Nicholas A. Bokulich

Target-driven optimization of feature representation and model selection for microbiome sequencing data with ritme

ritme optimizes feature representation and model selection for microbiome data, improving performance and interpretability across multiple use cases.

Laccase-mediated biotransformation potential for fluorinated compounds by geographically diverse human gut microbiota

This study identifies laccase-coding genes in human gut microbiomes and demonstrates their ability to degrade fluorinated compounds from food and industry.

Decoding the microbiota of bors: multifunctional potential of a traditional Romanian beverage fermentation

This study characterizes the microbial community and functional traits of Romanian bors, identifying key bacterial and yeast species and their metabolic capabilities.

Ecological inference and contaminant detection from fungal microbiome data with q2-fungal-traits

This paper demonstrates the value of fungal trait-based phenotyping in microbiome research by analyzing four case studies and introduces q2-fungal-traits, a QIIME2 plugin for integrating fungal taxonomy with ecological and functional traits.

Bidirectional interactions between gut microbiota and fluorochemical biotransformation and bioactivity

This study investigates bidirectional interactions between fluorinated chemicals and gut microbiota using ex vivo, in vitro, and in silico methods, revealing microbial biotransformation and potential detoxification effects.

Interaction of Environment and Vineyard Management Effects Shape Microbial Functionality, Terroir, and Grape Qualities

The paper examines how environmental factors and vineyard management practices influence microbial communities, soil properties, and grape quality in Pinot Noir vineyards across two Swiss regions.

HighALPS: Ultra-High-Throughput Marker-Gene Amplicon Library Preparation and Sequencing on the Illumina NextSeq and NovaSeq Platforms

HighALPS adapts existing microbiome protocols for newer Illumina platforms, enabling ultra-high-throughput sequencing of 16S rRNA and ITS markers with high read depth and reliability.

Rising together: Exploring Sourdough Fermentation Diversity through Co-design in the HealthFerm Citizen Science Initiative

The paper describes a citizen science initiative that collected sourdough fermentation data from over 1000 participants across Europe, revealing patterns in practices, motivations, and microbial characteristics.

Grape Expectations: Disentangling Environmental Drivers of Microbiome Establishment in Winegrowing Ecosystems

This study investigates environmental drivers of microbial communities in Swiss vineyards using multi-omics data and machine learning to link microbiome composition to wine characteristics.

Shipped and shifted: modeling collection-induced bias in microbiome multi-omics using a tractable fermentation system

This study models collection-induced bias in microbiome multi-omics using a fermentation system, showing temperature strongly affects microbial and metabolic profiles.

Spatial heterogeneity and microbial terroir: balancing dispersal limitation and cultivar as drivers of microbial diversity in viticulture

This study examines spatial heterogeneity and cultivar effects on microbial communities in vineyards, finding that spatial distance, not cultivar, drives microbial diversity and community similarity.

Evaluating long-term stool preservation methods for maximizing the recovery of viable human fecal microbiota

This study evaluates cryopreservation methods for stool samples to maintain viable microbiota, finding that simple methods like glycerol preservation and snap-freezing are as effective as more complex protocols.

Indoor environmental conditions shape the microbial landscape of food production facilities across space and time

The study examines how indoor environmental conditions affect microbial communities in food production facilities over space and time.

Tier-based standards for FAIR sequence data and metadata sharing in microbiome research

This paper proposes tiered badges and an evaluation tool to assess data sharing compliance in microbiome research and finds that nearly half of publications fail to meet minimum sequence data availability standards.

The Genetic Basis of Microbiome Recruitment in Grapevine and its Association with Fermentative and Pathogenic Taxa

This study identifies genetic loci in grapevine that influence berry-associated microbial communities, including pathogenic fungi and fermentative yeasts, revealing broad genetic control over microbiome assembly.

The gut microbiota and sleep in infants: a focus on diurnal rhythmicity patterns

This study examines links between gut microbiota diversity and sleep rhythmicity in infants, finding that higher alpha diversity correlates with more robust sleep rhythms.

A tale of two vineyards: parsing site-specific differences in bacterial and fungal communities of wine grapes from proximal vineyards, and their changes during processing in a single winery

This study tracks microbial changes in wine grapes from two nearby vineyards during processing, showing that site-specific microbial signatures persist despite shared farming practices and that winery environments contribute to the fermentation microbiome.

Integrating sequence composition information into microbial diversity analyses with k-mer frequency counting

This paper demonstrates that k-mer frequency counting can effectively estimate microbial diversity and improve supervised classification in microbiome studies, offering a reference-free alternative to traditional methods.

Domestic freezer storage: a solution for preserving stool microbiota integrity for at-home collection

This study shows that storing stool samples in domestic freezers for up to six months preserves microbial composition and metagenomic data integrity, making it a viable alternative to -80°C storage for at-home collection.

MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework

MOSHPIT provides a reproducible metagenome analysis tool built on QIIME 2, integrating validated tools and interfaces for scalable and accessible data science.

Standardising a microbiome pipeline for body fluid identification from complex crime scene stains

This study develops a random forest classifier to identify body fluids from complex crime scene stains using microbiome data, achieving an F1 score of 0.89 on forensic samples.

Reproducible acquisition, management, and meta-analysis of nucleotide sequence (meta)data using q2-fondue

This paper introduces q2-fondue, a software plugin for reproducibly acquiring, managing, and analyzing nucleotide sequence data from public repositories.

RESCRIPt: Reproducible sequence taxonomy reference database management for the masses

The paper introduces RESCRIPt, a software tool for reproducibly generating and managing nucleotide sequence taxonomy databases, showing that larger databases are not always better and highlighting the benefits of curation.

Revisiting microbe-metabolite interactions: doing better than random

The paper compares correlation/proportionality methods with MMvec for identifying microbe-metabolite interactions and finds MMvec performs better on real data due to its handling of sparsity.

Species abundance information improves sequence taxonomy classification accuracy

This paper shows that incorporating species abundance data improves taxonomy classification accuracy for amplicon sequences.

q2-sample-classifier: machine-learning tools for microbiome classification and regression

The paper benchmarks supervised learning methods for microbiome classification and regression, introducing a QIIME 2 plugin to apply these methods to microbiome data.

Lack of Evidence that Ursodeoxycholic Acid’s Effects on the Gut Microbiome Influence Colorectal Adenoma Risk

This paper investigates whether UDCA's effects on the gut microbiome influence colorectal adenoma risk and finds no association between UDCA-induced microbiome changes and adenoma risk.

q2-longitudinal: a QIIME 2 plugin for longitudinal and paired-sample analyses of microbiome data

The paper introduces q2-longitudinal, a QIIME 2 plugin for analyzing longitudinal and paired microbiome data, offering methods like linear mixed effects models and volatility analysis.