Biology subjects

Zou, H.

Publications and source records attributed to Zou, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Modulating Prestimulus Alpha and Beta Power with tRNS Establishes Their Causal Role in Visual Perception

Variability in visual perception in response to consistent stimuli is a fundamental phenomenon linked to fluctuations in prestimulus low-frequency neural oscillations--particularly in the alpha (8-13 Hz) and beta (13-30 Hz) bands--typically measured by their power in electroencephalography (EEG) signals. However, the causal role of these prestimulus alpha and beta power fluctuations in visual perception remains unestablished. In this study, we investigated whether prestimulus alpha and beta power causally affect visual perception using transcranial random noise stimulation (tRNS). In a sham-controlled, single-blind, within-subject design, 29 participants performed a visual detection task while receiving occipital tRNS. Online functional near-infrared spectroscopy (fNIRS) was used to measure cortical excitability during stimulation, and offline EEG signals were collected after stimulation. Mental fatigue was incorporated as a state-dependent factor influencing tRNS effects. Our findings demonstrate that, primarily under low fatigue states, tRNS increased cortical excitability during stimulation (indicated by increased fNIRS oxyhemoglobin amplitude), decreased subsequent prestimulus EEG alpha and beta power, and consequently reduced the visual contrast threshold (VCT), indicating enhanced visual perception. Sensitivity analysis revealed that alpha oscillations contributed more significantly to visual perception than beta oscillations under low fatigue. Additionally, the state-dependent effects of tRNS may result from different sensitivities of VCT to neural oscillations across fatigue states. These results provide causal evidence linking prestimulus alpha and beta power to visual perception and underscore the importance of considering brain states in neuromodulation research. Our study advances the understanding of the neural mechanisms underlying visual perception and suggests potential therapeutic applications targeting neural oscillations. Significance statementUnderstanding why we perceive identical visual stimuli differently is a fundamental question in neuroscience. This study provides causal evidence that prestimulus alpha and beta neural oscillations directly influence visual perception, particularly under low mental fatigue state. By using tRNS alongside fNIRS and EEG recordings, we demonstrate that modulating neural excitability can alter perceptual outcomes. Our findings highlight the importance of considering brain state--such as fatigue levels--in neuromodulation research. This work advances our understanding of the neural mechanisms underlying visual perception and opens avenues for developing targeted interventions to enhance sensory processing and cognitive functions, potentially benefiting individuals with perceptual or attentional disorders.

neuroscience↗

bioRxiv2024

AER-270 and TGN-020 are not aquaporin-4 water channel blockers

Aquaporin-4 (AQP4) is the most abundant water channel protein in the brain. It controls water homeostasis, facilitates glymphatic function and is a drug target for brain edema following injury or stroke. Dysregulation of brain water homeostasis affects millions of people every year leading to death, disability and cognitive decline, for which no medicines are available. Two compounds, AER-270 and TGN-020, are sold as AQP4 inhibitors and a prodrug of AER-270 is currently in a phase I human trial. However, the direct effect of these compounds on AQP4 function has not been unequivocally demonstrated. Our data across multiple cellular and molecular assay systems demonstrate, unexpectedly, that AER-270 and TGN-020 do not inhibit AQP4. Although we observed an apparent inhibitory effect of AER-270 and TGN-020 in the Xenopus laevis oocyte assay, there was no effect in assays using reconstituted recombinant AQP4 or mammalian cells expressing exogenous or endogenous AQP4. We identify alternative mechanisms of action for both molecules that may explain previously reported in vivo results that were interpreted in the context of AQP4 inhibition. Overall, we conclude that AER-270 and TGN-020 should not be used to investigate the AQP4-dependence of biological processes in the brain.

biophysics↗

bioRxiv2024

Genomic diversity and underlying metabolic variations of the human gut microbiome between populations at single nucleotide resolution

BackgroundA comprehensive and representative reference database is crucial for accurate taxonomic and functional profiling of the human gut microbiome in population-level studies. However, with 70% of current microbial reference data derived from Europeans and the Americans, East Asia, especially China, remain underrepresented. MethodsWe constructed the human Gut Microbiome Reference (GMR), comprising 478,588 high-quality microbial genomes from Chinese (247,134) and non-Chinese (231,454) populations. Species-level clustering and protein annotations were performed to characterize microbial diversity and function. We further integrated novel genomes into taxonomic profiling database and validated the improvements using independent cohort data. ResultsThe GMR dataset spans 6,664 species, including 26.4% newly classified species, and encodes over 20 million unique proteins, with 47% lacking known functional annotations. Notably, we observed that 35.35% and 32.46% of species unique to Chinese and non-Chinese populations, respectively. For 2,145 species shared between populations, 74% of 304 species with balanced prevalence between populations exhibited population-specific phylogenetic stratification, involving health relevant functionalities such as antibiotic resistance. Integration of novel genomes into taxonomic improved population-level species profiling by up to 23% and uncovered replicable associations between novel species and host physiological traits. ConclusionsOur study largely expands the compositional and functional landscape of the human gut microbiome, providing a crucial resource for studying the role of gut microbiome for regional health disparities.

genomics↗

bioRxiv2024

Endothelial cell Nrf2 controls neuroinflammation following a systemic insult

Systemic inflammation can lead to neuroinflammation with acute consequences such as delirium and long-lasting deleterious effects including cognitive decline and the exacerbation of neurodegenerative disease progression. Here we show that transcription factor Nrf2 controls brain endothelial cell homeostasis and barrier strength. We found that peripheral inflammation caused infiltration of macrophages, microglial activation and inflammatory reactive astrogliosis, all of which could be prevented by RTA-404, an activator of the transcription factor Nrf2 and close structural relative of the recently FDA-approved Nrf2 activator RTA-408 (Omaveloxolone). To identify the key cellular mediator(s), we generated an endothelial cell-specific Nrf2 knockout mouse. Strikingly, the effects of RTA-404 on brain endothelial activation and downstream neuroinflammatory events was abolished by endothelial cell-specific Nrf2 deletion. This places endothelial cell Nrf2 as a peripherally accessible therapeutic target to reduce the CNS-adverse consequences of systemic inflammation.

neuroscience↗

bioRxiv2024

Discovery and Biosynthesis of Sulfenicin and Its New-to-Nature Acylsulfenic Acid Functional Group

Lifes organic molecules are built with diverse functional groups that enable biology by fine tuning intimate connections through time and space. As such, the discovery of new-to-nature functional groups can expand our understanding of the natural world and motivate new applications in biotechnology and biomedicine. Herein we report the genome-aided discovery of sulfenicin, a novel polyketide-nonribosomal peptide hybrid natural product from a marine Streptomyces bacterium bearing a unique acylsulfenic acid functionality. Through a series of heterologous biosynthesis, functional genetics, and enzymatic reconstitution experiments, we show that this previously described synthetic functional group is biologically assembled by a set of enzymes from both primary and secondary metabolism, including a novel flavin-dependent S-hydroxylase that hydroxylates a thiocarboxylic acids sulfur atom. While the sulfenicin biosynthetic gene cluster is presently without parallel in public databases, acylsulfenic acid-encoding enzymes are widely distributed in bacterial genomes, implying that this labile functional group may similarly have a broad distribution among specialized metabolites.

biochemistry↗

bioRxiv2024

The Phylogeny and the Evolution of Parasitic Strategies in Trematoda

Trematodes are obligatory parasites that generally must transmit between hosts to complete their life cycle. They parasitize varying numbers of intermediate hosts (0, 1 or 2), but the evolutionary history of these strategies and the ancestral states remain unknown. We conducted the ancestral state reconstruction of the number of intermediate hosts using mitogenomic (Trematoda) and nuclear-genomic (Neodermata) topologies. Aspidogastrea was identified as the sister-group ("basal") to all other Trematoda using a range of approaches, so it is crucial for studying the evolutionary history of trematodes. However, there is only one transcriptome available for this lineage, and mitochondrial genomes (mitogenomes) remain unavailable. Herein, we sequenced mitogenomes of two aspidogastreans: Aspidogaster ijimai and Aspidogaster conchicola. As the ancestral state reconstruction analysis is topology-sensitive, we tested multiple phylogenetic strategies, comprising the outgroup selection, phylogenetic models, partitioning strategies, and topological constraints. These mitogenomic phylogenies exhibited pronounced topological instability, with Aspidogastrea resolved as the "basal" radiation in most, but not all, topologies. Based on our analyses, Cestoda was the optimal outgroup choice, and the "heterogeneous" CAT-GTR model in PhyloBayes was the optimal model choice. We inferred the time tree and conducted ancestral state reconstruction analyses using this "optimal" topology, as well as constrained mitogenomic and nuclear genomic topologies. Results were ambiguous for some lineages, but scenario that received the strongest support is the direct life cycle (no intermediate hosts) in the ancestors of Trematoda (proto-trematodes) and Aspidogastrea (proto-aspidogastreans), while the ancestor of Digenea (proto-digeneans) had two intermediate hosts. The inferred scenario indicates that host strategies are relatively plastic among trematodes, putatively comprising several independent host gains, and multiple host losses. We propose a timeline for these events and discuss the role that alternating sexual and asexual generations putatively played in the evolution of complex parasitic life histories in digeneans.

evolutionary biology↗

bioRxiv2024

3D Brain Vascular Niche Model Captures Invasive Behavior and Gene Signatures of Glioblastoma

Glioblastoma (GBM) is a lethal brain cancer with no effective treatment; understanding how GBM cells respond to tumor microenvironment remains challenging as conventional cell cultures lack proper cytoarchitecture while in vivo animal models present complexity all at once. Developing a culture system to bridge the gap is thus crucial. Here, we employed a multicellular approach using human glia and vascular cells to optimize a 3-dimensional (3D) brain vascular niche model that enabled not only long-term culture of patient derived GBM cells but also recapitulation of key features of GBM heterogeneity, in particular invasion behavior and vascular association. Comparative transcriptomics of identical patient derived GBM cells in 3D and in vivo xenotransplants models revealed that glia-vascular contact induced genes concerning neural/glia development, synaptic regulation, as well as immune suppression. This gene signature displayed region specific enrichment in the leading edge and microvascular proliferation zones in human GBM and predicted poor prognosis. Gene variance analysis also uncovered histone demethylation and xylosyltransferase activity as main themes for gene adaption of GBM cells in vivo. Furthermore, our 3D model also demonstrated the capacity to provide a quiescence and a protective niche against chemotherapy. In summary, an advanced 3D brain vascular model can bridge the gap between 2D cultures and in vivo models in capturing key features of GBM heterogeneity and unveil previously unrecognized influence of glia-vascular contact for transcriptional adaption in GBM cells featuring neural/synaptic interaction and immunosuppression.

bioengineering↗

bioRxiv2024

Structural Basis for the Activation of Proteinase-Activated Receptors (PARs) by Endogenous Ligands

The proteinase-activated receptor (PAR) subfamily of G protein-coupled receptors (GPCRs) include four members, PAR1-PAR4, that play critical roles in hemostasis, thrombosis, embryonic development, wound healing, inflammation, and cancer progression. The PARs share a unique activation mechanism driven by proteinase cleavage at a specific site within the extracellular amino-terminus, exposing a tethered ligand that self-activates the receptor. Subsequent activation allows PAR family members to initiate complex intracellular signaling networks via traditional G protein-mediated pathways and beta-arrestin signaling and, in this way, the PARs link extracellular protease signaling molecules to cellular functions. Despite a primary reliance on biochemical studies for understanding tethered ligand recognition, direct structural visualization of these ligand-receptor complexes has been elusive. Here, we present structural snapshots of activated PAR1 and PAR2 bound to their endogenous tethered ligands, revealing, for the first time, shallow and constricted orthosteric binding pockets and highlighting critical residues involved in ligand recognition and receptor activation. Surprisingly, comparisons with antagonist-bound structures show minimal conformational changes in the TM6 helix, a typical signature of GPCR activation, with large movements of TM7 observed upon activation. These insights lead to the identification of a common mechanism for PAR1 and PAR2 activation and provide a structural template for designing novel antagonists targeting the orthosteric binding site, potentially opening new avenues for therapeutic interventions.

biochemistry↗

bioRxiv2024

LncCE: Landscape of Cellular-Elevated LncRNAs in Single Cells Across Normal and Cancer Tissues

Long non-coding RNAs (lncRNAs) have emerged as significant players for maintaining the morphology and function of tissues or cells. The precise regulatory effectiveness of lncRNA is closely associated with the spatial expression patterns across tissues and cells. Here, we proposed the Cellular-Elevated LncRNA (LncCE) database to systematically explore cellular-elevated (CE) lncRNAs across normal and cancer tissues in single cells. LncCE encompasses 87,946 CE lncRNAs of 149 cell types by analyzing 181 single-cell RNA sequencing (scRNA-seq) datasets, involved in 20 fetal normal tissues, 59 adult normal tissues, as well as 32 adult and 5 pediatric cancer tissues.Two main search options were provided via a given lncRNA name or a cell type. The output results emphasize both qualitative and quantitative expression features of lncRNAs across different cell types, co-expression with protein-coding genes as well as their involved in biological functions. For cancers, LncCE particularly provided quantitative figures for exhibiting their expression changes compared to control samples and clinical associations with patient overall survivals. Together, LncCE offers an extensive, quantitative and user-friendly interface to investigate cellular-elevated expression atlas for lncRNAs across normal and cancers tissues at single-cell level. The LncCE database is available at http://bio-bigdata.hrbmu.edu.cn/LncCE.

cancer biology↗

bioRxiv2024

Invasion of glioma cells through confined space requires membrane tension regulation and mechano-electrical coupling via Plexin-B2

Glioblastoma (GBM) is a malignant brain tumor with uncontrolled invasive growth. Here, we demonstrate how GBM cells usurp guidance receptor Plexin-B2 to gain biomechanical plasticity for polarized migration through confined space. Using live-cell imaging to track GBM cells negotiating microchannels, we reveal active endocytosis at cell front and filamentous actin assembly at rear to propel GBM cells through constrictions. These two processes are interconnected and governed by Plexin-B2 that orchestrates cortical actin and membrane tension, shown by biomechanical assays. Molecular dynamics simulations predict that balanced membrane and actin tension are required for optimal migratory velocity and consistency. Furthermore, Plexin-B2 mechanosensitive function requires a bendable extracellular ring structure and affects membrane internalization, permeability, phospholipid composition, as well as inner membrane surface charge. Together, our studies unveil a key element of membrane tension and mechanoelectrical coupling via Plexin-B2 that enables GBM cells to adapt to physical constraints and achieve polarized confined migration.

cancer biology↗

bioRxiv2023

Synthetic mucus barrier arrays as a nanoparticle formulation screening platform

A mucus gel layer lines the luminal surface of tissues throughout the body to protect them from infectious agents and particulates. As a result, nanoparticle drug delivery systems delivered to these sites may become trapped in mucus and subsequently cleared before they can reach target cells. As such, optimizing the properties of nanoparticle delivery vehicles, such as their surface chemistry and size, is essential to improving their penetration through the mucus barrier. In previous work, we developed a mucin-based hydrogel that has viscoelastic properties like that of native mucus which can be further tailored to mimic specific mucosal tissues and disease states. Using this biomimetic hydrogel system, a 3D-printed array containing synthetic mucus barriers was created that is compatible with a 96-well plate enabling its use as a high-throughput screening platform for nanoparticle drug delivery applications. To validate this system, we evaluated several established design parameters to determine their impact on nanoparticle penetration through synthetic mucus barriers. Consistent with the literature, we found nanoparticles of smaller size and coated with a protective PEG layer more efficiently penetrated through synthetic mucus barriers. In addition, we evaluated a mucolytic (tris (2-carboxyethyl) phosphine, TCEP) for use as a permeation enhancer for mucosal drug delivery. In comparison to N-acetyl cysteine (NAC), we found TCEP significantly improved nanoparticle penetration through a disease-like synthetic mucus barrier. Overall, our results establish a new high-throughput screening approach using synthetic mucus barrier arrays to identify promising nanoparticle formulation strategies for drug delivery to mucosal tissues.

bioengineering↗

bioRxiv2023

Xanthomonas citri subsp. citri type III effector PthA4 directs the dynamical expression of a putative citrus carbohydrate-binding gene for canker formation

Xanthomonas citri subsp. citri (Xcc), the causal agent of citrus canker, elicits canker symptoms in citrus plants because of the transcriptional activator-like (TAL) effector PthA4, which activates the expression of the citrus susceptibility gene CsLOB1. This study reports the regulation of the putative carbohydrate-binding protein gene Cs9g12620 by PthA4-mediated induction of CsLOB1 during Xcc infection. We found that the transcription of Cs9g12620 was induced by infection with Xcc in a PthA4-dependent manner. Even though it specifically bound to a putative TAL effector-binding element in the Cs9g12620 promoter, PthA4 exerted a suppressive effect on the promoter activity. In contrast, CsLOB1 bound to the Cs9g12620 promoter to activate its expression. The silencing of CsLOB1 significantly reduced the level of expression of Cs9g12620, which demonstrated that Cs9g12620 was directly regulated by CsLOB1. Intriguingly, PhtA4 interacted with CsLOB1 and exerted feedback control that suppressed the induction of expression of Cs9g12620 by CsLOB1. Transient overexpression and gene silencing revealed that Cs9g12620 was required for the optimal development of canker symptoms. These results support the hypothesis that the expression of Cs9g12620 is dynamically directed by PthA4 for canker formation through the PthA4-mediated induction of CsLOB1.

plant biology↗

bioRxiv2023

Bacterial community characterization by deep learning aided image analysis in soil chips

Soil microbes play an important role in governing global processes such as carbon cycling, but it is challenging to study them embedded in their natural environment and at the single cell level due to the opaque nature of the soil. Nonetheless, progress has been achieved in recent years towards visualizing microbial activities and organo-mineral interaction at the pore scale, especially thanks to the development of microfluidic soil chips creating transparent soil model habitats. Image-based analyses come with new challenges as manual counting of bacteria in thousands of digital images taken from the soil chips is excessively time-consuming, while simple thresholding cannot be applied due to the background of soil minerals and debris. Here, we adopt the well-developed deep learning algorithm Mask-RCNN to quantitatively analyse the bacterial communities in soil samples from different locations in the world. This work demonstrates analysis of bacterial abundance from three contrasting locations (Greenland, Sweden and Kenya) using deep learning in microfluidic soil chips in order to characterize population and community dynamics. We additionally quantified cell- and colony morphology including cell size, shape and the cell aggregation level via calculation of the distance to the nearest neighbor. This approach allows for the first time an automated visual investigation of soil bacterial communities, and a crude biodiversity measure based on phenotypic cell morphology, which could become a valuable complement to molecular studies.

ecology↗

bioRxiv2023

Aryl hydrocarbon receptor restricts axon regeneration of DRG neurons in response to injury

Neurons must balance stress responses with regenerative demands following injury, but the mechanism is unclear. Here, we identify the aryl hydrocarbon receptor (AhR), a ligand-activated bHLH-PAS transcription factor, as a key regulator of this stress-growth switch. We show that ligand mediated AhR signaling restrains axon growth, whereas neuronal deletion or pharmacological inhibition of AhR promotes axonal regeneration and functional recovery in both peripheral nerve and spinal cord injury models. Mechanistic studies revealed that axotomy-induced AhR activation in dorsal root ganglion (DRG) neurons enforces proteostasis and stress-response programs to preserve tissue integrity. In contrast, AhR ablation redirects the neuronal response toward elevated de novo translation and pro-growth signaling, enabling axon regeneration. This growth-promoting effect required HIF-1, with shared transcriptional targets enriched for metabolic and regenerative pathways. Single-cell and epigenomic analyses further revealed that the AhR regulon engages the integrated stress response (ISR) and DNA hydroxymethylation to rewire neuronal injury programs. Together, our findings establish AhR as a neuronal brake on axon regeneration, integrating environmental sensing, protein homeostasis, and metabolic signaling to control the balance between stress adaptation and axonal repair.

neuroscience↗

bioRxiv2023

Gut microbial genomes with paired isolates from China signify probiotic and cardiometabolic effects

The gut microbiome displays significant genetic differences between populations while systematic characterization of the genomic landscape of the gut microbiome in Asia populations remains limited. Here, we present the Chinese gut microbial reference (CGMR) set, comprising 101,060 high quality metagenomic assembled genomes (MAGs) of 3,707 non-redundant species paired with 1,376 live isolates from a national wide collection of 3,234 fecal samples across China. This improved reference set contains 987 novel species compared with existing resources worldwide. By associating MAGs with geographic and phenotypic characteristics, we observed regional-specific coexisting MAGs and MAGs with probiotic and cardiometabolic functionalities. We further conducted mice experiments to confirm the probiotic effects of two Faecalibacterium intestinalis isolates in alleviating constipation, the cardiometabolic influences of three Bacteroides fragilis_A isolates in obesity, and the functional potential of isolates from the two new species belonging to the genera Parabacteroides and Lactobacillus in host lipids metabolism. Our study not only expands the current microbial genomes with paired isolates but also demonstrates their probiotic and cardiometabolic effects on hosts, contributing to the mechanistic understanding of host-microbe interactions and the translation of microbiome-based personalized therapies.

microbiology↗

bioRxiv2023

Antibody Humanization via Protein Language Model and Neighbor Retrieval

Antibody (Ab), also known as immunoglobulin (Ig), is an essential macromolecule involved in human immune response and plays an increasingly vital role in drug discovery. However, the development of antibody drugs heavily relies on humanization of murine antibodies, which often necessitates multiple rounds of sequence optimizations through laborious experimental processes. In recent years, the remarkable capabilities of machine learning have revolutionized the field of natural sciences and have also demonstrated promising applications in the field of antibody humanization. Here, we present Protein-LAnguage-model-knN (PLAN), a machine learning model leveraging protein language model and information retrieval for improving humanization of antibodies. Further, we propose DE, a computed value shows a positive correlation with antigen-binding affinity. Our in silico experimental results demonstrate that 1) the PLAN-humanized sequences average humanness score reaches 0.592, improving over the best existing method by 44.7%; 2) a 63% overlap between the PLAN-proposed mutations and the mutations validated through wet lab experiments, which is 16.7% higher than the best existing result; 3) comparable antigen-binding affinity after DE guided back mutation.

bioinformatics↗

bioRxiv2023

Prominent contributions of selective neuronal subtypes to pediatric drug-resistant focal dysplasia

About 75% cases of epilepsy begin during childhood, and 10 - 30% of pediatric epilepsy patients are resistant to drug treatment. The predominant seizure type in children is focal cortical dysplasia (FCD) which is highly associated with drug-resistant epilepsy, but its underlying cause is poorly understood. We performed single-cell RNA sequencing and patch-clamp recording on fresh brain tissues obtained from pediatric FCD patients shortly after surgery to reveal critical factors contributing to FCD. We report that known epilepsy genes or significant transcriptomic alterations occur in only a few neuronal subgroups, suggesting that epilepsy-associated neurons cluster into only a few neuronal subtypes. These epilepsy-subtypes displayed significant epilepsy-related transcriptomic alterations, especially in the genes associated with excitation/inhibition balance and neuron functional signal pathways. Among eight epilepsy-subtypes, L2_4_CUX2_YWHAH and PVALB_RGS5 subtypes showed the most prominent alterations in FCD patient tissues. Supporting PV-neurons being important, recording from fast-spiking/parvalbumin-containing neurons in acute FCD patient brain slices revealed reduced excitatory synaptic inputs, implicating lower activity in these neurons and fewer synaptic inputs onto them. A higher percentage of mitochondria genes, and likely higher activity in the pathways associated with oxidative phosphorylation and ATP biosynthetic process, was observed in the epilepsy-subtypes, suggesting a high energy expenditure in them. Interestingly, the activity of the above two pathways in most epilepsy-subtypes was lower in the FCD patients, suggesting these subtypes may be more vulnerable to energy deficit in epilepsy. Altogether, transcriptomics is significantly altered in only a few neuronal subtypes in pediatric FCD patient brains. These selective epilepsy-subtypes may play prominent roles in the genesis of pediatric drug-resistant seizure and targeting them may provide new treatment options.

bioinformatics↗

bioRxiv2023

Temporal colonization of the gut microbiome in neonatal Bos taurus at single nucleotide resolution

BackgroundThe rumen of neonatal calves is underdeveloped and exhibits limited functionality during early life. Thus, the acquisition and colonization of microbes in the gut are key to establishing a healthy host-microbiome symbiosis for neonatal calves. Microbiome-linked health outcomes appear to be the consequences of individual strains of specific microbes. However, the temporal colonization of pioneering microbial strains and their linkages to the health and growth of neonatal calves are poorly understood. ResultsTo address this, we longitudinally profiled the gut microbiome of 36 neonatal calves from birth up to 2 months postpartum and carried out microbial transplantation (MT) to reshape their gut microbiome. Genomic reconstruction of deeply sequenced fecal samples resulted in a total of 3,931 metagenomic assembled genomes (MAGs), of which 397 were identified as new species when compared with existing databases of Bos taurus. Single nucleotide level metagenomic profiling shows a rapid influx of microbes after birth, followed by strong selection during the first few weeks of life. MT was found to reshape the genetic makeup of 33 MAGs (FDR<0.05), mainly from Prevotella and Bacteroides species. We further linked over 20 million microbial single nucleotide variations (SNVs) to 736 plasma metabolites, which enabled us to characterize 24 study-wide significant associations (P < 4.4x10-9) that identify the potential microbial genetic regulation of host immune and neuro-related metabolites, including glutathione and L-dopa. Our integration analyses further revealed that microbial genetic variations may influence the health status and growth performance of neonatal calves by modulating metabolites via structural regulation of their encoded proteins. For instance, we found that the albumin levels and total antioxidant capacity in neonatal calves were correlated with L-dopa, which was determined by SNVs via structural regulations of metabolic enzymes. ConclusionsThe current results indicate that the temporal colonization of microbial strains and MT-induced strain replacement are integral in the development of the gut microbiome of neonatal calves and may help to develop strategies that can improve the health status and growth performance of neonatal calves.

microbiology↗