Biology subjects

Wang, B.

Publications and source records attributed to Wang, B..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Deep learning enables quantitative subcellular analysis of plant-microbe interfaces

Specialized host-microbe interfaces are central to cellular interactions in plants. Intracellular structures such as haustoria formed by filamentous pathogens mediate nutrient exchange and effector delivery to host cells. Despite their biological importance, the lack of quantitative frameworks has largely confined the study of these interfaces to qualitative observations, limiting our ability to compare infection strategies, cellular responses, and spatial organization across cells and tissues. Here, we present HFinder, a deep learning-based framework for automated detection, segmentation, and quantitative analysis of plant-microbe interfaces in confocal images. Using an object-centric deep learning approach, HFinder enables robust identification of haustoria, microbial hyphae, and host organelles across diverse imaging conditions and pathosystems. We demonstrate that this framework supports quantitative analyses of subcellular processes at host-microbe interfaces, including effector secretion, perturbation of host cellular processes, and immune receptor accumulation at haustoria. HFinder provides a practical and scalable solution for the systematic digitalization of plant infection imaging data and establishes a general framework for quantitative studies of cellular dynamics at host-microbe contact zones.

cell biology↗

bioRxiv2026

The genetic repertoire of the deep sea: from sequence to structure and function

The deep sea as the largest and maybe most hostile environment on Earth is still underexplored especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures, and used it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity, yet substantial structural conservation of proteins. Especially proteins involved in replication, recombination, and repair were identified to be under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as a unique evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.

bioinformatics↗

bioRxiv2026

Predicting evolutionary rate as a pretraining task improves genome language model representations

Genome language models (gLM) have the potential to further understanding of regulatory genomics without requiring labeled data. Most gLMs are pretrained using sequence reconstruction tasks inspired by natural language processing, but recent studies have shown that these gLMs often fail to capture biological signal. To overcome this, we introduce pretraining tasks that predict the rate of evolution. These tasks are designed so that they can be composed with sequence reconstruction, enabling a controlled comparison of predicting sequence only, evolutionary rate only, or both. To address gaps in existing evaluations, we developed a suite of biologically grounded benchmarks. Across these tasks, and for established variant effect prediction benchmarks, models pretrained on both sequence and evolutionary rate outperform those trained on sequence alone, and training on evolutionary rate can make the even the relatively small models in our work competitive with much larger existing gLMs for some tasks. These results establish evolution as a key training target for genome-scale models.

genomics↗

bioRxiv2026

A genetically encoded ionic-stress sensor reveals protons as a sleep driver

Dynamic ionic changes are hallmarks of physiological and behavioral state transitions, including sleep in animals. Although biosensors for specific cellular ions are widely available, real-time monitoring of overall ionic strength in living organisms remains challenging. Here, we present a genetically encoded nuclear translocation ionic sensor (GENTIS) that enables direct visualization of ionic stress in vivo. Using GENTIS in C. elegans, we uncover rhythmic elevations in ionic strength during larval molting transitions that coincide with the lethargus sleep. Cytosolic proton ionic increase through inhibition of v-ATPase is sufficient to induce GENTIS nuclear translocation and evoke behavioral quiescence, characterized by reduced feeding and activation of sleep-active neurons. Apical membrane v-ATPases undergo disassembly during lethargus and under sleep-inducing stress conditions, leading to proton accumulation. Notably, this proton-mediated sleep is suppressed by proton buffering with ammonium. Together, these findings establish GENTIS as a powerful tool for tracking ionic strength dynamics in living organisms and support protons as a physiological driver of sleep.

animal behavior and cognition↗

bioRxiv2026

Reproducible in vivo applications of the p16-3MR model in senescence research

The p16-3MR mouse model has been widely used to visualize and conditionally eliminate p16-expressing senescent cells in vivo and has been applied across diverse biological contexts, including tissue repair, fibrosis, cancer, therapy response, and aging. Despite the development of multiple senescence reporter and ablation systems, p16-3MR stands out for its broad and sustained adoption across independent laboratories. Here, we review the extensive published literature supporting the reproducibility and utility of the p16-3MR system and present new validation data across acute and chronic senescence-inducing conditions. We demonstrate reproducible induction of p16-associated bioluminescence during wound healing, chemotherapy, and aging, as well as partial but consistent reduction following ganciclovir treatment. We further delineate the strengths and limitations of the individual components of the 3MR construct, including HSV-thymidine kinase-mediated clearance, Renilla luciferase- based bioluminescence, and monomeric red fluorescent protein, and discuss how factors such as cell abundance, tissue context, pigmentation, and substrate chemistry influence detection sensitivity. Together, these data confirm that the p16-3MR model is a functional and versatile tool for studying senescent cells in vivo when used with appropriate experimental design and interpretation, and they provide support for its continued application alongside emerging senescence models.

cell biology↗

bioRxiv2026

Conditioning dentinal collagen by glycation improves long-term bond strength

ObjectivesThis study examined methylglyoxal (MGO) as a collagen crosslinker to reinforce demineralized dentin, enhance its enzymatic resistance, and improve long-term durability of the resin-dentin bond. MethodsDemineralized dentinal collagen films were treated with 0.5, 1, or 3 M MGO and subsequently exposed to collagenase to assess their resistance to enzymatic degradation. MGO-induced crosslink formation was monitored using Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR) spectroscopy by tracking the carbohydrate-associated band at 1180 cm-{superscript 1}. The apparent elastic modulus of the treated specimens was measured using a three-point bending test. For bond strength evaluation, resin-dentin beams were prepared and tested using microtensile bond strength (TBS) to assess the influence of MGO pretreatment on interfacial adhesion. ResultsThe ATR-FTIR spectra demonstrated increased intensity in the carbohydrate double bands (1000-1180 cm-{superscript 1}) in glycated samples compared to the control. Glycation with 3 M MGO exhibited the highest resistance to enzymatic degradation, persisting for up to 60 hours with a 78-fold increase in resistance factor compared to the control group (p < 0.05). Furthermore, glycation with 3 M MGO resulted in a 4-fold increase in elastic modulus compared with the control group. Notably, the functionalized dentin retained its improved mechanical properties even after collagenase exposure, whereas the control group experienced a significant 68.2% reduction in elastic modulus (p = 0.002). While MGO pretreatment did not influence resin infiltration or initial TBS ({approx}30-35 MPa), it maintained its original bond strength after one month of collagenase challenge. In contrast, the control group exhibited a significant reduction, decreasing to 17 {+/-} 5.5 MPa compared with its initial value (p < 0.01). ConclusionMGO demonstrated efficacy in enhancing the mechanical properties and enzymatic stability of collagen as well as improving the resistance of the bonded interface to enzymatic degradation. SignificanceMGO pretreatment maintains the long-term stability of the resin-dentin interface by protecting dentinal collagen from enzymatic degradation, without compromising initial bonding performance. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/701305v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@54ae32org.highwire.dtl.DTLVardef@1787fdforg.highwire.dtl.DTLVardef@130b40org.highwire.dtl.DTLVardef@47c5f9_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Structural and Spectroscopic Basis for Catalysis by a Class C Radical S-adenosylmethionine Methylase Involved in Nosiheptide/Nocathiacin Biosynthesis

Nosiheptide (NOS) is a ribosomally synthesized and post-translationally modified peptide (RiPP) natural product that exhibits potent antibiotic activity against multiple bacterial pathogens. NOS features a core macrocyclic peptide containing thiazoles, dehydrated serine and threonine residues, and a 3-hydroxypyridine ring. In addition to the macrocycle, NOS possesses a side-ring system formed by a 3-methyl-2-indolic acid (MIA) bridge that connects to glutamyl and cysteinyl residues on the core peptide via ester and thioester linkages. This unique side-ring is installed by the class C radical S-adenosylmethionine (SAM) methylase NosN. Here, we report three X-ray crystal structures of the NosN homolog, NocN, at resolutions of 1.4 [A], 1.84 [A], and 1.78 [A] under anaerobic conditions, representing the first structural characterization of a class C radical SAM methylase. The structures reveal clear electron density for two bound SAM molecules. Remarkably, the C5' atom of SAMI, which coordinates to the [Fe4S4] cluster, lies 3.5 [A] from the methyl group of SAMII and is properly positioned for direct hydrogen atom abstraction. A structure containing a product mimic illustrates how NocN engages its substrate and identifies Tyr276 as a key catalytic residue. The structure further suggests that the sulfonium center of SAMII may undergo epimerization to facilitate radical attack. Finally, electron paramagnetic resonance spectroscopy identifies a paramagnetic species consistent with the addition of the SAMII-derived methylene radical to the MIA substrate.

biochemistry↗

bioRxiv2026

Dynamic Supercoiling Sponsors Transcription Amplification by MYC

MYC dysregulation occurs in most cancers provoking, profound changes in gene expression. Although sometimes considered to be an E-box-dependent transcription factor, an alternate model posits MYC to be a universal amplifier of active genes. Although MYC is associated with accelerated pause release, the full extent of its participation in the transcription cycle remains poorly illuminated. MYC also stimulates topoisomerases to resolve topological issues that complicate DNA transactions; whether and how this stimulation is coordinated with or independent of its transcriptional role has not been examined. We have developed a genetic tool that discriminates between MYCs ability to activate versus amplify reporter gene expression in any cell. This system enables the interrogation of genes, cofactors, and compounds that execute or modulate MYC activity. Using a combination of biochemical and cellular assays, we reveal the dynamic interplay between MYC-driven transcription amplification and DNA supercoiling. The early stages of transcription are highly sensitive to the level of DNA supercoiling. Reducing the activity of TOP1 either through genetic knockdown or low-dose inhibition potentiates transcription amplification by MYC. This enhancement is associated with pre-initiation complex (PIC) stabilization by DNA supercoiling. MYC helps to mobilize these stabilized PICs. Significance StatementMYC is dysregulated in most cancers, yet its precise functions in transcription are poorly understood. Using a genetic system that distinguishes transcriptional activation from amplification, we reveal a functional interplay between MYC-driven amplification and DNA supercoiling. Reduced topoisomerase I activity increases DNA-supercoiling that in turn stabilizes PICs to provide more substrate for MYC-dependent transcription amplification. Thus, DNA topology as a critical regulator of MYC-dependent transcription.

molecular biology↗

bioRxiv2026

Covalent Leader Peptide Probes Enable Proteome-Level Mapping of RiPP Enzymes beyond Biosynthetic Gene Clusters

Genome-based analyses have enabled widespread discovery and biosynthetic annotation of ribosomally synthesized and post-translationally modified peptides (RiPPs) pathways, yet often fail to capture all participating enzymes, particularly those encoded outside canonical biosynthetic gene clusters. In this study, leveraging the central role of leader peptides (LPs) in RiPP enzyme-substrate recognition, we developed a substrate-guided chemical-proteomic strategy using covalent LP probes to directly identify LP-binding enzymes from native proteomes. Using the LctA-LctM and PatE-LynD systems, we demonstrate that LP probes carrying a photocrosslinker engage enzymes at their authentic LP-recognition sites while preserving full catalytic competence. Application of this strategy to a model strain Streptomyces sparsogenes uncovered lanthipeptide synthetases encoded outside canonical biosynthetic gene clusters and revealed graded cross-cluster activities among multiple RiPP pathways. This work establishes a proof-of-concept model platform for proteome-level discovery of LP-binding RiPP enzymes and highlights cross-cluster enzymatic crosstalk as a latent mechanism for structural diversification.

biochemistry↗

bioRxiv2026

Microglia Piezo1 aggravates cerebral ischemia and reperfusion injury by chemotactic recruitment of T lymphocytes

Cerebral ischemia reperfusion injury (CIRI) is a complex pathophysiological process involving multiple mechanisms. Piezo1, a stretch-activated ion channel, has recently emerged as a potential regulator of cellular responses to ischemic conditions. However, its role in specific cells during ischemic events is not well elucidated. Here, we showed that after experimentally induced CIRI, Piezo1 channel was highly expressed in peri-infarct area, where is upregulated and activated mainly in microglia. Behavioral tests, and infarct volume measurements demonstrated that conditional Piezo1 deficient in microglia markedly ameliorated the neurological deficits and reduced the infarct volumes. Flow cytometry and immunofluorescence staining showed decreased peripheral immune cells, especially T lymphocytes infiltration into the brain in microglia Piezo1 deficient mice after stroke. Multiplex chemokine immunoassay and T cell migration assays screened that Piezo1 deficient microglia blocked the CXC chemokine ligand 10 (CXCL10) release from astrocyte, which lead to the inhibited T cell recruitment in transwell co-cultured system. Furthermore, RNA-Sequencing analysis showed that defective Piezo1 in microglia lead to its polarization towards an anti-inflammatory phenotype in response to cerebral ischemia and reduced the secretion of tumor necrosis factor- (TNF-) and interferon-{gamma} (IFN-{gamma}). Collectively, Piezo1 deficiency inhibited the secretion of TNF- and IFN-{gamma} in microglia. The reduction of these inflammatory cytokines further blocked the CXCL10 release from astrocyte, and ultimately ameliorated the infiltration of peripheral T lymphocytes after stroke. Our results therefore highlight the critical role of Piezo1 in microglia-orchestrated neuroinflammation and suggest a potential means for reducing stroke-induced neurological injury.

neuroscience↗

bioRxiv2026

Rhythmic Nuclear Import Mediated by Importins Regulates the Neurospora Circadian Clock.

Circadian clocks in eukaryotes rely on precisely regulated negative feedback loops to generate daily rhythms. However, the delay mechanisms that extend this structurally simple feedback loop to [~]24 hours are not yet fully understood. In the filamentous fungal model organism Neurospora crassa, the negative arm complex, centered by FREQUENCY (FRQ), must enter the nucleus to repress the White Collar Complex (WCC) and close the feedback loop, but the mechanisms and dynamics of its nuclear transport have remained unresolved. Using long-term live-cell imaging and fluorescence recovery after photobleaching (FRAP), we demonstrate that FRQ nuclear import is an active circadian-regulated process that is fastest early in the subjective day and whose rate progressively decreases as nuclear FRQ approaches peak levels, corresponding to altered direct binding between FRQ and Importin . We further establish that Importin is required for the spatial regulation of FRQ and WCC, as well as the correct timing of Neurospora circadian clock, whereas the nuclear accumulation of non-clock-related free WC-2 doesnt require Importin . Analysis of the three Neurospora Importin {beta} homologs reveals that each of them contributes differently to the circadian clock through pathways beyond FRQ or WCC nuclear import. More specifically, we find a genetic interaction between Imp{beta}3 and the phosphatase PPH-4. Together, these findings indicate that nuclear import is a selective, dynamic, and rate-limiting regulatory step in the fungal circadian clock and reveal both conserved and fungal-specific mechanisms by which importins tune circadian timing.

cell biology↗

bioRxiv2025

Multimodal AI for Single cfDNA Profiling and Cancer Screening

Cell-free DNA (cfDNA) serves as a non-invasive biomarker for cancer detection, but conventional methods face challenges due to the ultra-low abundance of tumor-derived cfDNA (ctDNA) among normal cfDNA. Though nucleosome-bound cfDNA harbors rich epigenomic features that could enable ctDNA identification by single-molecule multi-omics cross-validation, this remains unexplored due to methodological limits. Here, we developed a cfDNA sequencing approach integrating methylation, fragmentomics, and histone modifications at the single-molecule level; together with gene semantics and epigenomic annotations, these modalities were vectorized and fused to represent each cfDNA molecule. We trained a Transformer-based model (cfAI) to profile and evaluate ctDNA likelihood at molecule, gene, and sample levels. cfAI achieved [~]10-fold enrichment of cancer-derived signals over noise and reached 72.6% sensitivity at 93.1% specificity for multi-cancer detection. Our study establishes an innovative framework that overcomes the inherent signal-to-noise limitations of conventional assays and reveals biological features at molecular resolution for cancer detection.

bioinformatics↗

bioRxiv2025

New potential antimicrobial peptides with amazing symmetrical structure in fungi and insects

We have discovered a new family of genes encoding potential antimicrobial peptides with unique compact and elegant structure in the genomes of several Fungi and some arthropod species. Their expression products are constituted of about 85 amino acids, including a signal peptide, and are folded into two -helical segments connected by a short unstructured coil. Three conserved disulphide bridges between cysteines located in symmetrically mirrored positions connect the two helical domains. The two ends of the chain are thus brought together and the elongated and compact shape suggests that of a nail, potentially able to penetrate the cell membrane. A high abundance of hydrophobic residues supports such hypothesis. These peptides, that we name Hairpin Loop Peptides (HLPs), have been found in the genomes of many Fungi species but only in selected clades. Orthologues have also been discovered in the genomes of some insects, notably Hemiptera, a few other arthropods and other organisms, but are absent in plants. They appear to have originated in Fungi and then migrated to insects through horizontal gene transfer. The antimicrobial activity of HLPs is predicted by several software programmes, although this still needs to be confirmed by experimental evidence. The occurrence of HLPs in several edible mushrooms supports potential uses of these peptides in food preservation and possibly also in medical applications. Their simple and nearly rigid structure can be easily modified to improve specificity, stability and solubility, thus making these molecular weapons suitable for a variety of different applications. Significance statementThe increasing emergence of bacteria resistant to current antibiotics has stimulated a rapid search for alternative treatments. In recent years, antimicrobial peptides have attracted considerable interest for their potential applications in medicine and as food preservatives. We have identified a new class of peptides primarily expressed in fungi, including edible mushrooms, and also detected in some insects and other arthropods, likely as a result of horizontal gene-transfer events. These peptides are particularly noteworthy because of their compact, elongated, and highly symmetrical structures, which give them a nail-like shape capable of penetrating cellular membranes. Such structural features suggest potential antimicrobial activity, a prediction supported by computational analyses. Their widespread presence in edible mushrooms further indicates the potential safety of these peptides for human use.

microbiology↗

bioRxiv2025

Mitochondrial membrane junction-mediated ATP channeling drives activity-dependent glucose metabolism

Neurons and brown adipocytes rely on rapid ATP production from accelerated glucose metabolism to sustain bursts of activity upon stimulation, a process known as activity-dependent glucose metabolism. The first committed step in this pathway, the hexokinase I (HK1)-catalyzed phosphorylation of glucose, consumes ATP, raising the question of how this reaction can be accelerated when cytosolic ATP becomes limiting during stimulation. We identify Cell Cycle Exit and Neuronal Differentiation protein 1 (CEND1), expressed in both cell types, as a critical regulator of this process. Loss of CEND1 impairs activity-dependent glucose utilization, ATP generation, and stimulation-evoked activity both in vitro and in vivo. Mechanistically, CEND1 assembles a complex with HK1, voltage-dependent anion channel 1 (VDAC1), and adenine nucleotide translocase 1 (ANT1) at hemifusion-like membrane junction between the outer/inner mitochondrial membrane, channeling mitochondrially derived ATP directly to HK1. These findings uncover a previously unrecognized mechanism that sustains activity-dependent glucose metabolism, with broad implications for energy homeostasis in specialized cell types.

physiology↗

bioRxiv2025

Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes

Comparative genomics provides a powerful framework to uncover the molecular and evolutionary mechanisms that shape genetic diversity within and across species, revealing how shared and lineage-specific processes influence their evolutionary trajectories through time. The nematode Caenorhabditis briggsae is distributed world-wide and is a comparative model to Caenorhabditis elegans in the biology of development, cellular mechanisms, neurobiology, genetic mappings of complex traits, and genome evolution. Following massive collection efforts by the nematode research community, we present the isolation of over 2,000 wild strains and analyses of genome sequences that catalog over six million single-nucleotide and insertion-deletion variants. This genome and strain resource provide a powerful means to interrogate the causal genetic bases of phenotypic variation for diverse traits. Additionally, we describe its global population structure and discover new and genetically distinct groups within this primarily self-fertilizing species, including groups of highly related strains that were sampled across different continents. We leverage expansive genetic variation to decipher the effects of linkage and selection on the distribution of genetic diversity across the genome and across geographic regions. Within the species, we find genomic regions with extremely high levels of genetic variation similar to hyper-divergent regions found in C. elegans and other species. These regions harbor new genes and variation enriched for environmental sensing and pathogen responses. In comparison to the outbreeding sister species Caenorhabditis nigoni, we conclude that long-term balancing selection has maintained substantial functional variation since the divergence from their outbreeding ancestor, likely in response to differences in the ecological niche. Overall, this massive strain resource enables future comparative genetics and genomics studies, including genome-wide association studies between Caenorhabditis species.

genomics↗

bioRxiv2025

Harnessing anti-CRISPR to suppress, subtract, and segregate Cas9 activity for precision CRISPR in Drosophila

Tissue-specific CRISPR (ts-CRISPR) is a powerful approach for studying cell and developmental biology by restricting mutagenesis to specific tissues. However, the precision of this approach is often compromised by non-specific, "leaky" Cas9 activity that confounds phenotypic analysis and destabilizes Cas9/gRNA stocks. To address these limitations in Drosophila, we developed a toolkit based on the Anti-CRISPR (Acr) protein AcrIIA4. We first identified AcrIIA4 as a potent in vivo Cas9 inhibitor with high stability and established the temporal requirements for its function. Based on these findings, we generated three classes of Acr tools. First, a collection of AcrIIA4-bearing balancers robustly suppresses Cas9 and enables the stable maintenance of complex Cas9/gRNA stocks. Importantly, maternal deposition of AcrIIA4 from these balancers provides a means of temporal control, delaying Cas9 activity until metamorphosis. Second, tissue-specific AcrIIA4 transgenes refine leaky Cas9 drivers in a "tissue-subtraction" strategy. Finally, germline-specific and soma-specific Acr tools efficiently segregate Cas9 activity, solving bidirectional leakiness between these two compartments. This comprehensive AcrIIA4 toolkit provides new levels of precision, versatility, and temporal control for Drosophila CRISPR applications.

genetics↗

bioRxiv2025

multiVIB: A unified probabilistic contrastive learning framework for atlas-scale integration of single-cell multi-omics data

Comprehensive brain cell atlases are essential for understanding neural function and advancing translational research. As single-cell technologies proliferate across platforms, species, and modalities, atlas construction increasingly depends on integration frameworks that are capable of aligning heterogeneous datasets without obscuring biological variations. However, existing methods are typically limited to narrow use cases, often requiring ad hoc workflows that may introduce artifacts. Here, we introduce multiVIB, a unified probabilistic contrastive learning framework for diverse scenarios of data integration. We demonstrate that multiVIB achieves state-of-the-art performance while minimizing spurious alignments. Applied to atlas-scale datasets generated by the BRAIN Initiative, multiVIB supports robust and scalable integration across data modalities and preserves species-specific variation in cross-species analyses. These results position multiVIB as a scalable, biologically faithful framework for the construction of next-generation brain cell atlases.

bioinformatics↗

bioRxiv2025

Modifications to the gut microbiome alter bone matrix proteomics and fracture toughness at the cellular scale

The gut microbiome can regulate the strength of bone matrix but the specific changes in matrix function and composition are not yet understood. Here we introduce micropillar splitting to determine the fracture toughness of matrix at the cellular scale in concert with proteomic analysis of bone matrix when the gut microbiome was altered by oral antibiotics (ampicillin+neomycin). Male mice were divided into four groups (n = 3-4/group): (1) Unaltered (no alteration), (2) Continuous (alteration from 4-24 weeks), (3) Delayed (alteration from 16-24 weeks) and (4) Reconstituted (alteration from 1-16 weeks following by reconstitution). Micropillars (5 {micro}m diameter) were fabricated using focused ion beam milling on femur cross-sections in regions of matrix formed either before or after changes in the microbiome (16 weeks) (n = 4/group). Proteomics was used to identify differences in matrix protein composition. Micropillar fracture toughness differed by group (p < 0.001) and region (p < 0.001). Fracture toughness in the Unaltered group (1.34 {+/-} 0.32 MPa{surd}m, mean {+/-} SD) was substantially greater than the Continuous group (0.95 {+/-} 0.20) and the Delayed group (0.90 {+/-} 0.21) but not different from the Reconstituted group (1.22 {+/-} 0.25). Bone matrix formed from 16-24 weeks of age had lower fracture toughness than matrix formed before 16 weeks of age in all groups. Notably, micropillar splitting was substantially more precise than whole bone testing; whole bone notched 3-point bending tests did not detect differences in fracture toughness. Proteomics identified 46 extracellular matrix proteins that were differentially abundant between groups, including decreased abundance of Periostin (q < 0.001) and Emilin-1 (q < 0.001) in groups with impaired bone matrix. These findings demonstrate that modifications to the gut microbiome lead to changes in bone matrix throughout cortical bone volume and establish micropillar splitting as a high-precision approach for characterizing matrix material properties. Plain Language SummaryThis study investigated the effect of the gut microbiome on the brittleness of bone as a material. We used a new technique for measuring the brittleness of bone that involves making microscopic pillars on the bone surface and splitting them down the middle to measure a material property called fracture toughness. Mice with altered gut microbiomes had bone with reduced fracture toughness (by 35-40%). Restoration of an altered gut microbiome for two months reversed the effects. The effect of the microbiome on bone occurred throughout the whole bone and was not limited to regions of the bone formed after a change in the gut microbiome.

bioengineering↗