Biology subjects

Mazel, F.

Publications and source records attributed to Mazel, F..

13 recordsLinked to original sources

bioRxiv2026

Species boundaries structure competitive interactions among honeybee gut bacteria

Bacterial species often harbor extensive strain-level diversity, raising the question of whether strains, rather than species, are the relevant ecological units. We quantified pairwise interactions among 12 strains from four prevalent Lactobacillus species of the honeybee gut microbiota using gnotobiotic bees. Microbiota-depleted bees were colonized with individual strains and all 66 pairwise combinations, with strain abundances measured by colony counts and strain-resolved amplicon sequencing. Negative interactions predominated, with most significant interactions involving mutual inhibition. Within-species interactions were stronger and more asymmetric than between-species interactions, producing less even community compositions. Across repeated cycles of colonization in microbiota-depleted bees, three of four within-species pairs lost one strain, whereas all four between-species pairs persisted. These results indicate that closely related strains experience greater niche overlap and stronger competition than strains from different species, supporting bacterial species as ecologically differentiated units while highlighting the importance of strain-specific traits in shaping community assembly and stability.

microbiology↗

bioRxiv2025

Host and microbial factors influence bacterial colonization of the honey bee gut

The guts of many animals are colonized by host-specific microbes, yet the extent to which host filtering (host-derived constraints) shapes microbial colonization and host specificity remains poorly understood. Here, we used gnotobiotic honey bees (Apis mellifera) as a model system to systematically assess the colonization potential of a phylogenetically and ecologically diverse panel of 56 bacterial strains, spanning native symbionts, opportunistic bee-associated taxa, gut microbes from other bee species, and non-bee environmental isolates. Bacterial load and colonization frequency were quantified by strain-specific qPCR seven days post-inoculation, in monocolonization and in the presence of a synthetic community composed of native honeybee core bacteria. Bacterial load was highest for native strains and declined with increasing phylogenetic distance from native symbionts. Co-colonization with the synthetic community reduces load across all groups, but native strains were least affected. Across strains, completeness of KEGG metabolic pathways correlated with bacterial load in some ecological groups; however, metabolic capacity alone did not fully explain colonization patterns, either in monocolonization or under competitive conditions. A key finding was that in vitro sensitivity to antimicrobial peptide (AMPs; apidaecin, abaecin, defensins, hymenoptaecin) varied widely among strains and was highest in closely related bee-associated bacteria. Notably, even highly successful colonizers such as Gilliamella and Snodgrassella were AMP-sensitive. AMP sensitivity showed a negative correlation with bacterial load, but not with the frequency of host colonization. These findings suggest that AMPs modulate symbiont abundance rather than acting as strict barriers to colonization. Overall, our results reveal that host filtering in the bee gut is multifaceted, integrating immune-mediated barriers, microbial traits, and competitive interactions.

microbiology↗

bioRxiv2025

Gut microbiota variation across sympatric stingless bee species and honey bees in the Neotropics

Stingless bees (Meliponini) are ecologically and culturally important pollinators with a long tradition of human management in the Neotropics. Yet, little is known about how their gut microbiota vary across geographic regions or whether microbial exchange occurs with managed honey bees (Apis mellifera), which are often kept in close proximity. Using full-length 16S rRNA gene sequencing of individual bees sampled from 167 colonies, we characterized gut microbial community structure through a hierarchical, taxonomic and phylogenetic comparative framework, contrasting the microbiota of Melipona quadrifasciata and Melipona mondury with that of Apis mellifera across their shared geographic range in Brazil. The core microbiota of Melipona was dominated by Lactobacillus, Bifidobacterium, Apilactobacillus, Bombella, and Floricoccus, and showed inverse variation in relative abundance with lower-prevalence bacterial taxa. Although the core microbiota of the two stingless bee species overlapped only partially with that of Apis mellifera, they exhibited comparable alpha-diversity and beta-diversity dispersion, indicating broadly similar community assembly processes and dynamics. Nevertheless, we found that 6% of all amplicon sequence variants (ASVs) were shared between hosts, encompassing nearly all canonical honey bee "core" symbionts, indicating frequent spillover. Remarkably, several ASVs of Snodgrassella, a genus typically rare in stingless bees, reached high abundance in several M. quadrifasciata individuals and formed a deeply divergent clade ([~]96% 16S rRNA gene identity to S. alvi). These patterns are consistent with the hypothesis that human-mediated management practices, such as mixed apiaries and artificial feeding, create opportunities for microbial exchange between native and non-native bees. Together, our findings indicate that stingless bee gut microbiomes are compositionally stable yet ecologically permeable, shaped by both long-term host specificity and recent anthropogenic contact.

ecology↗

bioRxiv2025

Priority effects determine community composition at the strain level in the honeybee gut microbiota

Gut microbial communities often differ at the strain level among individual hosts, but the mechanisms driving this variation remain poorly understood. One potential factor is priority effects, a process in which differences in the timing and order of microbial colonization influence subsequent community assembly ("first come, first served" dynamics). We hypothesize that such priority effects operate at the strain level within species, where closely related bacteria exhibit niche overlap, and that these dynamics can lead to community divergence even under similar environmental conditions. We tested these predictions, using the gut microbiota of honeybees, which harbor conserved microbial communities that differ in strain composition among individual bees. We sequentially colonized microbiota-depleted honeybees with two distinct microbial communities composed of the same twelve core microbiota species but different strains, ensuring that individuals shared species-level composition but differed at the strain level. We found that firstcomer strains consistently dominated the resulting communities, suggesting strong priority effects. Dropout experiments in which the firstcomer strain of a species was removed led to only partial increases in the colonization success of the conspecific latecomer, suggesting that both intra- and inter-species interactions contribute to priority effects. Our findings highlight the significant role of priority effects in strain-level community assembly and reveal their influence in shaping the specialized gut microbiota of honeybees, with important implications for the development of probiotic strategies in beekeeping. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/689826v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@b0930eorg.highwire.dtl.DTLVardef@8687c5org.highwire.dtl.DTLVardef@3ba838org.highwire.dtl.DTLVardef@a10c3e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Strain-level translocation and enrichment mechanisms of oral bacteria in the lower gastrointestinal tract of stunted children

Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of oral origin are continuously translocating from the oral cavity to the lower gastrointestinal tract or are locally adapted and persist in their respective niches. We investigated strain translocation dynamics in 44 healthy and stunted children from Bangui, Central African Republic. Using cross-sectional shotgun metagenomic sequencing of saliva, gastric, duodenal and fecal samples, and isolation and whole genome sequencing of 87 Streptococcus salivarius isolates, we showed translocation of members of the genera Streptococcus, Veillonella, Rothia and Haemophilus. Fecal isolates were more closely related to oral isolates from the same individuals than those from other individuals. Additionally, saliva showed higher S. salivarius nucleotide diversity compared to other compartments, suggesting a source-sink dynamic in which S. salivarius populations are continuously seeded from the oral cavity without durably establishing in the lower gastrointestinal tract. Last, we showed that overrepresentation of oral bacteria in the duodenum of stunted children is due to increased biomass, while in the colon it is linked to depletion of overall biomass, including in butyrate-producing strains. Our study quantifies mechanisms of oral-to-gut translocation and enrichment of oral taxa, providing key insights into microbiota disruption in stunted children.

microbiology↗

bioRxiv2025

Strain-level and phenotypic stability contrasts with plasmid and phage variability in water kefir communities

Microbial communities can change in response to top-down factors, such as phages, and bottom-up factors, such as nutrient availability. Previous studies have successfully investigated bacterial species-level dynamics, but diversity and interactions beyond the species-level is usually lacking. Traditional fermented foods, such as water kefir, provide ideal systems to study ecological and evolutionary dynamics beyond the species-level, as they are simple and trackable systems that are cultivated in non-sterile, nutrient-rich environments which foster microbial growth and invasion. Despite the central role of only a few lactic acid bacteria for fermentation, little is known about the genomic diversity and dynamics of these community members over time. Within the framework of a graduate course, 35 students propagated water kefir across several generations under different nutrient conditions and in different households to study microbial responses over time. We found that water kefir communities were generally stable at the species-level, with only rare bacterial species replaced over long timescales (more than 2 years). While we observed little strain-level diversity with few strain replacements over long timescales, closely related strains exhibited variation in accessory gene content, often encoded on plasmids, particularly those involved in ecologically meaningful functions such as sugar utilization pathways and phage defense systems. We hypothesise that these genomic variations could reflect the adaptations of strains to different sugars and phages. Consistent with this, we observed a diverse array of phages, many likely originating from the unique household environments. By documenting the genomic landscape of microbial species, strains, plasmids, and phages, this study advances our understanding of the diversity and dynamics of microbial communities in fermented foods. Furthermore, our course material is publicly available and offers a blueprint for bridging the gap between teaching and research, inspiring the next generation of scientists to unravel the complexities of microbial ecosystems. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/640646v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@56db6borg.highwire.dtl.DTLVardef@5f6dc6org.highwire.dtl.DTLVardef@11fff14org.highwire.dtl.DTLVardef@1a37a9f_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Symbiont loss and gain, rather than co-diversification shapes honeybee gut microbiota diversity and function

Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 worker bees from five honeybee species, we recover thousands of metagenome-assembled genomes and identify several novel bacterial species. While microbial communities were mostly host-specific, we found both specialists and generalists, even among closely related bacterial species, with notable variation between honeybee hosts. Some bacterial generalists emerged host-specific only at the strain level, suggesting recent host switches. While we found some signal of co-diversification between hosts and symbionts, this was not more than expected by chance and was much less pronounced than what has been observed for gut bacteria of hominids and small mammals. Instead, symbiont gains, losses, and replacements emerged as the predominant process for honeybees. This highly dynamic evolution of the specialized honey bee gut microbiota has led to taxonomic and functional differences across hosts, such as the ability to degrade pollen-derived pectin. Our results provide new insights into the evolutionary processes govern gut microbiota diversity across closely related hosts and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.

microbiology↗

bioRxiv2024

Genomic and phenotypic imprints of microbial domestication on cheese starter cultures

Domestication - the artificial selection of wild species to obtain variants with traits of human interest- was integral to the rise of civilization. During the neolithic, the oversupply of food enabled by the domestication of crop plants and farm animals was associated with the invention of food preservation strategies through microbial fermentation. However, it remains unclear whether fermented food microbes show similar signs of domestication by humans like plants or animals. Only a few eukaroytic have been studied so far in this respect (e.g., yeasts used in mantou or wine), whereas little is known for bacteria. Here, we tested if cheese starter cultures harbour typical hallmarks of domestication by characterising over 100 community samples and over 100 individual strains isolated from historical and modern traditional Swiss cheese starter cultures. We find that cheese starter cultures have low genetic diversity both at the species and strain-level and are taxonomically and phenotypically stable. Our analyses further suggest that the evolutionary origin of the bacteria in cheese starter cultures coincided with the start of cheesemaking as reported from archeological records. Finally, we find evidence for ongoing genome decay and pseudogenization via transposon insertion related to a reduction of their niche breadth. These characteristics suggest that cheese starter cultures were domesticated by humans before knowing about microbes, potentially starting as early as the neolithics Future work documenting the prevalence of these hallmarks across diverse fermented food systems and geographic regions will be key to unveiling the joint history of humanity with fermented food microbes.

microbiology↗

bioRxiv2024

Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation

Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of S. epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.

microbiology↗

bioRxiv2022

Deep divergence and genomic diversification of gut symbionts of neotropical stingless bees

Social bees harbor conserved gut microbiota that may have been acquired in a common ancestor of social bees and subsequently co-diversified with their hosts. However, most of this knowledge is based on studies on the gut microbiota of honey bees and bumble bees. Much less is known about the gut microbiota of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiota presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumble bee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host indicating that the evolution of the social bee gut microbiota was not driven by strict co-diversification, but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumble bee microbiota, we find substantial genomic divergence among strains of stingless bee gut bacteria suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota, and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota. ImportanceStingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found in honey bees and bumble bees and that are likely important for bee health. Few bacteria have been cultured from the gut of stingless bees which has prevented characterization of their genomic diversity and functional potential. Here, we established cultures of major community members of the gut microbiota of six stingless bee species and sequenced their genomes. We find that most stingless bee isolates belong to novel bacterial species distantly related to those found in honey bees and bumble bees and encoding similar functional capabilities. Our study offers a new perspective on the evolution of the social bee gut microbiota and presents the basis to characterize the symbiotic relationships between gut bacteria and stingless bees.

microbiology↗

bioRxiv2020

An integrated, modular approach to data science education in the life sciences

We live in an increasingly data-driven world, where high-throughput sequencing and mass spectrometry platforms are transforming biology into an information science. This has shifted major challenges in biological research from data generation and processing to interpretation and knowledge translation. However, post-secondary training in bioinformatics, or more generally data science for life scientists, lags behind current demand. In particular, development of accessible, undergraduate data science curricula has potential to improve research and learning outcomes and better prepare students in the life sciences to thrive in public and private sector careers. Here, we describe the Experiential Data science for Undergraduate Cross-Disciplinary Education (EDUCE) initiative, which aims to progressively build data science competency across several years of integrated practice. Through EDUCE, students complete data science modules integrated into required and elective courses augmented with coordinated co-curricular activities. The EDUCE initiative draws on a community of practice consisting of teaching assistants, postdocs, instructors and research faculty from multiple disciplines to overcome several reported barriers to data science for life scientists, including instructor capacity, student prior knowledge, and relevance to discipline-specific problems. Preliminary survey results indicate that even a single module improves student self-reported interest and/or experience in bioinformatics and computer science. Thus, EDUCE provides a flexible and extensible active learning framework for integration of data science curriculum into undergraduate courses and programs across the life sciences. Availability and implementationThe EDUCE teaching and learning framework is accessible at educe-ubc.github.io

scientific communication and education↗

bioRxiv2018

Is phylogenetic diversity a surrogate for functional diversity across clades and space?

In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have advocated for a \"phylogenetic gambit\": maximizing phylogenetic diversity (PD) should indirectly capture FD. For the first time, we empirically test this gambit using data from >15,000 vertebrate species and ecologically-relevant traits. Maximizing PD results in an average gain of 18% of FD relative to random choice. However, this average gain hides the fact that in over 1/3 of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky strategy.\n\nStatement of authorshipFM, MP, MC, SD, GVDR, RG, AOM, CT and WP conceived the design of the study. FM and GVDR conducted the analysis. FM, RG, MP and WP interpreted the results and wrote the first draft of the manuscript. All authors edited the final version.\n\nData accessibility statementMost of the data is publicly available (see methods). The Fish data is available upon request.\n\nCode accessibility statementR functions developed in this paper are available at https://github.com/FloMazel/FD_PD_Max

ecology↗

bioRxiv2017

Conserving Phylogenetic Diversity Can Be A Poor Strategy For Conserving Functional Diversity

For decades, academic biologists have advocated for making conservation decisions in light of evolutionary history. Specifically, they suggest that policymakers should prioritize conserving phylogenetically diverse assemblages. The most prominent argument is that conserving phylogenetic diversity (PD) will also conserve diversity in traits and features (functional diversity; FD), which may be valuable for a number of reasons. The claim that PD-maximized ( maxPD) sets of taxa will also have high FD is often taken at face value and in cases where researchers have actually tested it, they have done so by measuring the phylogenetic signal in ecologically important functional traits. The rationale is that if traits closely mirror phylogeny, then saving the maxPD set of taxa will tend to maximize FD and if traits do not have phylogenetic structure, then saving the maxPD set of taxa will be no better at capturing FD than criteria that ignore PD. Here, we suggest that measuring the phylogenetic signal in traits is uninformative for evaluating the effectiveness of using PD in conservation. We evolve traits under several different models and, for the first time, directly compare the FD of a set of taxa that maximize PD to the FD of a random set of the same size. Under many common models of trait evolution and tree shapes, conserving the maxPD set of taxa will conserve more FD than conserving a random set of the same size. However, this result cannot be generalized to other classes of models. We find that under biologically plausible scenarios, using PD to select species can actually lead to less FD compared to a random set. Critically, this can occur even when there is phylogenetic signal in the traits. Predicting exactly when we expect using PD to be a good strategy for conserving FD is challenging, as it depends on complex interactions between tree shape and the assumptions of the evolutionary model. Nonetheless, if our goal is to maintain trait diversity, the fact that conserving taxa based on PD will not reliably conserve at least as much FD as choosing randomly raises serious concerns about the general utility of PD in conservation.

ecology↗