Vanja Klepac-Ceraj

Wellesley College · Department of Biological Sciences

Myelination is a fundamental process of neurodevelopment that facilitates the efficient brain messaging and connectivity that underlies the emergence and refinement of cognitive skills and abilities. Healthy maturation of the myelinated white matter requires appropriate neural activity and coordinated delivery of key nutritional building blocks, in...

Characterizing the dynamics of microbial community succession in the infant gut microbiome is crucial for understanding child health and development, but no normative model currently exists. Here, we estimate child age using gut microbial taxonomic relative abundances from metagenomes, with high temporal resolution (±3 months) for the first 1.5 yea...

Infancy is a time of rapid brain development supporting foundational sensory learning. The gut microbiome, also undergoing extensive developmental changes in early life, may influence brain development through metabolism of neuroactive compounds. Here, we show across the first 18 months of life that microbial genes encoding enzymes that produce and...

Background Identifying modifiable risk factors of autism spectrum disorders (ASDs) may inform interventions to reduce financial burden. The infant/toddler gut microbiome is one such feature that has been associated with social behaviors, but results vary between cohorts. We aimed to identify consistent overall and sex-specific associations between...

Prenatal alcohol exposure (PAE) affects neurodevelopment in over 59 million individuals globally. Prior studies using dichotomous categorization of alcohol use and comorbid substance exposures provide limited knowledge of how prenatal alcohol specifically impacts early human neurodevelopment. In this longitudinal cohort study from Cape Town, South...

The term ‘executive functions’ (EFs) refers to a set of skills that support flexible control over thought and action. Classic EFs (working memory, inhibitory control, and cognitive flexibility) do not show measurable stable function until after the third year of life and continue to develop into early adulthood. However, even at the earliest ages,...

Emerging evidence implicates gut microbial metabolism in neurodevelopmental disorders, but its influence on typical neurodevelopment has not been explored in detail. We investigated the relationship between the microbiome and neuroanatomy and cognition of 381 healthy children, demonstrating that differences in microbial taxa and genes are associate...

Despite affecting up to 20% of infants in the United States, there is no cure for atopic dermatitis (AD), also known as eczema. Atopy usually manifests during the first six months of an infant's life and is one predictor of later allergic health problems. A diet of human milk may offer protection against developing atopic dermatitis. One milk compo...

Understanding the drivers that affect soil bacterial and fungal communities is essential to understanding and mitigating the impacts of human activity on vulnerable ecosystems like those on the Galápagos Islands. The volcanic slopes of these Islands lead to steep elevation gradients that generate distinct microclimates across small spatial scales....

In lakes, seasonal phytoplankton blooms and allochthonous plant debris intensify particulate organic carbon fluxes to the lakebed. Microbes associated with these particles likely vary with organic substrate lability and redox conditions. To explore microbial compositional responses to these variables, we analyzed particle‐associated and free‐living...

Understanding the major drivers that influence soil bacterial and fungal communities is essential to mitigate the impacts of human activity on vulnerable ecosystems, like those found on the Galápagos Islands. Located ~1000 km off the coast of Ecuador, the volcanically formed islands are situated within distinct oceanic currents, which provide seaso...

Microbial assemblages associated with biogenic particles are phylogenetically distinct from free-living counterparts, yet biogeochemically coupled. Compositions may vary with organic carbon and inorganic substrate availability and with redox conditions, which determine reductant and oxidant availability. To explore microbial assemblage compositiona...

Bifidobacterium longum subsp. infantis (B. infantis) is one of a few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis. All three organisms are classified in the same species group...

Bokashi is an organic soil amendment that makes use of microbial processes to break down agricultural waste and create a nutrient-rich fertilizer. The benefits of various types of bokashi on soil fertility and plant growth are well documented, however the changes in microbial community composition and nutrients during bokashi maturation remain poor...

Background: While early life exposures such as mode of birth, breastfeeding, and antibiotic use are established regulators of microbiome composition in early childhood, recent research suggests that the social environment may also exert influence. Two recent studies in adults demonstrated associations between socioeconomic factors and microbiome c...

The colonization of the human gut microbiome begins at birth, and over time, these microbial communities become increasingly complex. Most of what we currently know about the human microbiome, especially in early stages of development, was described using culture-independent sequencing methods that allow us to identify the taxonomic composition of...

Herein, we report the abundance and prevalence of HMO-metabolizing genes, specifically those of Bifidobacterium infantis, in fecal samples from human infants. Forty dyads were enrolled, and each mother collected a fecal sample from her infant at six months of age. Genomic DNA was extracted, and quantitative real-time PCR was used to determine gene...

Objectives To benefit from the complex oligosaccharides found in human milk, an infant relies on microbial metabolism of these compounds. The main objective of this study was to determine the abundance of Bifidobacterium infantis human milk oligosaccharide (HMO) metabolizing genes in infant fecal samples. Methods Fecal samples from 40 6-mos-old in...

Bifidobacterium longum subsp. infantis (B. infantis) is one of few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis, by molecular methods. These two organisms are classified in the...

The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, United States, and investigated the roles of organic electron donors and terminal electron accep...

The colonization of the human gut microbiome begins at birth, and, over time, these microbial communities become increasingly complex. Most of what we currently know about the human microbiome, especially in early stages of development, was described using culture-independent sequencing methods that allow us to identify the taxonomic composition of...

The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, and investigated the roles of organic electron donors and terminal electron acceptors in shaping...

Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts...

Both the brain and microbiome of humans develop rapidly in the first years of life, enabling extensive signaling between the gut and central nervous system (dubbed the “microbiome-gut-brain axis”). Emerging evidence implicates gut microorganisms and microbiota composition in cognitive outcomes and neurodevelopmental disorders (e.g., autism), but th...

Oxygenic photosynthesis supplies organic carbon to the modern biosphere, but it is uncertain when this metabolism originated. It has previously been proposed1,2 that photosynthetic reaction centres capable of splitting water arose by about 3 billion years ago on the basis of the inferred presence of manganese oxides in Archaean sedimentary rocks. H...

Insects, like all animals, are exposed to diverse environmental microbes throughout their life cycle. Yet, we know little about variation in the microbial communities associated with the majority of wild, unmanaged insect species. Here, we use a 16S rRNA gene metabarcoding approach to characterize temporal and geographic variation in the gut bacter...

Erwinia tracheiphila is a virulent phytopathogen that infects two genera of cucurbit crop plants, Cucurbita spp. (pumpkin and squash) and Cucumis spp. (muskmelon and cucumber). One of the unusual ecological traits of this pathogen is that it is limited to temperate eastern North America. Here, we complete the first large-scale sequencing of an E. t...

Erwinia tracheiphila is the causal agent of bacterial wilt of cucurbits, an economically important phytopathogen affecting few cultivated Cucurbitaceae host plant species in temperate Eastern North America. However, essentially nothing is known about E. tracheiphila population structure or genetic diversity. To address this shortcoming, a represent...

Course-based undergraduate research experiences (CUREs) have been shown to increase student retention and learning in the biological sciences. Most CURES cover only one aspect of gene regulation, such as transcriptional control. Here we present a new inquiry-based lab that engages understanding of gene expression from multiple perspectives. Student...

The microorganisms that inhabit cheese contribute greatly to the flavor and development of the final product. While the rind and curd microbiota have been characterized separately, there is limited information on how the structure and function of microbial communities in rinds and curds vary within and amongst cheeses. To better understand the diff...

Microbial fossils and textures are commonly preserved in Ediacaran and early Cambrian coarse-grained siliciclastic sediments that were deposited in tidal and intertidal marine settings. In contrast, the fossilization of micro-organisms in similar marine environments of post-Cambrian age is less frequently reported. Thus, temporal discrepancies in m...

Ooids are sedimentary grains that are distributed widely in the geologic record. Their formation is still actively debated, which limits our understanding of the significance and meaning of these grains in Earth's history. Central questions include the role played by microbes in the formation of ooids and the sources of ubiquitous organic matter wi...

Despite the impact of the human microbiome on health, an appreciation of microbial ecology has yet to be translated into mainstream medical training and practice. The human microbiota plays a role in the development of the immune system, in the development and function of the brain, in digestion, and in host defense, and we anticipate that many mor...

Ooids are small, concentrically laminated carbonate grains, typically limited to shallow tropical coastal settings in modern environments (e.g. Bahamas, Persian Gulf). However, they are common in the geological record, particularly in the Precambrian[1] and after mass extinction events[2]. Despite their geological significance and much interest, co...

Bacterial profiles of saliva in subjects with periodontitis and dental caries have been demonstrated to differ from that of oral health. The aim of this comparative analysis of existing data generated by the Human Oral Microbe Identification Microarray (HOMIM) from 293 stimulated saliva samples was to compare bacterial profiles of saliva in subject...

Understanding the composition of the microbiome of human associated insects can shed light on the sources of potential human pathogens. The human head louse, Pediculus humanus capitis, is an obligate symbiont found in the hair of humans, especially children. It is known to harbor an obligate endosymbiont, Candidatus Reisia. However, a complete surv...

Studies of the fecal microbiome have implicated the gut microbiota in obesity, but few studies have examined the microbial diversity at other sites. The association between obesity and the upper gastrointestinal (UGI) microbial diversity was explored. The UGI microbiome of 659 healthy Chinese adults with a measured body mass index (BMI) range of 15...

Tobacco causes many adverse health conditions and may alter the upper gastrointestinal (UGI) microbiome. However, the few studies that studied the association between tobacco use and the microbiome were small and underpowered. Therefore, we investigated the association between tobacco use and the UGI microbiome in Chinese men. We included 278 men w...

Background and objective: Aggressive periodontitis (AgP) is prevalent and shows a rapid course in African individuals. Although a strong focus has been placed on Aggregatibacter actinomycetemcomitans, new methods support the existence of a complex subgingival microflora in AgP. The purpose of the present study was to map the subgingival microbiota...

Bacteria affect oral health, but few studies have systematically examined the role of bacterial communities in oral diseases. We examined this relationship in a large population-based Chinese cancer screening cohort. Human Oral Microbe Identification Microarrays were used to test for the presence of 272 human oral bacterial species (97 genera) in u...

Objective: Next-generation sequencing (NGS) platforms can provide a plethora of 16S rDNA sequence data, however, analyses typically identify taxa only at the genus or higher levels. Using the Human Oral Microbe Identification Microarray (HOMIM), species-level identification of about 270 species could be obtained. The objective of this study was to...

Microbe-mediated soil uptake is the largest and most uncertain variable in the budget of atmospheric hydrogen (H2). The diversity and ecophysiological role of soil microorganisms that can consume low atmospheric abundances of H2 with high-affinity [NiFe]-hydrogenases is unknown. We expanded the library of atmospheric H2-consuming strains to include...

The human upper digestive tract microbial community (microbiota) is not well characterized and few studies have explored how it relates to human health. We examined the relationship between upper digestive tract microbiota and two cancer-predisposing states, serum pepsinogen I/pepsinogen II ratio (PGI/II; predictor of gastric cancer risk) and esoph...

Background and objective The bacterial profile of saliva is composed of bacteria from different oral surfaces. The objective of this study was to determine whether different diet intake, lifestyle, or socioeconomic status is associated with characteristic bacterial saliva profiles. Design Stimulated saliva samples from 292 participants with low le...

The aim of this study was to learn whether presence of caries in an adult population was associated with a salivary bacterial profile different from that of individuals without untreated caries. Stimulated saliva samples from 621 participants of the Danish Health Examination Survey were analyzed using the Human Oral Microbe Identification Microarra...

The objective of this study was to determine whether the detection of Aggregatibacter actinomycetemcomitans (Aa) correlates with the clinical and immunoinflammatory profile of Localized Aggressive Periodontitis (LAP), as determined by by 16S rRNA gene-based microarray. Subgingival plaque samples from the deepest diseased site of 30 LAP patients [PD...

Alkali production by oral bacteria via the arginine deiminase system (ADS) increases the pH of oral biofilms and reduces the risk for development of carious lesions. This study tested the hypothesis that increased availability of arginine in the oral environment through an exogenous source enhances the ADS activity levels in dental plaque and saliv...

Periodontitis is a multifactorial disease in which subgingival bacteria play an important role in the pathogenesis of the disease. The objective of this study was to determine if periodontitis is associated with a characteristic salivary bacterial profile. This was accomplished by comparing the bacterial profile of saliva from subjects with chronic...

Background: The purpose of this study is to investigate the antimicrobial effects of minocycline hydrochloride microspheres versus infrared light at 810 nm from a diode laser on multispecies oral biofilms in vitro. These biofilms were grown from dental plaque inoculum (oral microcosms) and were obtained from six systemically healthy individuals wi...

The primary goal of the human microbiome initiative has been to increase our understanding of the structure and function of our indigenous microbiota and their effects on human health and predisposition to disease. Because of its clinical importance and accessibility for in vivo study, the oral biofilm is one of the best-understood microbial commun...

Objective: To analyze salivary bacteria associated with body weight categories in female Kuwaiti children. Methods: Salivary and plaque samples were collected from 85 females (10.4 ± 0.6 year-old) during a pilot study in Kuwaiti children. Height, weight, and age were recorded and BMI percentile calculations were made using CDC software. The child...

Objective: Although Next Generation Sequencing platforms, such as Illumina, provide massive amounts of 16S rDNA sequence data, phylogenetic analyses primarily identify taxa only at the genus or higher level. Species-specific sequences were used for analysis of an Illumina dataset to determine microbial profiles in clinical samples, but at the speci...

Objective: The oral microflora comprising more than 700 bacterial species is generally considered beneficial. However, at present it is unknown whether oral or systemic diseases are reflected in qualitative changes of the microflora detected in saliva. Molecular methods, including Human Oral Microbe Identification Microarray (HOMIM), have increased...

Objectives: Inadequately maintained dentures can contribute to oral mucosal infections. Consequently, the initial microbial composition of denture surfaces must be determined to identify putative etiologic agents. Methods: Thirteen healthy subjects (7 females and 6 males), 60±9 yrs old (mean±SD), with maxillary complete denture were enrolled. Bru...

Recent studies implicate the gut microbiome in the etiology of obesity. However, the contribution of the microbiome remains uncertain due to conflicting results. Previous studies have examined different populations and ages, but most have focused on the fecal microbiome, while few studies have examined the role of microbial diversity at other body...

Some modern filamentous oxygenic photosynthetic bacteria (cyanobacteria) form macroscopic tufts, laminated cones and ridges that are very similar to some Archean and Proterozoic stromatolites. However, it remains unclear whether microbes that constructed Archean clumps, tufts, cones and ridges also produced oxygen. Here, we address this question by...

Unlabelled: The objective of this study was to characterize the subgingival microbiota of African-American children with Localized Aggressive Periodontitis (LAP). Fifty-one children were included. Subgingival plaque samples were taken from diseased (DD) and healthy sites (DH) in LAP and from healthy sites in HS and HC and analyzed by 16S rRNA-base...

While much is known about how virulence factors affect pathogens and host tissues in vitro, far less is understood about their dynamics in vivo. As a step towards characterizing the chemistry of infected environments, we measured phenazine abundance in the lungs of cystic fibrosis patients. Phenazines are redox-active small molecules produced by Ps...

Modern conical microbialites are similar to some ancient conical stromatolites, but growth, behavior and diversity of cyanobacteria in modern conical microbialites remain poorly characterized. Here, we analyze the diversity of cyanobacterial 16S rRNA gene sequences in conical microbialites from 14 ponds fed by four thermal sources in Yellowstone Na...

Objective: Metabolic Syndrome (MS) is constellation of symptoms including obesity, high blood pressure, high blood glucose, insulin resistance and high blood lipids leading for increased incidence of diabetes. The rates of increased body mass index and prevalence of obesity among Kuwaiti adults are higher than in other countries at the Gulf Region....

Background Dental caries is one of the most common diseases in the world. However, our understanding of how the microbial community composition changes in vivo as caries develops is lacking. Objective An in vivo model was used in a longitudinal cohort study to investigate shifts in the microbial community composition associated with the development...

Mahoney Lake, British Columbia, Canada, is a stratified, 15-m deep saline lake with a euxinic (anoxic, sulfidic) hypolimnion. A dense plate of phototrophic purple sulfur bacteria is found at the chemocline, but to date the rest of the Mahoney Lake microbial ecosystem has been underexamined. In particular, the microbial community that resides in the...

Abundance of taxa from phylum to order for the three methods used. The number of OTUs is shown for Phylochip, the number of total sequences for 454 pyrotags, and the number of sequences for each separate clone library (Bacteria and Archaea). Abundance was determined as the percentage of the total for each strategy. In bold are the subtotals for eac...

Phylogenetic reconstruction of sequences from El Coquito hot spring. Green branches indicate unique sequences obtained by Phylochip, dark blue branches indicate unique sequences obtained by 454 pyrotags, light blue indicates unclassified sequences of 454 pyrotags, red branches indicate unique sequences obtained by clone libraries, and black branche...

Many different systems of bacterial interactions have been described. However, relatively few studies have explored how interactions between different microorganisms might influence bacterial development. To explore such interspecies interactions, we focused on Bacillus subtilis, which characteristically develops into matrix-producing cannibals bef...