines in both motor function and muscle structure. However, the consequences of age-related motor deficits on behavior have not ... Full text Link to item Cite