Biology subjects

He, J.

Publications and source records attributed to He, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Alignment-free phylogenetic inference via hyperbolic protein language models

Conventional phylogenetic methods rely on multiple sequence alignments which are computationally intensive and often fail for highly divergent lineages. Here, we introduce LucaPhylo, an alignment-free framework that infers evolutionary relationships directly from unaligned sequences. Through a cascaded learning strategy LucaPhylo integrates protein language models with hyperbolic geometry, a representation space naturally suited to hierarchical branching, to capture deep evolutionary constraints without explicit homology matching. Using highly divergent RNA virosphere as a test case, LucaPhylo places unaligned sequences into phylogenetic trees with an accuracy comparable to leading alignment-based tree construction tools, while retaining divergent sequences that conventional pipelines frequently discard. It further enables the integration of divergent viral lineages into phylogenetic trees, thereby expanding the evolutionary landscape of RNA viruses. Together, LucaPhylo establishes an AI-driven, alignment-free paradigm for phylogenetic inference and provides a robust computational foundation for resolving deep evolutionary relationships among RNA viruses and other biological systems.

evolutionary biology↗

bioRxiv2026

Molecular evolution of baculovirus IE1 protein, an essential multi-functional regulator of transcription and replication

Immediate-early protein IE1 is an essential protein of baculoviruses that is involved in transcription and replication. In the present study, we provide several lines of evidence for how ancient IE1 evolved into its current version. Using progressive truncations and site-directed mutations coupled with fluorescence microscopy, surprisingly, we showed that the previously identified nuclear localization sequence (NLS), basic domain II, was essential for sequence non-specific DNA binding, but not required for IE1 nuclear import, and demonstrated that, BmNPV IE1 (BmIE1) possesses not only a unique bipartite NLS that contains a monopartite NLS but also a cryptic non-canonical NLS that is correlated with sequence non-specific DNA binding. The non-canonical NLS alone was sufficient to launch infection. We also found that N-terminally truncated IE1 can enter the nucleus through its sequence non-specific binding ability. Remarkably, the monopartite NLS, when fused to the N-terminus of EGFP, can form a novel NLS that is also functional in a mammalian cell line. Moreover, residues 58 to 151 of BmIE1 were shown to be dispensable, and residue 152 was found to be critical for launching a productive infection. To gain insight into how ancient IE1 acquired its multi-functionality, we reorganized the N-terminal 23 aa and 132 aa of BmIE1 with EGFP in a variety of manners and found that both fragments are separable and transferable. Notably, we observed that the nuclear levels of BmIE1 should reach certain thresholds to initiate infection. Additionally, we found that BmNPV could launch infection more efficiently in a BmN cell line over another BmN cell line by increasing transcription levels of immediate early genes. Collectively, these findings suggest a hypothesis where ancient IE1 might have evolved the two additional NLSs and acquired the N-terminal 132 aa through gene fusion so as to reach infection-initiating thresholds at a faster pace. Author SummaryBasic domain II was previously shown to be the NLS of AcMNPV IE1 protein. In the present study, we demonstrated that it is essential for sequence non-specific DNA binding, but not required for IE1 nuclear import, and found that BmNPV IE1 (BmIE1) possesses not only a unique bipartite NLS that contains a monopartite NLS but also a cryptic non-canonical NLS that is correlated with sequence non-specific DNA binding. We also found that N-terminally truncated BmIE1 can enter the nucleus through its sequence non-specific binding ability. Remarkably, the monopartite NLS, when fused to the N-terminus of EGFP, can form a novel NLS that is also functional in a mammalian cell line. Moreover, the domains of BmIE1 was shown to be separable and transferable. We also demonstrated that higher expression of functionally impaired BmIE1 achieved by higher MOIs or higher transfection efficiency can partially complement its compromised functions. Consistently, we found that BmNPV could launch infection more efficiently in a BmN cell line over another BmN cell line by increasing transcription levels of immediate early genes.

microbiology↗

bioRxiv2026

The effect of cell death on DNA-replication-based estimates of microbial population growth

Inferring bacterial growth rates is fundamental to understanding microbial interactions and community dynamics, but remains difficult in natural settings where time points are limited or organisms are unculturable. In these cases, a widely used method is the origin-to-terminus ratio, or peak-to-trough ratio (PTR), which estimates DNA replication activity from origin and terminus copy numbers. Although PTR is theoretically related to bacterial growth rate, it is frequently benchmarked against population growth rate, which reflects the balance between cell division and loss. Understanding when and why these measures diverge is therefore important for validating PTR-based approaches. To quantify how departures from steady growth affect PTR, population growth rate, and bacterial growth rate, we developed a stochastic, cell-based model that explicitly tracks DNA replication, cell division, and cell death. We show that transient stress-induced mortality and heterogeneous survival can cause PTR to fail to reflect population growth rate while still reflecting bacterial growth rate. We experimentally validated these predictions by exposing \textit{Escherichia coli} to osmotic shock or antibiotics, and measuring population growth rate and DNA replication activity. We further show that initial physiological state, lag before replication resumes, and abrupt growth arrest can alter the relationship between PTR and population growth rate. In the presence of mortality, lag can increase PTR's correspondence with population growth rate while decreasing its correspondence with bacterial growth rate. These results provide a mechanistic and quantitative framework for interpreting PTR across changing growth states, mortality regimes, and environmental perturbations.

microbiology↗

bioRxiv2026

Pre-transplant TCR Network Topology Predicts Kidney Allograft Rejection Independent of HLA Mismatch

Despite extensive pretransplant serological screening and HLA matching, 10-15% of kidney allografts experience acute rejection within the first year. Currently, risk stratification for transplantation relies primarily on antibody reactivity to HLA molecules, with no assessment of the T cell compartment before or after transplantation. In our previously established longitudinal cohort of 54 patients, T cell receptor {beta} (TCR{beta}) sequencing was performed on paired kidney biopsy and peripheral blood samples. Here, we further analyzed the data to construct a comprehensive set of sequence-similarity networks and quantify over 30 network metrics. After adjusting for repertoire size, graft status was the strongest signal for the underlying differences in network metrics. Individuals who rejected the kidney graft generally exhibited more fragmented and less connected networks at baseline, with fewer interconnect T cell clones and more isolated sequences. Notably, pre-transplant peripheral blood mononuclear cell (PBMC) network topology alone predicted non-stable outcomes with an area under the curve (AUC) of 0.81, sensitivity of 76%, and specificity of 76%. The performance of this prediction model was independent of HLA mismatch, while changes in network topology at three months post-transplantation further improved prediction to an AUC of 0.88 (permutation p = 0.009). Collectively, TCR sequencing and network analysis represent a potential novel, non-invasive approach for pre-transplant risk stratification and immune monitoring, capturing functional immunological risk that may not be accessible through HLA genotyping or serology.

immunology↗

bioRxiv2026

The Par complex regulates apical-basal cell polarity through modulation of FAK signaling homeostasis

Cell polarity complexes are essential for embryogenesis, but their regulatory mechanisms during early developmental transitions remain incompletely understood. Here, we individually deleted the Crumbs, Par, and Scrib polarity complexes in mouse embryonic stem cells (mESCs). While loss of any single complex did not affect pluripotency or proliferation, deletion of Par complex disrupted the naive-to-primed transition and impaired subsequent differentiation, particularly lumen formation in neural tube organoids. Mechanistically, Par complex deficiency led to hyperphosphorylation of focal adhesion kinase (FAK) at the primed stage, driving a morphological shift from flat monolayer clusters to dome-shaped colonies. FAK inhibition rescued the aberrant morphology. Upstream, Par complex loss increased AKT phosphorylation, which remodeled extracellular matrix (ECM) and regulated integrin signaling via FURIN-LEFTY, ultimately modulating FAK activity. In addition, conditioned medium from wild-type cells partially rescued differentiation defects in Par knockout cells in a LEFTY-dependent manner. These phenotypes were consistently observed in naive-to-primed transition, neural stem cell differentiation, embryoid body formation, teratoma assays, and neural tube organoid differentiation. Together, these findings establish a Par complex-AKT-FURIN-LEFTY-ECM-integrin-FAK signaling cascade that links apical-basal polarity to early lineage specification and morphogenesis, providing a mechanistic framework for how polarity cues are translated into developmental outcomes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/722465v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@179e0adorg.highwire.dtl.DTLVardef@8d83bdorg.highwire.dtl.DTLVardef@c425fforg.highwire.dtl.DTLVardef@19a8ee5_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementThis study elucidates the molecular mechanism by which the Par complex regulates the establishment of cell polarity. The authors demonstrate that the Par complex promotes the expression of the protein convertase FURIN via AKT signaling, thereby enhancing the maturation and secretion of LEFTY protein. This process remodels the ECM and modulates integrin signaling, ultimately regulating FAK activity and controlling the establishment of cell polarity. These findings reveal how polarity cues govern early lineage specification and morphogenesis, with implications across multiple developmental contexts.

developmental biology↗

bioRxiv2026

Engineering Dual-Target Chimeric Lysins for Synergistic Eradication of Porphyromonas gingivalis

Periodontitis is a chronic inflammatory disease driven by complex subgingival multispecies biofilms, in which Porphyromonas gingivalis plays a central role in coordinating microbial interactions. Together with host-associated factors, these microbial communities create dual constraints that limit antimicrobial efficacy. In this study, we engineered a library of recombinant lysins by fusing membrane-destabilizing peptides to the periodontal pathogen-derived lysin LysPd078 and identified four optimized variants (PlyPd06, PlyPd19, PlyPd27, and PlyPd44) with enhanced salt tolerance, environmental stability, and bactericidal activity. In a clinically derived polymicrobial oral biofilm, PlyPd44 at only 25 g/mL eradicated 96.6% of P. gingivalis. In a humanized oral microbiota mouse model of periodontitis, selected PlyPds significantly reduced inflammation and inhibited alveolar bone loss compared with LysPd078 and minocycline. Collectively, these results establish membrane-destabilizing peptide-enabled lysins as a promising platform for developing microenvironment-adapted precision antimicrobials for periodontitis.

microbiology↗

bioRxiv2026

High Purity Differential Expression of Genes across Spatial Domains

Spatial transcriptomics maps gene expression within tissue architecture, offering deep insights into cellular function. A key yet overlooked phenomenon is the systematic imbalance in gene regulation within spatial domains, contrasting with traditional analyses. We define and validate this as a prevalent hallmark--High-Purity Differential Expression (HiP-DEP)--where genes in a domain shift predominantly in one direction (i.e., predominantly up- or downregulated). We introduce a Spatial Purity index to quantify it. Analysis of 190 diverse datasets across diverse tissues, diseases, and technologies revealed that spatial domains possess significantly higher purity than conventional bulk (p = 5.4 x 10-11) or single-cell data (p = 6.9 x 10-14), establishing HiP- DEP as a core hallmark of spatial biology. Using our HiP-DEP framework, we show its utility in: decoding core oncogenic regulation and its spatial gradient in breast cancer; uncovering hidden phenotypic divergence between morphologically similar Alzheimers plaques; and identifying active cellular communication niches in normal brain tissue. By shifting focus from individual genes to coordinated transcriptional programs, HiP-DEP provides a new paradigm for precision spatial omics analysis.

bioinformatics↗

bioRxiv2026

In utero transduction resolves gut cell lineages and enables conditional gene perturbation in the developing enteric nervous system

How diverse cell lineages emerge and are genetically regulated during organogenesis are central questions in understanding the developmental origins of disease. However, the mouse gut, including its intrinsic enteric nervous system (ENS) derived from migratory neural crest, has remained difficult to experimentally target. Here, we introduce an in utero lentiviral nano-injection strategy that enables early and efficient access to progenitor cells of all major cell types within the developing gut as well as gut-innervating ganglia. Leveraging this approach in combination with DNA barcoding and single cell transcriptomics, we resolve clonal relationships in all gut lineages, including epithelial, neural, immune, and mesenchymal cell types. Clonal coupling between distinct subsets of fibroblasts and either pericytes, mesothelial cells, or interstitial cells of Cajal, suggested a developmental logic whereby the mesenchymal compartment arises from a set of fate-biased progenitors. Yet, mesenchymal regionalization along the anterior-posterior axis establishes early, whereas the ENS displays broad clonal dispersion across gut regions and acquires subsequent regional identities. We further adapted the platform for temporally controlled cell-type specific gene manipulation and, as a proof-of-principle, show that induced expression of the proneural factor Ascl1 biases ENS progenitor cells toward neuronal differentiation. Together, this work provides insights into refined spatiotemporal lineage relationships within a multigerm-layer organ and establishes a broadly applicable in vivo framework for probing gene function during gastrointestinal and neural crest development. SIGNIFICANCEThe gastrointestinal tract comprises diverse cell types originating from all three germ layers and includes the neural crest-derived enteric nervous system (ENS). Progress in defining these lineages and their gene regulation is challenged by the limited experimental access to the developing gut. Here, we establish in utero lentiviral transduction as an efficient approach to resolve clonal lineages and address gene functions in defined gut cell types. We show that mesenchyme assumes positional allocation early and differentiates through fate-restricted progenitors, linking specialized mesenchymal cell types to different fibroblasts. In contrast, the ENS differentiates stochastically and acquires late regional identities. Our study reveals fundamental principles of multi-lineage organogenesis and provides a framework to dissect the contribution of developmental programs to visceral dysfunction.

developmental biology↗

bioRxiv2026

Structure-based similarity network accelerates the discovery of lysins as oral microbiome modulators targeting periodontal pathogens

Microorganisms significantly influence human health, and dysbiosis of the oral microbiome plays a critical role in the development and progression of both oral and systemic diseases. This highlights the urgent need for novel therapeutics targeting specific pathogens. Here, we presented a structure-based pipeline to efficiently identify potential phage-derived periodontal lysins (LysPds) from nearly one million proteins. We predicted the structures of candidate lysins using AlphaFold2 and developed an innovative structure-based similarity network to classify them into distinct clusters, each with unique functional properties. A systematic characterization of 16 representative LysPds from 11 superfamilies revealed that over 90% demonstrated potent antibacterial activity against key periodontal pathogens. Among these, LysPd078 was identified as a promising preclinical drug candidate, effectively reconfiguring microbiome communities while demonstrating significant efficacy and safety in mouse models of periodontitis and calvarial infection. Our findings highlight the effectiveness of structure-based similarity networks in exploring vast protein spaces and underscore the potential of LysPd078 as a targeted modulating agent for the oral microbiome.

microbiology↗

bioRxiv2026

FOXA1 preserves cell polarity and restrains lysosome biogenesis in non-small cell lung adenocarcinoma

BackgroundThis study investigates the role of the pioneer transcription factor FOXA1 as a master gene in sustaining epithelial cell polarization in early-stage lung adenocarcinoma. The partial loss of FOXA1 is explored to determine if it will affect plasticity and progression of lung adenocarcinoma. The study also addresses the transcriptional circuitry that links polarity defects to lysosome homeostasis. MethodsA multiomics approach was used to define the status of the chromatin in epithelial and mesenchymal states of A549 adenocarcinoma cells obtained with a newly synthetized TGF-{beta} receptor inhibitor or TGF-{beta} respectively. The study leveraged ATAC-seq, RNA sequencing, Cut&Tag sequencing of FOXA1 and histone marks profiling. The functional impact of FOXA1 was examined by partial silencing in vitro and by heterozygous FOXA1 deletion in a KrasG12D mouse model. Three-dimensional organoid culture, high-resolution electron microscopy, spatial transcriptomics and multiplex immunohistochemistry assessed carcinoma cell polarity, proliferation, the tumor microenvironment and organelle content. Group differences were evaluated with two-tailed t tests or one-way analysis of variance. ResultsFOXA1 binding and expression were highest in cells harboring an epithelial phenotype. In mouse KrasG12D LUAD tumors FOXA1 marked polarized, CDH1-positive cells; heterozygous loss diminished CDH1, disrupted apical-basal architecture, lowered organoid-forming efficiency and remodeled the immune microenvironment. Spatial transcriptomics and ultrastructural analyses showed that FOXA1-deficient carcinoma cells accumulated lysosomes, down-regulated vesicle fusion genes of the SNARE family and activated the lysosomal CLEAR gene network. FOXA1 occupied enhancers of lysosome-associated genes and competed with the transcription factor TFE3, thereby suppressing transcription of cathepsin B and cathepsin C and restricting lysosome biogenesis. ConclusionsFOXA1 is a central regulator that preserves epithelial cell polarity and limits lysosome formation in lung adenocarcinoma. Targeting the FOXA1-TFE3-lysosome axis may affect tumor plasticity and provide new therapeutic opportunities.

cancer biology↗

bioRxiv2026

Levosimendan inhibits HIV-1 infection in myeloid cells in the RIOK1-dependent manner

Despite of the highly potent antiretroviral therapies, HIV-1 establishes persistent infection and causes chronic inflammation in AIDS patients. Beyond CD4+ T cells, HIV-1 infects myeloid cells, including circulating monocytes and tissue-resident macrophages, and integrates with host genomes to form stable viral reservoirs. To achieve a functional HIV cure, latency-promoting agents (LPAs) have been developed for the "block-and-lock" strategy to reinforce deep HIV-1 latency and permanently silence proviruses. However, most LPAs have been tested mainly in CD4+ T cells, and their efficacy in myeloid cells remains unclear. In this study, we reported that levosimendan (LSM), a drug approved for clinic use to treat heart failures, is able to inhibit HIV lytic infection and reactivation in myeloid cells. LSM blocked viral lytic reactivation in HIV-1 latently infected monocytic cells (TH89GFP, U1) and microglial cells (HC69). LSM also inhibited HIV infection in human induced pluripotent stem cell (iPSC) derived microglia (iMG), primary human resident liver macrophages (Kupffer cells) as well as human monocyte-derived macrophages (MDMs). Furthermore, we demonstrated that overexpression of a predicted drug target of LSM, the conserved serine/threonine kinase RIOK1 (RIO kinase 1), overcomes LSMs anti-HIV effect. Overall, our studies concluded that LSM is a promising LPA to inhibit HIV-1 infection in myeloid cells in the RIOK1-dependent manner.

microbiology↗

bioRxiv2026

IMMREP25: Unseen Peptides

T cell receptors (TCRs) can bind to peptides presented by MHC molecules (pMHC) as a first step to trigger a T cell response. Reliable approaches to predict TCR:pMHC binding would have broad applications in clinical diagnostics, therapeutics, and the fundamental understanding of molecular interactions. IMMREP is a community organized series of prediction contests that asks participants to predict TCR:pMHC binding on unpublished datasets. Previous iterations in 2022 and 2023 showed multiple approaches can predict TCR-pMHC binding with significant accuracy (median AUC_0.1[≥]0.7) for peptides where experimental data is available ("seen" peptides). In contrast, models did not outperform random guessing for peptides that have no such data available ("unseen" peptides). Here we report on the results of IMMREP25, which focused solely on unseen peptides in order to evaluate the cutting edge of the field. We received 126 named submissions predicting the specificity of 1,000 TCRs against twenty unseen peptides restricted by one of two MHC molecules (HLA-A*02:01 and HLA-B*40:01). The best performing methods showed a macro-AUC_0.1 of 0.60, significantly better than random, demonstrating significant advances in the field. The top performing methods incorporated structural modeling into their approach, indicating that especially for unseen peptides, a structural understanding aids in the prediction of TCR:pMHC interactions. The results from this benchmark highlight the significant challenges remaining for TCR:pMHC predictions and will inform future method development.

bioinformatics↗

bioRxiv2026

LATTE for locus-specific quantification of transposable element expression across species

Transposable elements (TEs) are pivotal drivers of eukaryotic genome evolution and phenotypic diversity. However, their functional contributions to complex traits remain largely obscured by expression quantification challenges arising from high sequence homology and multi-mapping ambiguities. Here, we present LATTE, an efficient computational framework for defining and quantifying TE expression at locus-specific resolution by leveraging an innovative multi-indicator Expectation-Maximization (EM) algorithm. Extensive benchmarking against simulated datasets demonstrated that LATTE significantly outperformed existing state-of-the-art tools, achieving an accuracy of 0.998 at the subfamily level and 0.839 at the locus-specific level. Applying LATTE to 813 RNA-seq datasets across humans, cattle, and chickens, we quantified expression profiles of 2,703 TEs, followed by TE-expression quantitative trait loci (TE-eQTL) mapping. The colocalization rates between TE-eQTL and host gene-eQTL was low, revealing a distinct regulatory landscape of TE expression. This decoupled correlation between TEs and host genes are likely mediated by the differential expression of alternative transcripts. Through integrated TE-eQTL and genome-wide association studies on 3,746 complex traits across three species, we demonstrated that TEs constitute 204 (8.7%) additional associations with complex traits beyond gene-eQTL. More specifically, the Sjogrens syndrome-associated variant rs10954213 acts as a TE-eQTL that shifts the splicing landscape of IRF5, upregulating TE-containing transcripts while simultaneously suppressing canonical ones. Collectively, LATTE provides an efficient framework for studying TE expression across species, and our findings highlight the key role of TEs in understanding the genetic architecture of complex phenotypes.

bioinformatics↗

bioRxiv2026

Generalizable Finger Movement Decoding from Intracranial Recordings Across Static and Dynamic Actions

Reliable decoding of finger movements requires brain-computer interfaces (BCIs) that generalize across the diverse static and dynamic actions performed in daily life. Static postures and dynamic movement sequences rely on partially distinct neural representations, and the balance between these components varies widely across tasks. Yet most BCI decoding pipelines are optimized for a narrow task domain, limiting their ability to transfer to new scenarios. Here we show that standard intracranial decoding approaches show notable performance drops when applied to previously unseen finger tasks with different static-dynamic compositions, and that generalization critically depends on multiple elements of the decoding pipeline. High gamma features and short temporal windows yield the most robust cross task transfer. Although nonlinear models perform best when examples of all tasks are represented during training, linear decoders generalize better to novel, particularly dynamic, actions. We identify a consistent static-dynamic structure across tasks that may provide a useful basis for improving generalization. Finally, we show that anatomical heterogeneity between tasks also constrains generalization. Together, these results establish design principles for BCIs that generalize reliably across the rich repertoire of human finger movements.

neuroscience↗

bioRxiv2026

Species-specific regulation of porcine STING stability and antiviral signaling via its K61 mediated K48 ubiquitination and proteasome degradation

The cGAS-STING pathway has been widely recognized as a critical DNA-sensing pathway that plays a broad-spectrum antiviral role. Livestock, especially pigs, represents one of the most important meat sources. In this study, we identified a key lysine 61 (K61) of porcine STING (pSTING) that plays an essential role in its degradation and antiviral signaling in a species-specific manner, with K61 as the major lysine of pSTING for K48-linked ubiquitination. After virus infection, pSTING recruits the E3 ligase, RNF5, which specifically assembles a K48-linked ubiquitin chain at K61, thereby mediating pSTING proteasomal degradation and reducing its antiviral activity. Meanwhile, the deubiquitylation of K61 is mediated mainly by deubiquitinase USP20, which enhances the stability and antiviral activity of pSTING. Together, given the relatively few lysine numbers in livestock STINGs and species-specific K61 regulation of pSTING stability and antiviral function, the K61 and its specific regulatory enzymes of pSTING could serve as potential targets for breeding of antiviral pigs and design of antiviral drugs, respectively.

immunology↗

bioRxiv2026

Effect of dietary Chitosan supplementation on Intestinal Barrier Function and Growth Performance in weaned piglets challenged by Enterohemorrhagic haemolytic Escherichia coli

Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is an important zoonotic pathogen that disrupts intestinal epithelial barrier integrity and induces excessive inflammatory responses, thereby leading to impaired growth performance and intestinal injury. EHEC is also an important cause Hemolytic Uremic Syndrome (HUS) in children and older adults. In pig production, chitosan is considered a promising alternative to antibiotics due to its bioadhesive and antimicrobial properties, but the effects and underlying mechanisms of chitosan (COS) under pathogenic challenge remain to be elucidated. One hundred and eight pigs were randomly divided into three treatments: an unchallenged control group (CON), an EHEC-challenged control group (ECON), and an EHEC-challenged group supplemented with 100 mg/kg COS (ECOS). Results show that EHEC challenge increased the feed conversion ratio (FCR), increased inflammatory cytokine levels, disrupted intestinal morphology, and downregulated tight junction and nutrient transporter gene expression (P<0.05). Dietary COS supplementation significantly improved average daily gain (ADG) and FCR during day 6-14 (P<0.05). Moreover, COS reduced fecal shedding of total E. coli (P = 0.085) and EHEC, attenuated systemic inflammation by decreasing serum TNF- and IL-6 levels, and enhanced humoral immunity as indicated by increased IgA and IgM concentrations (P<0.05). Importantly, COS alleviated EHEC-induced intestinal injury by restoring villus height and villus-to-crypt ratio, with enhanced mucosal digestive enzyme activities, and upregulated expression of tight junction proteins (ZO-1 and occludin) and nutrient transporters (SGLT-1 and PEPT1) (P<0.05). In conclusion, these findings indicate that dietary COS improves growth performance in EHEC-challenged weaned pigs, with enhanced intestinal barrier integrity and nutrient transport capacity.

microbiology↗

bioRxiv2026

Microencapsulation of a novel Bacteroides thetaiotaomicron strain: a promising strategy to fortify intestinal barrier fortification in weaned pig model

Porcine Bacteroides thetaiotaomicron LYH5 demonstrated in vitro antimicrobial activity, suggesting probiotic potential. Due to poor gastric juice tolerance, LYH5 was encapsulated via extrusion using sodium alginate (SA) and gellan gum. Box-Behnken design optimization yielded optimal parameters: SA 1.5%, gellan gum 0.4%, CaCl2 0.9%, bacteria:glue ratio 1:4, achieving an encapsulation rate of 84.22{+/-}0.17%. Its effect on weaned piglet intestinal health was evaluated using 78 piglets (7.69{+/-}0.52 kg) randomly assigned to 4 groups for 40 days: CON (control), T (basal diet + LYH5 live bacteria, 1x10{superscript 1} CFU/mL), TJ (basal diet + LYH5 microcapsules, 1x10{superscript 1} CFU/mL, J (basal diet + empty capsules). The results of this experiment showed that compared with the control group, LYH5 microcapsule can improve the intestinal barrier function without affecting the growth performance of piglets, and provide ideas and references for the development of human next-generation probiotics (NGP). IMPORTANCEThis study addresses the key bottleneck of poor gastric acid tolerance of probiotics via microencapsulation and provides a practical reference for the development of human next-generation probiotics.

microbiology↗

bioRxiv2026

Multi-component functionalized Bifidobacterium longum hydrogel for multi-target integrated therapy of colitis-associated anxiety and depression

Inflammatory bowel diseases (IBDs) are frequently accompanied by anxiety and depression, largely driven by perturbed gut-brain axis signaling. However, current oral therapies remain constrained by the spatial and functional separation between intestinal inflammation and central nervous system dysfunction. Here, we present a comprehensive gut-brain dual region integrated therapeutic strategy based on functionalized Bifidobacterium longum hydrogel (INPs@BL@Gel), in which baicalin and tyrosine are coordinated with Fe(III) to form infinite coordination polymers (ICPs), coated with inulin, assembled onto Bifidobacterium longum (BL), and subsequently encapsulated within a pH- and matrix metalloproteinase-responsive silk fibroin-gelatin hydrogel. INPs@BL@Gel exhibits high drug-loading, effective gastric protection, inflammation-triggered release, and long-term intestinal colonization. Within the inflamed intestine, BL and components synergistically suppress inflammatory responses, restore gut microbiota homeostasis, and promote intestinal barrier repair through multi-target integrated therapy. Importantly, BL combined with components markedly enhances the production of beneficial neuroactive metabolites such as homovanillic acid and short-chain fatty acids, which integrated regulate neuroinflammation, preserve synaptic function, and facilitate blood-brain barrier repair via the gut-brain axis. In vivo studies demonstrate that INPs@BL@Gel not only exert potent therapeutic efficacy against colitis and effectively alleviate associated depression, but also reshape the gut microbiota and restore barrier integrity, achieving an remarkable comprehensive therapeutic effect. O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/710940v1_fig1a.gif" ALT="Figure 11"> View larger version (59K): org.highwire.dtl.DTLVardef@1a831f3org.highwire.dtl.DTLVardef@1676617org.highwire.dtl.DTLVardef@15f99c1org.highwire.dtl.DTLVardef@1677cc4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOScheme 1.C_FLOATNO (a) Schematic diagram of the design and preparation of functionalized Bifidobacterium longum hydrogel. (b) Exploration of the mechanism of INPs@BL@Gel in treating colitis-associated anxiety and depression through a dual-site multi-target synergistic strategy. C_FIG

pathology↗