Nicholas Bokulich

Last Name

Bokulich

First Name

Nicholas

ORCID

0000-0002-1784-8935

Organisational unit

09714 - Bokulich, Nicholas / Bokulich, Nicholas

Show all metadata

Search Results

Publications 1 - 10 of 112

Composition of the Vaginal Microbiome Associated with High Risk HPV Infection and Increased Risk for Cervical Cancer
Madhivanan, P.; Bokulich, Nicholas; Coudray, M.; et al. (2020)
Cancer Epidemiology, Biomarkers and Prevention
Impact of the [GAR+] Prion on Fermentation and Bacterial Community Composition with Saccharomyces cerevisiae UCD932
Walker, Gordon A.; Hjelmeland, Anna; Bokulich, Nicholas; et al. (2016)
American Journal of Enology and Viticulture
The efficiency and efficacy of alcoholic fermentation by yeast is crucial for the winemaking process. Sluggish or arrested fermentations can negatively affect winery operations and wine quality. Here, we present a novel mechanism by which problem fermentations can arise. Yeast can induce a prion known as [GAR+] that allows the cell to circumvent glucose repression of alternative carbon substrates. We have confirmed that Saccharomyces cerevisiae strain UCD932 can spontaneously generate the [GAR+] phenotype and that this phenotype exhibits the genetic traits of a prion. Differences were observed in the fermentative behavior of UCD932 wild-type [gar−] versus [GAR+] yeasts in laboratory-scale model juice fermentations. To further understand these differences, fermentations were performed in Chardonnay juice to study the interaction of the [GAR+] prion and presence of sulfur dioxide (SO2) on fermentation kinetics, bacterial community composition, and volatile compound production. Cells harboring the [GAR+] prion displayed reduced fermentation capacity, which was especially evident in the absence of SO2. Presence of SO2 and fermentation time had the most significant effects on the types of bacteria present in the fermentation. However, [GAR+] yeasts without added SO2 were especially sensitive to bacterial competition. This difference was also reflected in the bacterial and volatile profiles of the finished wine. We hypothesize that the bacterial induction of the [GAR+] prion by yeast during fermentation is another possible mechanism by which stuck or sluggish fermentations may become established. © 2016 American Society for Enology and Viticulture.
Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate
Bokulich, Nicholas; Thorngate, John H.; Richardson, Paul M.; et al. (2014)
Proceedings of the National Academy of Sciences of the United States of America
We demonstrate that grape-associated microbial biogeography is nonrandomly associated with regional, varietal, and climatic factors across multiscale viticultural zones. This poses a paradigm shift in our understanding of food and agricultural systems beyond grape and wine production, wherein patterning of whole microbial communities associated with agricultural products may associate with downstream quality characteristics. Elucidating the relationship between production region, climate, and microbial patterns may enhance biological control within these systems, improving the supply, consumer acceptance, and economic value of important agricultural commodities.
Microbial biogeography of the transnational fermented milk matsoni
Bokulich, Nicholas; Amiranashvili, Lia; Chitchyan, Karine; et al. (2015)
Food Microbiology
The fermented milk matsoni is a traditional, national food product of both Georgia and Armenia. Little is known about the effects of biogeography and milk type on the microbial biodiversity of matsoni or the fungal composition of matsoni fermentations. High-throughput marker-gene sequencing was used to survey the bacterial and fungal communities of matsoni from different milk types and regions throughout Armenia and Georgia. Results demonstrate that both production region and milk type influence matsoni microbiota, suggesting that the traditional production methods preserve the transfer of unique regional microbiota from batch to batch. Bacterial profiles were dominated by Lactobacillus and Streptococcus species. Yeast profiles varied dramatically, with Kluyveromyces marxianus, Candida famata, Saccharomyces cerevisiae, Lodderomyces elongisporus, and Kluyveromyces lactis being the most important species distinguishing production regions and milk types. This survey will enable more detailed capture and characterization of specific microbiota detected within these fermentations. © 2015 Elsevier Ltd.
Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: differentiation by vineyard management
Burns, Kayla N.; Bokulich, Nicholas; Cantu, Dario; et al. (2016)
Soil Biology and Biochemistry
Little is known about the hierarchical effects of management practices, soil attributes and location factors on structure of vineyard soil microbiota. A hierarchical effect occurs when the specific influence of an experimental factor (e.g. cover crop type, compost application) on soil-borne bacterial communities is greater within a subset composing the larger set but not across the entire set (e.g. bacterial communities only respond to a management practice within a subset of soil types but not across the entire set composed of all soil types). To address this concept, we measured differences in soil bacterial and archaeal diversity in wine-grape vineyard soils throughout Napa Valley, California. We describe how vineyard management practices influence soil resources, which in turn determine shifts in soil-borne bacterial communities. Soil bacterial communities were structured with respect to management practices, specifically cover crop presence and cover crop mix, tillage, and agricultural system designation, i.e. conventional, organic and biodynamic production systems. Distinctions with respect to management were associated with differences in pH and soil resource pools: total carbon and total nitrogen of the <53 and 53–250 μm particulate organic matter fractions, and potentially mineralizable nitrogen. Findings in this study suggest management practices in vineyard production systems directly influence soil microbial community structure, as mediated by shifts in soil resource pools. However, hierarchical effects occur, in which β-diversity is more strongly affected by specific management practices only within certain soil types, tillage or no-till soils or winegrowing region. This work allows for subsequent assessments of interrelationships of vineyard management, microbial biodiversity and their combined influence on soil quality, vine health, and berry quality.
Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants
Bokulich, Nicholas; Mills, David A. (2013)
Applied and Environmental Microbiology
Cheese fermentations involve the growth of complex microbial consortia, which often originate in the processing environment and drive the development of regional product qualities. However, the microbial milieus of cheesemaking facilities are largely unexplored and the true nature of the fermentation-facility relationship remains nebulous. Thus, a highthroughput sequencing approach was employed to investigate the microbial ecosystems of two artisanal cheesemaking plants, with the goal of elucidating how the processing environment influences microbial community assemblages. Results demonstrate that fermentation-associated microbes dominated most surfaces, primarily Debaryomyces and Lactococcus, indicating that establishment of these organisms on processing surfaces may play an important role in microbial transfer, beneficially directing the course of sequential fermentations. Environmental organisms detected in processing environments dominated the surface microbiota of washed-rind cheeses maturing in both facilities, demonstrating the importance of the processing environment for populating cheese microbial communities, even in inoculated cheeses. Spatial diversification within both facilities reflects the functional adaptations of microbial communities inhabiting different surfaces and the existence of facility-specific "house" microbiota, which may play a role in shaping site-specific product characteristics. © 2013 American Society for Microbiology.
A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses
O'Rourke, Devon R.; Bokulich, Nicholas; MacManes, Matthew D.; et al. (2020)
Ecology and Evolution
Metabarcoding studies provide a powerful approach to estimate the diversity and abundance of organisms in mixed communities in nature. While strategies exist for optimizing sample and sequence library preparation, best practices for bioinformatic processing of amplicon sequence data are lacking in animal diet studies. Here we evaluate how decisions made in core bioinformatic processes, including sequence filtering, database design, and classification, can influence animal metabarcoding results. We show that denoising methods have lower error rates compared to traditional clustering methods, although these differences are largely mitigated by removing low-abundance sequence variants. We also found that available reference datasets from GenBank and BOLD for the animal marker gene cytochrome oxidase I (COI) can be complementary, and we discuss methods to improve existing databases to include versioned releases. Taxonomic classification methods can dramatically affect results. For example, the commonly used Barcode of Life Database (BOLD) Classification API assigned fewer names to samples from order through species levels using both a mock community and bat guano samples compared to all other classifiers (vsearch-SINTAX and q2-feature-classifier's BLAST + LCA, VSEARCH + LCA, and Naive Bayes classifiers). The lack of consensus on bioinformatics best practices limits comparisons among studies and may introduce biases. Our work suggests that biological mock communities offer a useful standard to evaluate the myriad computational decisions impacting animal metabarcoding accuracy. Further, these comparisons highlight the need for continual evaluations as new tools are adopted to ensure that the inferences drawn reflect meaningful biology instead of digital artifacts.
RESCRIPt: Reproducible sequence taxonomy reference database management
Robeson II, Michael S.; O'Rourke, Devon R.; Kaehler, Benjamin D.; et al. (2021)
PLoS Computational Biology
Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, and evaluating nucleotide sequence and taxonomy reference databases creates a significant bottleneck for researchers aiming to generate custom sequence databases. Furthermore, database composition drastically influences results, and lack of standardization limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a Python 3 software package and QIIME 2 plugin for reproducible generation and management of reference sequence taxonomy databases, including dedicated functions that streamline creating databases from popular sources, and functions for evaluating, comparing, and interactively exploring qualitative and quantitative characteristics across reference databases. To highlight the breadth and capabilities of RESCRIPt, we provide several examples for working with popular databases for microbiome profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA and diet metabarcoding surveys (BOLD, GenBank), as well as for genome comparison. We show that bigger is not always better, and reference databases with standardized taxonomies and those that focus on type strains have quantitative advantages, though may not be appropriate for all use cases. Most databases appear to benefit from some curation (quality filtering), though sequence clustering appears detrimental to database quality. Finally, we demonstrate the breadth and extensibility of RESCRIPt for reproducible workflows with a comparison of global hepatitis genomes. RESCRIPt provides tools to democratize the process of reference database acquisition and management, enabling researchers to reproducibly and transparently create reference materials for diverse research applications. RESCRIPt is released under a permissive BSD-3 license at https://github.com/bokulich-lab/RESCRIPt.
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
Bokulich, Nicholas; Subramanian, Sathish; Faith, Jeremiah J.; et al. (2013)
Nature Methods
High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and α-diversity assessment for microbial communities. We demonstrate that high-quality read length and abundance are the primary factors differentiating correct from erroneous reads produced by Illumina GAIIx, HiSeq and MiSeq instruments. We present guidelines for user-defined quality-filtering strategies, enabling efficient extraction of high-quality data and facilitating interpretation of Illumina sequencing results.
A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments
Bokulich, Nicholas; Rideout, Jai Ram; Kopylova, Evguenia; et al. (2015)
PeerJ Preprints
Background: Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms. Results: We present three advances in our ability to assign and interpret taxonomic classifications of short marker gene sequences: two new methods for taxonomy assignment, which reduce runtime up to two-fold and achieve high-precision genus-level assignments; an evaluation of classification methods that highlights differences in performance with different marker genes and at different levels of taxonomic resolution; and an extensible framework for evaluating and optimizing new classification methods, which we hope will serve as a model for standardized and reproducible bioinformatics methods evaluations. Conclusions: Our new methods are accessible in QIIME 1.9.0, and our evaluation framework will support ongoing optimization of classification methods to complement rapidly evolving short-amplicon sequencing and bioinformatics technologies. Static versions of all of the analysis notebooks generated with this framework, which contain all code and analysis results, can be viewed at http://bit.ly/srta-012 .

Publications 1 - 10 of 112

Nicholas Bokulich

Last Name

First Name

ORCID

Organisational unit

Filters

Search Results