Honors & Awards
Walter V. and Idun Berry Postdoctoral Fellowship, Stanford University (2009-2013)
K99 Pathway to Independence Award, NIH/NICHD (2013-2016)
Education & Certifications
Postdoc, Stanford University (2013)
Postdoc, University of Colorado Boulder (2009)
PhD, University of Colorado Boulder (2007)
BS, Cornell University (1999)
Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant.
2017; 7 (1): 3764
Genital mycoplasmas, which can be vertically transmitted, have been implicated in preterm birth, neonatal infections, and chronic lung disease of prematurity. Our prior work uncovered 16S rRNA genes belonging to a novel, as-yet-uncultivated mycoplasma (lineage 'Mnola') in the oral cavity of a premature neonate. Here, we characterize the organism's associated community, growth status, metabolic potential, and population diversity. Sequencing of genomic DNA from the infant's saliva yielded 1.44 Gbp of high-quality, non-human read data, from which we recovered three essentially complete (including 'Mnola') and three partial draft genomes (including Trichomonas vaginalis). The completed 629,409-bp 'Mnola' genome (Candidatus Mycoplasma girerdii str. UC-B3) was distinct at the strain level from its closest relative, vaginally-derived Ca. M. girerdii str. VCU-M1, which is also associated with T. vaginalis. Replication rate measurements indicated growth of str. UC-B3 within the infant. Genes encoding surface-associated proteins and restriction-modification systems were especially diverse within and between strains. In UC-B3, the population genetic underpinnings of phase variable expression were evident in vivo. Unique among mycoplasmas, Ca. M. girerdii encodes pyruvate-ferredoxin oxidoreductase and may be sensitive to metronidazole. This study reveals a metabolically unique mycoplasma colonizing a premature neonate, and establishes the value of genome-resolved metagenomics in tracking phase variation.
View details for DOI 10.1038/s41598-017-03821-7
View details for PubMedID 28630471
View details for PubMedCentralID PMC5476646
Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women.
Proceedings of the National Academy of Sciences of the United States of America
Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. Previous studies have suggested that the maternal vaginal microbiota contributes to the pathophysiology of PTB, but conflicting results in recent years have raised doubts. We conducted a study of PTB compared with term birth in two cohorts of pregnant women: one predominantly Caucasian (n = 39) at low risk for PTB, the second predominantly African American and at high-risk (n = 96). We profiled the taxonomic composition of 2,179 vaginal swabs collected prospectively and weekly during gestation using 16S rRNA gene sequencing. Previously proposed associations between PTB and lower Lactobacillus and higher Gardnerella abundances replicated in the low-risk cohort, but not in the high-risk cohort. High-resolution bioinformatics enabled taxonomic assignment to the species and subspecies levels, revealing that Lactobacillus crispatus was associated with low risk of PTB in both cohorts, while Lactobacillus iners was not, and that a subspecies clade of Gardnerella vaginalis explained the genus association with PTB. Patterns of cooccurrence between L. crispatus and Gardnerella were highly exclusive, while Gardnerella and L. iners often coexisted at high frequencies. We argue that the vaginal microbiota is better represented by the quantitative frequencies of these key taxa than by classifying communities into five community state types. Our findings extend and corroborate the association between the vaginal microbiota and PTB, demonstrate the benefits of high-resolution statistical bioinformatics in clinical microbiome studies, and suggest that previous conflicting results may reflect the different risk profile of women of black race.
View details for DOI 10.1073/pnas.1705899114
View details for PubMedID 28847941
Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea.
2016; 7: 10516-?
Marine mammals play crucial ecological roles in the oceans, but little is known about their microbiotas. Here we study the bacterial communities in 337 samples from 5 body sites in 48 healthy dolphins and 18 healthy sea lions, as well as those of adjacent seawater and other hosts. The bacterial taxonomic compositions are distinct from those of other mammals, dietary fish and seawater, are highly diverse and vary according to body site and host species. Dolphins harbour 30 bacterial phyla, with 25 of them in the mouth, several abundant but poorly characterized Tenericutes species in gastric fluid and a surprisingly paucity of Bacteroidetes in distal gut. About 70% of near-full length bacterial 16S ribosomal RNA sequences from dolphins are unique. Host habitat, diet and phylogeny all contribute to variation in marine mammal distal gut microbiota composition. Our findings help elucidate the factors structuring marine mammal microbiotas and may enhance monitoring of marine mammal health.
View details for DOI 10.1038/ncomms10516
View details for PubMedID 26839246
View details for PubMedCentralID PMC4742810
Temporal and spatial variation of the human microbiota during pregnancy
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2015; 112 (35): 11060-11065
Despite the critical role of the human microbiota in health, our understanding of microbiota compositional dynamics during and after pregnancy is incomplete. We conducted a case-control study of 49 pregnant women, 15 of whom delivered preterm. From 40 of these women, we analyzed bacterial taxonomic composition of 3,767 specimens collected prospectively and weekly during gestation and monthly after delivery from the vagina, distal gut, saliva, and tooth/gum. Linear mixed-effects modeling, medoid-based clustering, and Markov chain modeling were used to analyze community temporal trends, community structure, and vaginal community state transitions. Microbiota community taxonomic composition and diversity remained remarkably stable at all four body sites during pregnancy (P > 0.05 for trends over time). Prevalence of a Lactobacillus-poor vaginal community state type (CST 4) was inversely correlated with gestational age at delivery (P = 0.0039). Risk for preterm birth was more pronounced for subjects with CST 4 accompanied by elevated Gardnerella or Ureaplasma abundances. This finding was validated with a set of 246 vaginal specimens from nine women (four of whom delivered preterm). Most women experienced a postdelivery disturbance in the vaginal community characterized by a decrease in Lactobacillus species and an increase in diverse anaerobes such as Peptoniphilus, Prevotella, and Anaerococcus species. This disturbance was unrelated to gestational age at delivery and persisted for up to 1 y. These findings have important implications for predicting premature labor, a major global health problem, and for understanding the potential impact of a persistent, altered postpartum microbiota on maternal health, including outcomes of pregnancies following short interpregnancy intervals.
View details for DOI 10.1073/pnas.1502875112
View details for Web of Science ID 000360383200068
- Population health: immaturity in the gut microbial community. Nature 2014; 510 (7505): 344-345
Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2013; 110 (42): 17059-17064
We investigate how host mucus glycan composition interacts with dietary carbohydrate content to influence the composition and expressed functions of a human gut community. The humanized gnotobiotic mice mimic humans with a nonsecretor phenotype due to knockout of their α1-2 fucosyltransferase (Fut2) gene. The fecal microbiota of Fut2(-) mice that lack fucosylated host glycans show decreased alpha diversity relative to Fut2(+) mice and exhibit significant differences in community composition. A glucose-rich plant polysaccharide-deficient (PD) diet exerted a strong effect on the microbiota membership but eliminated the effect of Fut2 genotype. Additionally fecal metabolites predicted host genotype in mice on a polysaccharide-rich standard diet but not on a PD diet. A more detailed mechanistic analysis of these interactions involved colonization of gnotobiotic Fut2(+) and Fut2(-) mice with Bacteroides thetaiotaomicron, a prominent member of the human gut microbiota known to adaptively forage host mucosal glycans when dietary polysaccharides are absent. Within Fut2(-) mice, the B. thetaiotaomicron fucose catabolic pathway was markedly down-regulated, whereas BT4241-4247, an operon responsive to terminal β-galactose, the precursor that accumulates in the Fut2(-) mice, was significantly up-regulated. These changes in B. thetaiotaomicron gene expression were only evident in mice fed a PD diet, wherein B. thetaiotaomicron relies on host mucus consumption. Furthermore, up-regulation of the BT4241-4247 operon was also seen in humanized Fut2(-) mice. Together, these data demonstrate that differences in host genotype that affect the carbohydrate landscape of the distal gut interact with diet to alter the composition and function of resident microbes in a diet-dependent manner.
View details for DOI 10.1073/pnas.1306070110
View details for Web of Science ID 000325634200076
View details for PubMedID 24062455
View details for PubMedCentralID PMC3800993
Biphasic assembly of the murine intestinal microbiota during early development.
2013; 7 (6): 1112-1115
The birth canal provides mammals with a primary maternal inoculum, which develops into distinctive body site-specific microbial communities post-natally. We characterized the distal gut microbiota from birth to weaning in mice. One-day-old mice had colonic microbiota that resembled maternal vaginal communities, but at days 3 and 9 of age there was a substantial loss of intestinal bacterial diversity and dominance of Lactobacillus. By weaning (21 days), diverse intestinal bacteria had established, including strict anaerobes. Our results are consistent with vertical transmission of maternal microbiota and demonstrate a nonlinear ecological succession involving an early drop in bacterial diversity and shift in dominance from Streptococcus to Lactobacillus, followed by an increase in diversity of anaerobes, after the introduction of solid food. Mammalian newborns are born highly susceptible to colonization, and lactation may control microbiome assembly during early development.
View details for DOI 10.1038/ismej.2013.15
View details for PubMedID 23535917
View details for PubMedCentralID PMC3660675
Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States
2013; 8 (1)
Our current understanding of the composition and stability of the human distal gut microbiota is based largely on studies of infants and adults living in developed countries. In contrast, little is known about the gut microbiota and its variation over time in older children and adolescents, especially in developing countries.We compared the diversity, composition, and temporal stability of the fecal microbiota of healthy children, ages 9 to 14 years, living in an urban slum in Bangladesh with that of children of the same age range in an upper-middle class suburban community in the United States. We analyzed >8,000 near full-length 16S rRNA gene sequences and over 845,000 pyrosequencing reads of the 16S rRNA V1-V3 region. The distal gut of Bangladeshi children harbored significantly greater bacterial diversity than that of U.S. children, including novel lineages from several bacterial phyla. Bangladeshi and U.S. children had distinct fecal bacterial community membership and structure; the microbiota of Bangladeshi children was enriched in Prevotella, Butyrivibrio, and Oscillospira and depleted in Bacteroides relative to U.S. children (although similar to Bangladeshi adults). Furthermore, community membership and structure in Bangladeshi children was significantly less stable month-to-month than U.S. children.Together, these results suggest that differing environmental or genetic factors may shape the microbiota of healthy children in the two countries. Further investigation is necessary to understand the mechanisms and factors that underlie these differences, and to incorporate these findings into new strategies for the prevention and treatment of childhood and adolescent diseases.
View details for DOI 10.1371/journal.pone.0053838
View details for Web of Science ID 000314019100034
View details for PubMedID 23349750
View details for PubMedCentralID PMC3551965
Microbiome assembly across multiple body sites in low-birthweight infants.
2013; 4 (6): e00782-13
ABSTRACT The purpose of this study was to evaluate the composition and richness of bacterial communities associated with low-birthweight (LBW) infants in relation to host body site, individual, and age. Bacterial 16S rRNA genes from saliva samples, skin swabs, and stool samples collected on postnatal days 8, 10, 12, 15, 18, and 21 from six LBW (five premature) infants were amplified, pyrosequenced, and analyzed within a comparative framework that included analogous data from normal-birthweight (NBW) infants and healthy adults. We found that body site was the primary determinant of bacterial community composition in the LBW infants. However, site specificity depended on postnatal age: saliva and stool compositions diverged over time but were not significantly different until the babies were 15 days old. This divergence was primarily driven by progressive temporal turnover in the distal gut, which proceeded at a rate similar to that of age-matched NBW infants. Neonatal skin was the most adult-like in microbiota composition, while saliva and stool remained the least so. Compositional variation among infants was marked and depended on body site and age. Only the smallest, most premature infant received antibiotics during the study period; this heralded a coexpansion of Pseudomonas aeruginosa and a novel Mycoplasma sp. in the oral cavity of this vaginally delivered, intubated patient. We conclude that concurrent molecular surveillance of multiple body sites in LBW neonates reveals a delayed compositional differentiation of the oral cavity and distal gut microbiota and, in the case of one infant, an abundant, uncultivated oral Mycoplasma sp., recently detected in human vaginal samples. IMPORTANCE Complications of premature birth are the most common cause of neonatal mortality. Colonization by the indigenous microbiota, which begins at delivery, may predispose some high-risk newborns to invasive infection or necrotizing enterocolitis (NEC), and protect others, yet neonatal microbiome dynamics are poorly understood. Here, we present the first cultivation-independent time series tracking microbiota assembly across multiple body sites in a synchronous cohort of hospitalized low-birthweight (LBW) neonates. We take advantage of archived samples and publically available sequence data and compare our LBW infant findings to those from normal-birthweight (NBW) infants and healthy adults. Our results suggest potential windows of opportunity for the dispersal of microbes within and between hosts and support recent findings of substantial baseline spatiotemporal variation in microbiota composition among high-risk newborns.
View details for DOI 10.1128/mBio.00782-13
View details for PubMedID 24169577
View details for PubMedCentralID PMC3809564
Cohabiting family members share microbiota with one another and with their dogs.
Human-associated microbial communities vary across individuals: possible contributing factors include (genetic) relatedness, diet, and age. However, our surroundings, including individuals with whom we interact, also likely shape our microbial communities. To quantify this microbial exchange, we surveyed fecal, oral, and skin microbiota from 60 families (spousal units with children, dogs, both, or neither). Household members, particularly couples, shared more of their microbiota than individuals from different households, with stronger effects of co-habitation on skin than oral or fecal microbiota. Dog ownership significantly increased the shared skin microbiota in cohabiting adults, and dog-owning adults shared more 'skin' microbiota with their own dogs than with other dogs. Although the degree to which these shared microbes have a true niche on the human body, vs transient detection after direct contact, is unknown, these results suggest that direct and frequent contact with our cohabitants may significantly shape the composition of our microbial communities. DOI:http://dx.doi.org/10.7554/eLife.00458.001.
View details for DOI 10.7554/eLife.00458
View details for PubMedID 23599893
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents
2013; 7 (1): 85-95
The human skin harbors complex bacterial communities. Prior studies showing high inter-individual variation focused on subjects from developed countries. We therefore compared cutaneous bacterial communities of Amerindians in the Venezuelan Amazon with subjects in the United States. Forearm skin specimens were studied from healthy Amerindians in Platanillal village in Amazonas State, and from healthy persons in New York and Colorado. All skin sampling used similar swab/buffer techniques. Multiplexed V2-targeted 16S rRNA gene pyrosequencing yielded high quality sequences from 112 samples. The results show 20 phyla, with three (Proteobacteria, Firmicutes, Actinobacteria) predominating. US residents and Venezuelan Amerindians had significantly different forearm skin bacterial community compositions, with United States dominated by Propionibacterium. Among the Amerindians, there was a deep split based on bacterial community membership, with 30 and 42 samples, respectively, falling into each of the two groups, not associated with age, gender, or body mass index. One Amerindian group had diversity similar to the United States, but was dominated by Staphylococcus rather than Propionibacterium. The other Amerindian group was significantly more diverse and even than the US or the other Amerindian group, and featured a broad range of Proteobacteria. The results provide evidence that ethnicity, lifestyle and/or geography are associated with the structure of human cutaneous bacterial communities.
View details for DOI 10.1038/ismej.2012.81
View details for Web of Science ID 000313236000008
View details for PubMedID 22895161
View details for PubMedCentralID PMC3526177
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
2013; 23 (1): 111-120
The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial communities in 11 fecal samples collected from a premature infant during the first month of life. Ninety six percent of the sequencing reads were assembled into scaffolds of >500 bp in length that could be assigned to organisms at the strain level. Six essentially complete (∼99%) and two near-complete genomes were assembled for bacteria that comprised as little as 1% of the community, as well as nine partial genomes of bacteria representing as little as 0.05%. In addition, three viral genomes were assembled and assigned to their hosts. The relative abundance of three Staphylococcus epidermidis strains, as well as three phages that infect them, changed dramatically over time. Genes possibly related to these shifts include those for resistance to antibiotics, heavy metals, and phage. At the species level, we observed the decline of an early-colonizing Propionibacterium acnes strain similar to SK137 and the proliferation of novel Propionibacterium and Peptoniphilus species late in colonization. The Propionibacterium species differed in their ability to metabolize carbon compounds such as inositol and sialic acid, indicating that shifts in species composition likely impact the metabolic potential of the community. These results highlight the benefit of reconstructing complete genomes from metagenomic data and demonstrate methods for achieving this goal.
View details for DOI 10.1101/gr.142315.112
View details for Web of Science ID 000312963400010
View details for PubMedID 22936250
View details for PubMedCentralID PMC3530670
The Application of Ecological Theory Toward an Understanding of the Human Microbiome
2012; 336 (6086): 1255-1262
The human-microbial ecosystem plays a variety of important roles in human health and disease. Each person can be viewed as an island-like "patch" of habitat occupied by microbial assemblages formed by the fundamental processes of community ecology: dispersal, local diversification, environmental selection, and ecological drift. Community assembly theory, and metacommunity theory in particular, provides a framework for understanding the ecological dynamics of the human microbiome, such as compositional variability within and between hosts. We explore three core scenarios of human microbiome assembly: development in infants, representing assembly in previously unoccupied habitats; recovery from antibiotics, representing assembly after disturbance; and invasion by pathogens, representing assembly in the context of invasive species. Judicious application of ecological theory may lead to improved strategies for restoring and maintaining the microbiota and the crucial health-associated ecosystem services that it provides.
View details for DOI 10.1126/science.1224203
View details for Web of Science ID 000304905300034
View details for PubMedID 22674335
Sources of Bacteria in Outdoor Air across Cities in the Midwestern United States
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
2011; 77 (18): 6350-6356
Bacteria are abundant in the atmosphere, where they often represent a major portion of the organic aerosols. Potential pathogens of plants and livestock are commonly dispersed through the atmosphere, and airborne bacteria can have important effects on human health as pathogens or triggers of allergic asthma and seasonal allergies. Despite their importance, the diversity and biogeography of airborne microorganisms remain poorly understood. We used high-throughput pyrosequencing to analyze bacterial communities present in the aerosol fraction containing fine particulate matter of ≤2.5 μm from 96 near-surface atmospheric samples collected from cities throughout the midwestern United States and found that the communities are surprisingly diverse and strongly affected by the season. We also directly compared the airborne communities to those found in hundreds of samples representing potential source environments. We show that, in addition to the more predictable sources (soils and leaf surfaces), fecal material, most likely dog feces, often represents an unexpected source of bacteria in the atmosphere at more urbanized locations during the winter. Airborne bacteria are clearly an important, but understudied, component of air quality that needs to be better integrated into efforts to measure and model pollutants in the atmosphere.
View details for DOI 10.1128/AEM.05498-11
View details for Web of Science ID 000294691400005
View details for PubMedID 21803902
View details for PubMedCentralID PMC3187178
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
2011; 29 (5): 415-420
Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
View details for DOI 10.1038/nbt.1823
View details for Web of Science ID 000290301700021
View details for PubMedID 21552244
View details for PubMedCentralID PMC3367316
Supervised classification of human microbiota
FEMS MICROBIOLOGY REVIEWS
2011; 35 (2): 343-359
Recent advances in DNA sequencing technology have allowed the collection of high-dimensional data from human-associated microbial communities on an unprecedented scale. A major goal of these studies is the identification of important groups of microorganisms that vary according to physiological or disease states in the host, but the incidence of rare taxa and the large numbers of taxa observed make that goal difficult to obtain using traditional approaches. Fortunately, similar problems have been addressed by the machine learning community in other fields of study such as microarray analysis and text classification. In this review, we demonstrate that several existing supervised classifiers can be applied effectively to microbiota classification, both for selecting subsets of taxa that are highly discriminative of the type of community, and for building models that can accurately classify unlabeled data. To encourage the development of new approaches to supervised classification of microbiota, we discuss several structures inherent in microbial community data that may be available for exploitation in novel approaches, and we include as supplemental information several benchmark classification tasks for use by the community.
View details for DOI 10.1111/j.1574-6976.2010.00251.x
View details for Web of Science ID 000286837600006
View details for PubMedID 21039646
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2011; 108 (3): 1128-1133
The intestinal microbiome is a critical determinant of human health. Alterations in its composition have been correlated with chronic disorders, such as obesity and inflammatory bowel disease in adults, and may be associated with neonatal necrotizing enterocolitis in premature infants. Increasing evidence suggests that strain-level genomic variation may underpin distinct ecological trajectories within mixed populations, yet there have been few strain-resolved analyses of genotype-phenotype connections in the context of the human ecosystem. Here, we document strain-level genomic divergence during the first 3 wk of life within the fecal microbiota of an infant born at 28-wk gestation. We observed three compositional phases during colonization, and reconstructed and intensively curated population genomic datasets from the third phase. The relative abundance of two Citrobacter strains sharing ~99% nucleotide identity changed significantly over time within a community dominated by a nearly clonal Serratia population and harboring a lower abundance Enterococcus population and multiple plasmids and bacteriophage. Modeling of Citrobacter strain abundance suggests differences in growth rates and host colonization patterns. We identified genotypic variation potentially responsible for divergent strain ecologies, including hotspots of sequence variation in regulatory genes and intergenic regions, and in genes involved in transport, flagellar biosynthesis, substrate metabolism, and host colonization, as well as differences in the complements of these genes. Our results demonstrate that a community genomic approach can elucidate gut microbial colonization at the resolution required to discern medically relevant strain and species population dynamics, and hence improve our ability to diagnose and treat microbial community-mediated disorders.
View details for DOI 10.1073/pnas.1010992108
View details for Web of Science ID 000286310300046
View details for PubMedID 21191099
View details for PubMedCentralID PMC3024690
Global patterns in the biogeography of bacterial taxa
2011; 13 (1): 135-144
Bacteria control major nutrient cycles and directly influence plant, animal and human health. However, we know relatively little about the forces shaping their large-scale ecological ranges. Here, we reveal patterns in the distribution of individual bacterial taxa at multiple levels of phylogenetic resolution within and between Earth's major habitat types. Our analyses suggest that while macro-scale habitats structure bacterial distribution to some degree, abundant bacteria (i.e. detectable using 16S rRNA gene sequencing methods) are confined to single assemblages. Additionally, we show that the most cosmopolitan taxa are also the most abundant in individual assemblages. These results add to the growing body of data that support that the diversity of the overall bacterial metagenome is tremendous. The mechanisms governing microbial distribution remain poorly understood, but our analyses provide a framework with which to test the importance of macro-ecological environmental gradients, relative abundance, neutral processes and the ecological strategies of individual taxa in structuring microbial communities.
View details for DOI 10.1111/j.1462-2920.2010.02315.x
View details for Web of Science ID 000285876600012
View details for PubMedID 21199253
Moving pictures of the human microbiome
2011; 12 (5)
Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn’s disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.We find that despite stable differences between body sites and individuals, there is pronounced variability in an individual’s microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members.DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions.
View details for DOI 10.1186/gb-2011-12-5-r50
View details for Web of Science ID 000295732700014
View details for PubMedID 21624126
View details for PubMedCentralID PMC3271711
The bacterial microbiota in the oral mucosa of rural Amerindians
2010; 156: 3282-3287
The oral microbiota plays an important role in buccal health and in diseases such as periodontitis and meningitis. The study of the human oral bacteria has so far focused on subjects from Western societies, while little is known about subjects from isolated communities. This work determined the composition of the oral mucosa microbiota from six Amazon Amerindians, and tested a sample preservation alternative to freezing. Paired oral swabs were taken from six adults of Guahibo ethnicity living in the community of Platanillal, Amazonas State, Venezuela. Replicate swabs were preserved in liquid nitrogen and in Aware Messenger fluid (Calypte). Buccal DNA was extracted, and the V2 region of the 16S rRNA gene was amplified and pyrosequenced. A total of 17 214 oral bacterial sequences were obtained from the six subjects; these were binned into 1034 OTUs from 10 phyla, 30 families and 51 genera. The oral mucosa was highly dominated by four phyla: Firmicutes (mostly the genera Streptococcus and Veillonella), Proteobacteria (mostly Neisseria), Bacterioidetes (Prevotella) and Actinobacteria (Micrococcineae). Although the microbiota were similar at the phylum level, the Amerindians shared only 62 % of the families and 23 % of the genera with non-Amerindians from previous studies, and had a lower richness of genera (51 vs 177 reported in non-Amerindians). The Amerindians carried unidentified members of the phyla Bacteroidetes, Firmicutes and Proteobacteria and their microbiota included soil bacteria Gp1 (Acidobacteriaceae) and Xylanibacter (Prevotellaceae), and the rare genus Phocoenobacter (Pasteurellaceae). Preserving buccal swabs in the Aware Messenger oral fluid collection device substantially altered the bacterial composition in comparison to freezing, and therefore this method cannot be used to preserve samples for the study of microbial communities.
View details for DOI 10.1099/mic.0.043174-0
View details for Web of Science ID 000284660400009
View details for PubMedID 20847007
Postprandial remodeling of the gut microbiota in Burmese pythons
2010; 4 (11): 1375-1385
The vertebrate gut microbiota evolved in an environment typified by periodic fluctuations in nutrient availability, yet little is known about its responses to host feeding and fasting. As many model species (for example, mice) are adapted to lifestyles of frequent small meals, we turned to the Burmese python, a sit-and-wait foraging snake that consumes large prey at long intervals (>1 month), to examine the effects of a dynamic nutrient milieu on the gut microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities harvested from the intestines of fasted and digesting snakes, and from their rodent meal. In this unprecedented survey of a reptilian host, we found that Bacteroidetes and Firmicutes numerically dominated the python gut. In the large intestine, fasting was associated with increased abundances of the genera Bacteroides, Rikenella, Synergistes and Akkermansia, and with reduced overall diversity. A marked postprandial shift in bacterial community configuration occurred. Between 12 h and 3 days after feeding, Firmicutes, including the taxa Clostridium, Lactobacillus and Peptostreptococcaceae, gradually outnumbered the fasting-dominant Bacteroidetes, and overall 'species'-level diversity increased significantly. Most lineages seemed to be indigenous to the python rather than ingested with the meal, but a dietary source of Lactobacillus could not be ruled out. Thus, the observed large-scale alterations of the gut microbiota that accompany the Burmese python's own dramatic physiological and morphological changes during feeding and fasting emphasize the need to consider both microbial and host cellular responses to nutrient flux. The Burmese python may provide a unique model for dissecting these interrelationships.
View details for DOI 10.1038/ismej.2010.71
View details for Web of Science ID 000285793700003
View details for PubMedID 20520652
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2010; 107 (26): 11971-11975
Upon delivery, the neonate is exposed for the first time to a wide array of microbes from a variety of sources, including maternal bacteria. Although prior studies have suggested that delivery mode shapes the microbiota's establishment and, subsequently, its role in child health, most researchers have focused on specific bacterial taxa or on a single body habitat, the gut. Thus, the initiation stage of human microbiome development remains obscure. The goal of the present study was to obtain a community-wide perspective on the influence of delivery mode and body habitat on the neonate's first microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities from mothers and their newborn babies, four born vaginally and six born via Cesarean section. Mothers' skin, oral mucosa, and vagina were sampled 1 h before delivery, and neonates' skin, oral mucosa, and nasopharyngeal aspirate were sampled <5 min, and meconium <24 h, after delivery. We found that in direct contrast to the highly differentiated communities of their mothers, neonates harbored bacterial communities that were undifferentiated across multiple body habitats, regardless of delivery mode. Our results also show that vaginally delivered infants acquired bacterial communities resembling their own mother's vaginal microbiota, dominated by Lactobacillus, Prevotella, or Sneathia spp., and C-section infants harbored bacterial communities similar to those found on the skin surface, dominated by Staphylococcus, Corynebacterium, and Propionibacterium spp. These findings establish an important baseline for studies tracking the human microbiome's successional development in different body habitats following different delivery modes, and their associated effects on infant health.
View details for DOI 10.1073/pnas.1002601107
View details for Web of Science ID 000279332300057
View details for PubMedID 20566857
- QIIME allows analysis of high-throughput community sequencing data NATURE METHODS 2010; 7 (5): 335-336
Forensic identification using skin bacterial communities
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2010; 107 (14): 6477-6481
Recent work has demonstrated that the diversity of skin-associated bacterial communities is far higher than previously recognized, with a high degree of interindividual variability in the composition of bacterial communities. Given that skin bacterial communities are personalized, we hypothesized that we could use the residual skin bacteria left on objects for forensic identification, matching the bacteria on the object to the skin-associated bacteria of the individual who touched the object. Here we describe a series of studies de-monstrating the validity of this approach. We show that skin-associated bacteria can be readily recovered from surfaces (including single computer keys and computer mice) and that the structure of these communities can be used to differentiate objects handled by different individuals, even if those objects have been left untouched for up to 2 weeks at room temperature. Furthermore, we demonstrate that we can use a high-throughput pyrosequencing-based ap-proach to quantitatively compare the bacterial communities on objects and skin to match the object to the individual with a high degree of certainty. Although additional work is needed to further establish the utility of this approach, this series of studies introduces a forensics approach that could eventually be used to independently evaluate results obtained using more traditional forensic practices.
View details for DOI 10.1073/pnas.1000162107
View details for Web of Science ID 000276374400063
View details for PubMedID 20231444
Direct sequencing of the human microbiome readily reveals community differences
2010; 11 (5)
Culture-independent studies of human microbiota by direct genomic sequencing reveal quite distinct differences among communities, indicating that improved sequencing capacity can be most wisely utilized to study more samples, rather than more sequences per sample.
View details for DOI 10.1186/gb-2010-11-5-210
View details for Web of Science ID 000279631000009
View details for PubMedID 20441597
View details for PubMedCentralID PMC2898070
Bacterial Community Variation in Human Body Habitats Across Space and Time
2009; 326 (5960): 1694-1697
Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. To obtain an integrated view of the spatial and temporal distribution of the human microbiota, we surveyed bacteria from up to 27 sites in seven to nine healthy adults on four occasions. We found that community composition was determined primarily by body habitat. Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.
View details for DOI 10.1126/science.1177486
View details for Web of Science ID 000272839000053
View details for PubMedID 19892944
Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2009; 106 (27): 11276-11281
Studies in mice indicate that the gut microbiota promotes energy harvest and storage from components of the diet when these components are plentiful. Here we examine how the microbiota shapes host metabolic and physiologic adaptations to periods of nutrient deprivation. Germ-free (GF) mice and mice who had received a gut microbiota transplant from conventionally raised donors were compared in the fed and fasted states by using functional genomic, biochemical, and physiologic assays. A 24-h fast produces a marked change in gut microbial ecology. Short-chain fatty acids generated from microbial fermentation of available glycans are maintained at higher levels compared with GF controls. During fasting, a microbiota-dependent, Ppar alpha-regulated increase in hepatic ketogenesis occurs, and myocardial metabolism is directed to ketone body utilization. Analyses of heart rate, hydraulic work, and output, mitochondrial morphology, number, and respiration, plus ketone body, fatty acid, and glucose oxidation in isolated perfused working hearts from GF and colonized animals (combined with in vivo assessments of myocardial physiology) revealed that the fasted GF heart is able to sustain its performance by increasing glucose utilization, but heart weight, measured echocardiographically or as wet mass and normalized to tibial length or lean body weight, is significantly reduced in both fasted and fed mice. This myocardial-mass phenotype is completely reversed in GF mice by consumption of a ketogenic diet. Together, these results illustrate benefits provided by the gut microbiota during periods of nutrient deprivation, and emphasize the importance of further exploring the relationship between gut microbes and cardiovascular health.
View details for DOI 10.1073/pnas.0902366106
View details for Web of Science ID 000267796100074
View details for PubMedID 19549860
Soil CO2 flux and photoautotrophic community composition in high-elevation, 'barren' soil
2009; 11 (3): 674-686
Soil-dominated ecosystems, with little or no plant cover (i.e. deserts, polar regions, high-elevation areas and zones of glacial retreat), are often described as 'barren', despite their potential to host photoautotrophic microbial communities. In high-elevation, subnival zone soil (i.e. elevations higher than the zone of continuous vegetation), the structure and function of these photoautotrophic microbial communities remains essentially unknown. We measured soil CO(2) flux at three sites (above 3600 m) and used molecular techniques to determine the composition and distribution of soil photoautotrophs in the Colorado Front Range. Soil CO(2) flux data from 2002 and 2007 indicate that light-driven CO(2) uptake occurred on most dates. A diverse community of Cyanobacteria, Chloroflexi and eukaryotic algae was present in the top 2 cm of the soil, whereas these clades were nearly absent in deeper soils (2-4 cm). Cyanobacterial communities were composed of lineages most closely related to Microcoleus vaginatus and Phormidium murrayi, eukaryotic photoautotrophs were dominated by green algae, and three novel clades of Chloroflexi were also abundant in the surface soil. During the light hours of the 2007 snow-free measurement period, CO(2) uptake was conservatively estimated to be 23.7 g C m(-2) season(-1). Our study reveals that photoautotrophic microbial communities play an important role in the biogeochemical cycling of subnival zone soil.
View details for DOI 10.1111/j.1462-2920.2008.01844.x
View details for Web of Science ID 000263755700013
View details for PubMedID 19187281
Fumarole-Supported Islands of Biodiversity within a Hyperarid, High-Elevation Landscape on Socompa Volcano, Puna de Atacama, Andes
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
2009; 75 (3): 735-747
Fumarolic activity supports the growth of mat-like photoautotrophic communities near the summit (at 6,051 m) of Socompa Volcano in the arid core of the Andes mountains. These communities are isolated within a barren, high-elevation landscape where sparse vascular plants extend to only 4,600 m. Here, we combine biogeochemical and molecular-phylogenetic approaches to characterize the bacterial and eucaryotic assemblages associated with fumarolic and nonfumarolic grounds on Socompa. Small-subunit rRNA genes were PCR amplified, cloned, and sequenced from two fumarolic soil samples and two reference soil samples, including the volcanic debris that covers most of the mountain. The nonfumarolic, dry, volcanic soil was similar in nutrient status to the most extreme Antarctic Dry Valley or Atacama Desert soils, hosted relatively limited microbial communities dominated by Actinobacteria and Fungi, and contained no photoautotrophs. In contrast, modest fumarolic inputs were associated with elevated soil moisture and nutrient levels, the presence of chlorophyll a, and (13)C-rich soil organic carbon. Moreover, this soil hosted diverse photoautotroph-dominated assemblages that contained novel lineages and exhibited structure and composition comparable to those of a wetland near the base of Socompa (3,661-m elevation). Fumarole-associated eucaryotes were particularly diverse, with an abundance of green algal lineages and a novel clade of microarthropods. Our data suggest that volcanic degassing of water and (13)C-rich CO(2) sustains fumarole-associated primary producers, leading to a complex microbial ecosystem within this otherwise barren landscape. Finally, we found that human activities have likely impacted the fumarolic soils and that fumarole-supported photoautotrophic communities may be exceptionally sensitive to anthropogenic disturbance.
View details for DOI 10.1128/AEM.01469-08
View details for Web of Science ID 000262690100024
View details for PubMedID 19074608
Environmental DNA sequencing primers for eutardigrades and bdelloid rotifers.
2009; 9: 25-?
The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms.Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly from soil. Our PCR primers, specific to the 18s small-subunit rRNA gene, were developed for both eutardigrades and bdelloid rotifers.The developed primers successfully amplified DNA of their target organism from various soil DNA extracts. This was confirmed by both the BLAST similarity searches and phylogenetic analyses. Tardigrades showed much better phylogenetic resolution than bdelloids. Both groups of organisms exhibited varying levels of endemism.The development of clade-specific primers for characterizing eutardigrades and bdelloid rotifers from environmental samples should greatly increase our ability to characterize the composition of these taxa in environmental samples. Environmental sequencing as shown here differs from other molecular survey methods in that there is no need to pre-isolate the organisms of interest from soil in order to amplify their DNA. The DNA sequences obtained from methods that do not require culturing can be identified post-hoc and placed phylogenetically as additional closely related sequences are obtained from morphologically identified conspecifics. Our non-cultured environmental sequence based approach will be able to provide a rapid and large-scale screening of the presence, absence and diversity of Bdelloidea and Eutardigrada in a variety of soils.
View details for DOI 10.1186/1472-6785-9-25
View details for PubMedID 20003362
The earliest stages of ecosystem succession in high-elevation (5000 metres above sea level), recently deglaciated soils
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
2008; 275 (1653): 2793-2802
Global climate change has accelerated the pace of glacial retreat in high-latitude and high-elevation environments, exposing lands that remain devoid of vegetation for many years. The exposure of 'new' soil is particularly apparent at high elevations (5000 metres above sea level) in the Peruvian Andes, where extreme environmental conditions hinder plant colonization. Nonetheless, these seemingly barren soils contain a diverse microbial community; yet the biogeochemical role of micro-organisms at these extreme elevations remains unknown. Using biogeochemical and molecular techniques, we investigated the biological community structure and ecosystem functioning of the pre-plant stages of primary succession in soils along a high-Andean chronosequence. We found that recently glaciated soils were colonized by a diverse community of cyanobacteria during the first 4-5 years following glacial retreat. This significant increase in cyanobacterial diversity corresponded with equally dramatic increases in soil stability, heterotrophic microbial biomass, soil enzyme activity and the presence and abundance of photosynthetic and photoprotective pigments. Furthermore, we found that soil nitrogen-fixation rates increased almost two orders of magnitude during the first 4-5 years of succession, many years before the establishment of mosses, lichens or vascular plants. Carbon analyses (pyrolysis-gas chromatography/mass spectroscopy) of soil organic matter suggested that soil carbon along the chronosequence was of microbial origin. This indicates that inputs of nutrients and organic matter during early ecosystem development at these sites are dominated by microbial carbon and nitrogen fixation. Overall, our results indicate that photosynthetic and nitrogen-fixing bacteria play important roles in acquiring nutrients and facilitating ecological succession in soils near some of the highest elevation receding glaciers on the Earth.
View details for DOI 10.1098/rspb.2008.0808
View details for Web of Science ID 000260611200003
View details for PubMedID 18755677
Biogeochemical consequences of rapid microbial turnover and seasonal succession in soil
2007; 88 (6): 1379-1385
Soil microbial communities have the metabolic and genetic capability to adapt to changing environmental conditions on very short time scales. In this paper we combine biogeochemical and molecular approaches to reveal this potential, showing that microbial biomass can turn over on time scales of days to months in soil, resulting in a succession of microbial communities over the course of a year. This new understanding of the year-round turnover and succession of microbial communities allows us for the first time to propose a temporally explicit N cycle that provides mechanistic hypotheses to explain both the loss and retention of dissolved organic N (DON) and inorganic N (DIN) throughout the year in terrestrial ecosystems. In addition, our results strongly support the hypothesis that turnover of the microbial community is the largest source of DON and DIN for plant uptake during the plant growing season. While this model of microbial biogeochemistry is derived from observed dynamics in the alpine, we present several examples from other ecosystems to indicate that the general ideas of biogeochemical fluxes being linked to turnover and succession of microbial communities are applicable to a wide range of terrestrial ecosystems.
View details for Web of Science ID 000247203100005
View details for PubMedID 17601130
Microbial diversity in alpine tundra wet meadow soil: novel Chloroflexi from a cold, water-saturated environment
2006; 8 (8): 1471-1486
Cold, water-saturated soils play important biogeochemical roles, yet almost nothing is known about the identity and habitat of microbes active under such conditions. We investigated the year-round microenvironment of an alpine tundra wet meadow soil in the Colorado Rocky Mountains, focusing on the biogeochemistry and microbial diversity of spring snowmelt--a dynamic time for alpine ecosystems. In situ measurements revealed spring and autumn periods of long-term temperature stability near 0 degrees C, and that deeper soil (30 cm) was more stable than surface soil, with more moderate summers and winters, and longer isothermal phases. The soil was saturated and water availability was limited by freezing rather than drying. Analyses of bioavailable redox species showed a shift from Mn reduction to net Fe reduction at 2-3 cm depth, elevated SO4(2-) and decreased soluble Zn at spring snowmelt. Terminal restriction fragment length polymorphism profiles detected a correlated shift in bacterial community composition at the surface to subsurface transition. Bacterial and archaeal small-subunit rRNA genes were amplified from saturated spring soil DNA pooled along a depth profile. The most remarkable feature of these subsurface-biased libraries was the high relative abundance of novel, uncultivated Chloroflexi-related sequences comprising the third largest bacterial division sampled, and representing seven new Chloroflexi subdivisions, thereby dramatically expanding the known diversity of this bacterial division. We suggest that these novel Chloroflexi are active at near -0 degrees C temperatures, under likely anoxic conditions, and utilize geochemical inputs such as sulfide from upslope weathering.
View details for DOI 10.1111/j.1462-2920.2006.01041.x
View details for Web of Science ID 000238885300015
View details for PubMedID 16872409
Structure and function of alpine and arctic soil microbial communities
RESEARCH IN MICROBIOLOGY
2005; 156 (7): 775-784
Cultivation-independent molecular phylogenetic techniques are now widely employed to examine environmental microbial diversity; however, the relationship between microbial community structure and ecosystem function is unclear. This review synthesizes cultivation-independent views of microbiological diversity with our current understanding of nutrient dynamics in alpine and arctic soils. Recently, we have begun to explore connections between microbial community structure and function in soils from the alpine Niwot Ridge LTER site in Colorado, USA, whose ecology has been extensively investigated for over 50 years. We examined the diversity of bacterial, eucaryal, and archaeal small subunit rRNA genes in tundra and talus soils across seasons in the alpine. This work has provided support for spatial and seasonal shifts in specific microbial groups, which correlate well with previously documented transitions in microbial processes. In addition, these preliminary results suggest that the physiologies of certain groups of organisms may scale up to the ecosystem level, providing the basis for testable hypotheses about the function of specific microbes in this system. These studies have also expanded on the known diversity of life, as these soils harbor bacterial and eucaryotic lineages that are distantly related to other known organisms. In contrast to the alpine, microbial diversity in the arctic has been little explored; only three published studies have used molecular techniques to examine these soils. Because of the importance of these systems, particularly to the global C cycle, and their vulnerability to current and impending climate change, the microbial diversity of these soils needs to be further investigated.
View details for DOI 10.1016/j.resmic.2005.03.004
View details for Web of Science ID 000232098000001
View details for PubMedID 15922566
The rate and pattern of cladogenesis in microbes
2004; 58 (5): 946-955
Theories of macroevolution rarely have been extended to include microbes; however, because microbes represent the most ancient and diverse assemblage of organismal diversity, such oversight limits our understanding of evolutionary history. Our analysis of phylogenetic trees for microbes suggests that macroevolution may differ between prokaryotes and both micro- and macroeukaryotes (mainly plants and animals). Phylogenetic trees inferred for prokaryotes and some microbial eukaryotes conformed to expectations assuming a constant rate of cladogenesis over time and among lineages: nevertheless, microbial eukaryote trees exhibited more variation in rates of cladogenesis than prokaryote trees. We hypothesize that the contrast of macroevolutionary dynamics between prokaryotes and many eukaryotes is due, at least in part, to differences in the prevalence of lateral gene transfer (LGT) between the two groups. Inheritance is predominantly, if not wholly, vertical within eukaryotes, a feature that allows for the emergence and maintenance of heritable variation among lineages. By contrast, frequent LGT in prokaryotes may ameliorate heritable variation in rate of cladogenesis resulting from the emergence of key innovations; thus, the inferred difference in macroevolution might reflect exclusivity of key innovations in eukaryotes and their promiscuous nature in prokaryotes.
View details for Web of Science ID 000221632700005
View details for PubMedID 15212376