Biology subjects

Bokulich, N. A.

Publications and source records attributed to Bokulich, N. A..

16 recordsLinked to original sources

bioRxiv2026

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

Fungi are key members of microbial communities, yet microbiome surveys often lack trait-based information required for ecologically meaningful interpretation of mycobiome data. To demonstrate the value of fungal trait-based phenotyping in microbiome research, we re-analyzed N=3,221 samples across four case studies spanning human, agricultural, and environmental systems. In human cancer and vineyard datasets, trait-based analysis detected fungi producing macroscopic fruiting bodies, likely introduced via airborne spore dispersal, indicating widespread contributions of transient or contaminant fungi that can confound interpretation of sequencing data from tumor biopsies and grape berries. In sourdough fermentations, filamentous fungi were highly abundant alongside traditionally-recognized yeast and occupied distinct ecological niches. In forest soils, increasing habitat disturbance was associated with increased prevalence and abundance of plant pathogens, and a marked decline in ectomycorrhizal and lichenized fungi. These changes were accompanied by a shift toward large-spored taxa in urban soils, consistent with enhanced stress tolerance. To facilitate broader adoption of fungal phenotyping in microbiome studies, we introduce q2-fungal-traits, a QIIME2 plugin for automated integration of fungal taxonomy derived from marker-gene or shotgun metagenome sequencing surveys with ecological and functional trait data. The plugin assigns lifestyle-related traits and spore size estimates through hierarchical taxonomic matching and integrates directly into standard microbiome workflows. Our case studies demonstrate that integrating trait-based ecology with mycobiota datasets can generate novel findings and testable hypotheses, enabling inference of the functional (ir)relevance of community constituents. Our work contributes to bridging the gap between descriptive community profiling and functional ecology in microbiome research.

microbiology↗

bioRxiv2026

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

The growing prevalence of synthetic organofluorine substances in agrochemicals, food packaging, and consumer products has led to increasing gastrointestinal exposure, with potential consequences for human health. Despite the extreme stability of fluorinated compounds, several microbial pathways for their transformation are known, including by laccases, a type of multicopper oxidase. However, the functionality of laccases in the gut microbiome, a natural contact point between food-associated chemicals and microbial biotransformation pathways, is poorly defined. Through a multi-study analysis of 1578 human gut metagenomes spanning a global gradient from hunter-gatherer societies to industrialized urban populations, we found that laccase-coding gene homologs are widely distributed in the human gut microbiome. We identified a significant association between both the abundance and phylogenetic diversity of laccase homologs with the degree of urbanization. As human gut microbial laccase activity has not been experimentally demonstrated, eight gut metagenome-derived laccases were heterologously expressed and screened for activity with a redox mediator system. Six of the eight laccases demonstrated activity. One of these gut microbial laccases and three previously characterized laccases were then tested for their capacity to deplete 11 different food-associated chemicals. All four effectively depleted the agrochemicals cyflumetofen and fluazinam, as well as the industrial chemical bisphenol AF to a lesser extent. By linking global gut metagenomes with activity assays, this work demonstrates the untapped potential of mining human gut metagenomes for laccases and other microbial enzymes that can actively modify various agricultural and industrial chemicals. ImportanceAs adverse effects of fluorinated compounds on human health are emerging, the responsible enzymes from the human gut microbiome of geographically diverse human cohorts mediating interactions with fluorinated compounds in the gastrointestinal tract remain poorly characterized. In a multi-study analysis of publicly available microbiome sequencing data, we linked the abundance, diversity, and phylogeny of laccases within the gut microbiome to the degree of urbanization of human cohorts, and experimentally demonstrated the ability of these laccases to deplete a range of food-associated fluorochemicals. Another significant contribution of our study is in the integration of rural catchment areas as a quantitative metric of urbanization in gut microbiome metagenomics and enzyme activity surveys.

microbiology↗

bioRxiv2025

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

Vineyards are complex agroecological systems, with geographically distinct microbial communities playing a central role in mediating vine health, grape quality, and ultimately local wine characteristics (terroir). However, the extent to which environmental factors and vineyard management practices interact to shape these microbial communities and their functions remains poorly understood. We implemented a multidisciplinary citizen science collaboration together with winegrowers to sample 19 Pinot Noir vineyards across two distinct Swiss regions (N=38 samples). This allowed us to evaluate how a combination of environmental conditions and management practices (such as cover cropping and fungicide use) collectively impact soil and grape microbiomes, soil enzymatic activities, nutrient concentration in leaves, and grape chemistry. Regional differences were the primary drivers of variation, but multivariate analysis revealed a distinct, secondary influence from management practices on soil and berries. Berry quality was linked to functional soil properties, including microbial activity, which were further associated with key fermentative yeasts likely involved in wine fermentation. These findings highlight the interconnected nature of environmental, microbial, and agronomic factors in grapevine systems and offer novel insights into functional aspects of microbial terroir.

microbiology↗

bioRxiv2025

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

The microbial communities inhabiting food production environments are distinguished from those of other built environments in their capacity to influence food quality and safety, impacting consumer health. However, how indoor environmental conditions drive the bacterial and fungal communities of food production facilities remains largely unknown. In this study of five commercial food production facilities, we employed remote wireless sensors paired with marker-gene amplicon sequencing (bacterial 16S rRNA genes and fungal ITS) of processing equipment and non-processing built environment surfaces (N=2,329) to profile spatial and longitudinal changes in bacterial and fungal communities, and their association with indoor climate. We identify multiple associations between indoor environmental conditions and microbial community structure, demonstrating the role of the indoor environment in shaping microbial communities on food processing and non-processing surfaces. This suggests that indoor climate could be manipulated to rationally modify surface communities, with the aim of enhancing food quality and safety.

microbiology↗

bioRxiv2025

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

The microbial communities inhabiting grapevines and wines exhibit spatiotemporal patterns linked to region, climate, and cultivar. However, the degree of spatial heterogeneity within and between vineyards and its relationship to cultivar-associated biodiversity selection has not been studied previously. We combined high-density sampling of grapevine microbiota (N = 230) with spatial modeling and satellite imagery in two experiments: (i) two monoclonal Chardonnay vineyards to examine spatial heterogeneity in a genetically homogenous population; and (ii) three old-vine vineyards interplanted with mixed cultivars to investigate the relative effects of spatial distance and cultivar on the microbiota. Contrary to expectations based on monoclonal vineyards, cultivar effects were not apparent in mixed-cultivar vineyards. Instead, we demonstrate extensive spatial variation in the bacterial and fungal communities inhabiting individual grapevines and vineyards, and that community similarity is correlated with spatial distance within and between vineyards. This suggests that dispersal limitation may play an important role in shaping grapevine microbiota, as well as cumulative diversity within the vineyard ecosystem (gamma diversity), with implications for both plant health and wine quality. Spatial models can identify abnormalities in microbial communities, such as contaminant sources within vineyards, and future studies examining microbiota in agricultural settings should account for spatial variation within the study design, e.g., by sufficiently dense spatial sampling or collection of grape musts to avoid undersampling bias. These findings add to the complicated story of microbial biogeography associated with winegrowing and wine quality (microbial terroir), highlighting the roles of dispersal and potential microclimate effects in agricultural settings.

microbiology↗

bioRxiv2025

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

Emerging evidence supports a bidirectional relationship between the gut microbiome and sleep, partly mediated by the microbiota-gut-brain axis. Circadian rhythms appear to influence early developmental processes and may play a role in shaping this relationship. While infancy is a critical window for both gut microbiota establishment and the maturation of sleep regulation, the role of gut bacteria in modulating infant sleep remains poorly understood. In this longitudinal study, we performed continuous within-subject sampling (monitoring across 48 hours) in 20 infants at 2, 4, and 6 months of age to examine associations between the establishment of gut microbiota and sleep patterns. We hypothesized that microbial diversity and sleep rhythmicity would be linked across both short (diurnal) and long (monthly) time scales. Gut microbiota profiles were characterized using 16S rRNA gene sequencing; gut melatonin concentrations were measured; and sleep metrics were quantified through wearable actimetry, parent-reported 24-hour sleep diaries, and the Brief Infant Sleep Questionnaire (BISQ). Parents additionally completed the Baby Care Questionnaire (BCQ), assessing parenting style, and the Ages and Stages Questionnaire (ASQ), evaluating infant behavioral development. In some infants, alpha diversity followed diurnal rhythmic patterns. Although bacterial rhythmicity was not significantly associated with sleep rhythmicity, as quantified with the Circadian Function Index, infants with higher alpha diversity had more robust sleep rhythmicity ({beta}Faith PD= 0.0721, SE = 0.0337). Infant age emerged as the strongest predictor of both gut microbiota diversity (observed features: {beta}age = 0.101, SE = 0.0172) and gut melatonin concentrations ({beta}age = 0.638, SE = 0.162). For the same age, gut microbiota temporal volatility - an indicator for bacterial community instability - was not associated with sleep patterns. This study demonstrates promising short- and long-term links between gut microbiota diversity and sleep-wake rhythm maturation in infancy. Further research is needed to elucidate the mechanistic role of the gut microbiome in sleep development.

microbiology↗

bioRxiv2025

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

Fermented foods are culturally significant and increasingly recognized for their potential health benefits, yet scientific data on household fermentation practices remain limited. We launched a co-designed citizen science (CS) initiative within the HealthFerm project to collect sourdough fermentation data across Europe. Over 1000 participants from 33 countries registered, with 671 samples submitted, enabling large-scale analysis of fermentation practices, motivations, and sourdough characteristics. Participants also completed standardized at-home experiments and sensory evaluations, generating a dataset linking baking habits with physicochemical and sensory profiles. Distinct patterns emerged: professional bakers used older, more frequently refreshed starters and fermented at higher temperatures. Ingredient choices and motivations varied by country, shaped by perceived health benefits. Beyond data collection, this initiative established a microbial biobank and harmonized metadata resource, while offering practical insights into co- design, logistics, and public engagement. The resulting framework provides a transferable model for participatory research in microbiology and food systems science.

scientific communication and education↗

bioRxiv2025

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

Microbial communities play an integral role in agricultural systems, where their composition and function are shaped by environmental factors and interactions with the plant host. In viticulture and winemaking, the resulting distinct microbial biogeographic patterns influence wine characteristics - a well-established concept termed microbial terroir. Yet, due to the complexity of interactions, the specific environmental drivers shaping these microbiomes remain poorly understood. We conducted a multi-year, large-scale survey (N = 680 samples) of Swiss vineyards (N = 95 sites), following a subset (N = 12, within 2.46 km) longitudinally over 3 years. We integrate microbiome (bacterial and fungal marker-gene sequencing), untargeted metabolomics (GC-MS and LC-MS/MS), environmental monitoring, and sensory data to disentangle abiotic factors influencing community assembly and interactions in vineyards and in wine fermentations. Results show that topography and climate collectively structure microbial communities, yet exhibit distinct influences on soil- and plant-associated microbiomes. Berry-associated fungal communities exhibit the strongest site-specific imprint, enabling machine-learning-based prediction of even subtle microclimatic differences. Climatic factors and berry chemistry exhibit an inverse relationship, selectively favoring either Hanseniaspora sp. or Saccharomyces cerevisiae - each correlating with distinct metabolite and aroma profiles. Additionally, plant stress-response metabolites were associated with shifts in microbial composition and fermentation outcomes. By integrating multi-omics and machine learning approaches, this study enhances our understanding of microbial biogeography and its role in winegrowing. Our findings highlight the need for further research on microbial transmission, vineyard management, and implications for wine quality, offering a foundation for a more precise, science-driven approach to terroir expression. Graphical AbstractWe sampled a total of 95 vineyards, with longitudinal sampling of 12 over three years, controlling for cultivar while capturing variations in topography, soil properties, and microclimate. Data collected in vineyards further included berry chemistry, vineyard management, and phenology. We sequenced microbial communities in both vineyard and fermentation samples, and the wines were additionally analysed with three different untargeted metabolomics approaches. Supervised and unsupervised modeling revealed spatio-temporal variability, the influence of environmental factors on microbial communities, and their impact on wine characteristics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/652874v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1ccb855org.highwire.dtl.DTLVardef@15a13f2org.highwire.dtl.DTLVardef@d39455org.highwire.dtl.DTLVardef@af8c29_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

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

O_LIWhile grapevine is an exceptional perennial model for studying host-microbiome interactions, the host genomes role in microbiome assembly is often masked by environmental factors. This research provides a first insight into the genetic mechanisms shaping berry-associated microbial communities. C_LIO_LIUsing QTL mapping in a newly established population of 140 F1-progeny grapevine genotypes in a complete random block design, we were able to control abiotic effects and investigate how the host genome influences grape berry-associated bacterial and fungal communities. C_LIO_LIWe identify significant associations between various microorganisms and the grape genome, including pathogenic fungi such as Botrytis spp. and fermentative yeasts such as Saccharomyces cerevisiae. Many of these taxa map to the same genetic loci associated with plant immune responses, suggesting that specific genetic loci broadly influence microbial community assembly in fruits. C_LIO_LIOur findings demonstrate that grapevine genetics significantly shape the microbiome, even under varying environmental conditions; moreover, that broad, rather than known symbiont-specific mechanisms control microbial colonization of fruit, revealing an emergent "domino" effect with implications for plant-fungal-bacterial interactions. We provide a framework for understanding genotype-microbiome interactions in perennial plants, enabling future targeted experiments to establish causal relationships in microbiome recruitment and offer a potential avenue for breeding programs advancing sustainable viticulture. C_LI

microbiology↗

bioRxiv2025

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

Wine is a microbial product, naturally transformed through fermentation by a consortium of fungi and bacteria that originate from the vineyard and the cellar, in addition to any microorganisms that are intentionally inoculated. Previous work has shown that grapevine-associated microbiota follow distinct biogeographic patterns, associated with climate and soil properties, and that even neighboring vineyards can harbor distinct microbial communities, but it is unclear whether these differences persist when controlling for variations in farming practices, cultivar, and climate, and whether site-specific microbial profiles change during processing in the winery. Here we investigated the bacterial and fungal microbiota of fruit pre- and post-harvest from two nearby vineyards planted to a single variety, geographically close to one another, and farmed the same way, and then processed in a single winery. These communities subtly changed during processing yet retained distinct site-specific signatures, indicating a partial contribution of the winery environment to the microbiota of grape must and juice pre-fermentation. We also profiled the microbiota of key microbial sources in the winery environment, including fruit flies and processing equipment, demonstrating that the microbiota at these sites reflect contact with plant material, harbor communities distinct from fruit, and appear to partially contribute to the fermentation assemblage, especially via the contribution of fermentative yeasts that are rare or missing in the vineyard environment. These results bolster previous reports of site-specific microbial signatures in winegrowing and make a first estimation of the changes to the grape-associated microbiome during early processing. ImportanceNative wine fermentations are driven by microbes carried over from the vineyard or introduced in the winery. In this study, we tracked the microbiome dynamics of wine fermentations from two Chardonnay vineyards planted in close proximity to examine the relative contribution of vineyard- and winery-resident microbiota on microbial succession during wine fermentation. By tracking microbial changes from vineyard to winery, we show that the winery environment, including processing equipment and fruit flies, contributes to the fermentation microbiome but does not override vineyard-specific microbial differences. These findings support the concept of microbial terroir and highlight the importance of vineyard microbiomes in shaping wine fermentation. This work advances our understanding of how microbial diversity influences wine production and provides insight into the ecological dynamics of fermentation. By identifying key microbial sources and their contributions, this study lays the groundwork for future microbiome research in viticulture and wine making.

microbiology↗

bioRxiv2025

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

Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems, but is fraught with technical hurdles. We introduce MOSHPIT (https://moshpit.readthedocs.io), software built on the QIIME 2 framework (Q2F) that integrates best-in-class CAMI2-validated metagenome tools with robust provenance tracking and multiple user interfaces, enabling streamlined, reproducible metagenome analysis for all expertise levels. By building on Q2F, MOSHPIT enhances scalability, interoperability, and reproducibility in complex workflows, democratizing and accelerating discovery at the frontiers of metagenomics.

bioinformatics↗

bioRxiv2024

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

K-mer frequency information in biological sequences is used for a wide range of applications, including taxonomy classification, sequence similarity estimation, and supervised learning. However, in spite of its widespread utility, k-mer counting has been largely neglected for diversity estimation. This work examines the application of k-mer counting for alpha and beta diversity as well as supervised classification from microbiome marker-gene sequencing datasets (16S rRNA gene and full-length fungal ITS sequences). Results demonstrate a close correspondence with phylogenetically aware diversity metrics, and advantages for using k-mer-based metrics for measuring microbial biodiversity in microbiome sequencing surveys. K-mer counting appears to be a suitable and efficient strategy for feature processing prior to diversity estimation as well as supervised learning in microbiome surveys. This allows incorporation of subsequence-level information into diversity estimation without the computational cost of pairwise sequence alignment. K-mer counting is proposed as a complementary approach for feature processing prior to diversity estimation and supervised learning analyses, enabling large-scale reference-free profiling of microbiomes in biogeography, ecology, and biomedical data. A method for k-mer counting from marker-gene sequence data is implemented in the QIIME 2 plugin q2-kmerizer (https://github.com/bokulich-lab/q2-kmerizer). ImportanceK-mers are all of the subsequences of length k that comprise a sequence. Comparing the frequency of k-mers in DNA sequences yields valuable information about the composition of these sequences and their similarity. This work demonstrates that k-mer frequencies from marker-gene sequence surveys can be used to inform diversity estimates and machine learning predictions that incorporate sequence composition information. Alpha and beta diversity estimates based on k-mer frequencies closely correspond to phylogenetically aware diversity metrics, suggesting that k-mer-based diversity estimates are useful proxy measurements especially when reliable phylogenies are not available, as is often the case for some DNA sequence targets such as for internal transcribed spacer sequences.

bioinformatics↗

bioRxiv2022

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

The volume of public nucleotide sequence data has blossomed over the past two decades, enabling novel discoveries via re-analysis, meta-analyses, and comparative studies for uncovering general biological trends. However, reproducible re-use and management of sequence datasets remains a challenge. We created the software plugin q2-fondue to enable user-friendly acquisition, re-use, and management of public nucleotide sequence (meta)data while adhering to open data principles. The software allows fully provenance-tracked programmatic access to and management of data from the Sequence Read Archive (SRA). Sequence data and accompanying metadata retrieved with q2-fondue follow a validated format, which is interoperable with the QIIME 2 ecosystem and its multiple user interfaces. To highlight the manifold capabilities of q2-fondue, we present several demonstration analyses using amplicon, whole genome, and shotgun metagenome datasets. These use cases demonstrate how q2-fondue increases analysis reproducibility and transparency from data download to final visualizations by including source details in the integrated provenance graph. We believe q2-fondue will lower existing barriers to comparative analyses of nucleotide sequence data, enabling more transparent, open, and reproducible conduct of meta-analyses. q2-fondue is a Python 3 package released under the BSD 3-clause license at https://github.com/bokulich-lab/q2-fondue.

bioinformatics↗

bioRxiv2020

RESCRIPt: Reproducible sequence taxonomy reference database management for the masses

BackgroundNucleotide 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 standardizations limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a software package 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. ResultsTo 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. ConclusionsRESCRIPt 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.

bioinformatics↗

bioRxiv2019

Rapidly processed stool swabs approximate stool microbiota profiles

Studies of the intestinal microbiome commonly utilize stool samples to measure microbial composition in the distal gut. However, collection of stool can be difficult from some subjects under certain experimental conditions. In this study we validate the use of swabs of fecal matter to approximate measurements of microbiota in stool using 16S rRNA gene Illumina amplicon sequencing, and evaluate the effects of shipping time at ambient temperatures on accuracy. Results indicate that swab samples reliably replicate stool microbiota bacterial composition, alpha diversity, and beta diversity when swabs are processed quickly (< 2 days), but sample quality quickly degrades after this period, accompanied by increased abundances of Enterobacteriaceae. Fresh swabs appear to be a viable alternative to stool sampling when standard collection methods are challenging, but extended exposure to ambient temperatures prior to processing threatens sample integrity.

microbiology↗

bioRxiv2017

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

ObjectiveWe previously reported that Ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduces risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colon cancer neoplasia have been postulated but evidence is limited to small cohorts and animal studies.\n\nDesignUsing banked stool samples collected as part of a phase III randomized clinical trial of UDCA for the prevention of colorectal neoplasia, we compared change in the microbiome composition after 3 years intervention in a subset of participants randomized to 8-10 mg/kg of body weight UDCA (n=198) to placebo (n=203). UDCA effects on the microbiome, sex and adenoma outcome were investigated.\n\nResultsStudy participants randomized to UDCA experienced compositional changes in their microbiome that were statistically more similar to other individuals in the UDCA arm than to those in the placebo arm. This change reflected an UDCA-associated shift in microbial community distance metrics (P <0.001), independent of sex, with no evidence of UDCA effect on microbial richness (P > 0.05). These UDCA-associated shifts in microbial community distance metrics from baseline to end-of-study were not associated with risk of any or advanced adenoma (all P> 0.05) in men or women.\n\nConclusionDespite a large sampling of randomized clinical trial participants, daily UDCA use only modestly influenced the relative abundance of microbial species in stool with no evidence for effects of UDCA on stool microbial community composition as a modifier of colorectal adenoma risk.\n\nSUMMARYO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIUrsodeoxycholic acid (UDCA) is a therapeutic bile acid used in the treatment of primary biliary cirrhosis (PBC) and investigated for anti-cancer activity in the colon\nC_LIO_LIIn humans, UDCA is produced in the colon from the conjugation of primary bile acids by intestinal bacteria\nC_LIO_LIIntestinal bacteria play a critical role in human intestinal health and disease including a hypothesized role in the development of colorectal cancer.\nC_LIO_LIUDCA was found to reduce the risk of more advanced colorectal adenoma with effects present in men but not women.\nC_LIO_LITherapeutic UDCA was recently shown to reduce the extent of bacterial dysbiosis in patients with PBC\nC_LI\n\nWhat are the new findings?O_LIAmong a population of patients with colorectal adenoma, low dose oral UDCA taken daily produced modest changes in fecal bacterial composition\nC_LIO_LIUDCA associated changes in the gut microbiome were similar in men and women.\nC_LIO_LIUDCA associated changes in the gut micobiome were not associated with risk of any or advanced colorectal adenoma in the patient population.\nC_LI\n\nHow might it impact on clinical practice in the foreseeable future?O_LIThese findings confirm effects of oral UDCA on the microbiome that may be beneficial for patients with PBC.\nC_LIO_LIThese findings suggest that the anti-cancer effects of UDCA for colorectal adenoma prevention are not due to major effects of UDCA on the gut microbiome.\nC_LI

cancer biology↗