43 Matching Annotations
  1. Oct 2025
  2. www.biorxiv.org www.biorxiv.org
    Protein Structure Informed Bacteriophage Genome Annotation with Phold
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    biorxiv.org/content/10.1101/2025.08.05.668817v1
  3. Jun 2025
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    Uniform bacterial genetic diversity along the guts of mice inoculated with human stool
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    biorxiv.org/content/10.1101/2025.01.28.635365v1
  5. Feb 2025
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    Genomic analysis of cultivated infant microbiomes identifies Bifidobacterium 2’-fucosyllactose utilization can be facilitated by co-existing species
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    biorxiv.org/content/10.1101/2023.03.10.532136v1
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    BMI and BPH correlate with urinary microbiome diversity and lower urinary tract symptoms in men
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    biorxiv.org/content/10.1101/2023.12.14.571758v1
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    Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome
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    biorxiv.org/content/10.1101/2024.09.30.615745v1
  9. www.medrxiv.org www.medrxiv.org
    Fecal microbiome predicts treatment response after the initiation of semaglutide or empagliflozin uptake
    1
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    medrxiv.org/content/10.1101/2024.07.19.24310611v1
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    Expanding the human gut microbiome atlas of Africa
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    biorxiv.org/content/10.1101/2024.03.13.584859v1
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    Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution
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    biorxiv.org/content/10.1101/2024.03.08.584156v1
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    A catalogue of small proteins from the global microbiome
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    biorxiv.org/content/10.1101/2023.12.27.573469v1
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    Viroid-like colonists of human microbiomes
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    biorxiv.org/content/10.1101/2024.01.20.576352v1
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    Pervasive selective sweeps across human gut microbiomes
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    biorxiv.org/content/10.1101/2023.12.22.573162v1
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    Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition
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    biorxiv.org/content/10.1101/2022.08.26.505490v2
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    Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut
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    biorxiv.org/content/10.1101/2023.02.28.530516v1
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    Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut
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    biorxiv.org/content/10.1101/2023.04.28.538771v2
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    The prevalence of Fusobacterium nucleatum subspecies in the oral cavity stratifies by local health status
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    biorxiv.org/content/10.1101/2023.10.25.563997v1
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    Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome
    1
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    biorxiv.org/content/10.1101/2023.01.24.525211v1
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    Steamed broccoli sprouts alleviate gut inflammation and retain gut microbiota against DSS-induced symptoms
    1
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    biorxiv.org/content/10.1101/2023.01.27.522641v2
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    Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children
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    biorxiv.org/content/10.1101/2020.02.13.944181v5
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    Detailed Social Network Interactions and Gut Microbiome Strain-Sharing Within Isolated Honduras Villages
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    biorxiv.org/content/10.1101/2023.04.06.535875v1
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    Functional and evolutionary significance of unknown genes from uncultivated taxa
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    biorxiv.org/content/10.1101/2022.01.26.477801v1
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    Exposure to environmental stress decreases the resistance of river microbial communities towards invasion by antimicrobial resistant bacteria
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    biorxiv.org/content/10.1101/2022.11.19.517188v1
  25. www.medrxiv.org www.medrxiv.org
    Longitudinal analysis at three oral sites links oral microbiota to clinical outcomes in allogeneic hematopoietic stem-cell transplant
    1
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    medrxiv.org/content/10.1101/2022.11.18.22282520v1
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    Time of Sample Collection Critical for Microbiome Replicability
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    biorxiv.org/content/10.1101/2022.10.26.513817v1
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    mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome
    1
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    biorxiv.org/content/10.1101/2022.11.07.515285v1
  28. www.biorxiv.org www.biorxiv.org
    A novel taurine-respiring murine gut bacterium contributes to colonization resistance against enteropathogens
    1
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    biorxiv.org/content/10.1101/2022.10.05.510937v1
  29. www.medrxiv.org www.medrxiv.org
    BugSigDB: accelerating microbiome research through systematic comparison to published microbial signatures
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    medrxiv.org/content/10.1101/2022.10.24.22281483v3
  30. www.biorxiv.org www.biorxiv.org
    Functional screens of barcoded expression libraries uncover new gene functions in carbon utilization among gut Bacteroidales
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    biorxiv.org/content/10.1101/2022.10.10.511384v2
  31. www.biorxiv.org www.biorxiv.org
    Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians
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    biorxiv.org/content/10.1101/2022.05.05.490740v1
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    Two Competing Guilds as a Core Microbiome Signature for Health Recovery
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    biorxiv.org/content/10.1101/2022.05.02.490290v2
  33. www.biorxiv.org www.biorxiv.org
    Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria is Governed by a Global Transcriptional Regulator NagR
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    biorxiv.org/content/10.1101/2022.04.06.487429v1
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    Axial spondyloarthritis patients have altered mucosal IgA response to oral and fecal microbiota
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    biorxiv.org/content/10.1101/2021.07.15.452558v1
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    LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis
    1
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    biorxiv.org/content/10.1101/2021.12.24.474111v1
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    Using strain-resolved analysis to identify contamination in metagenomics data
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    biorxiv.org/content/10.1101/2022.01.16.476537v1
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    The genetic and ecological landscape of plasmids in the human gut
    1
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    biorxiv.org/content/10.1101/2020.11.01.361691v2
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    A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae
    1
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    biorxiv.org/content/10.1101/2021.02.24.432587v1
  39. www.biorxiv.org www.biorxiv.org
    Short- and long-read metagenomics of South African gut microbiomes reveal a transitional composition and novel taxa
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    biorxiv.org/content/10.1101/2020.05.18.099820v2
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    The darkest place is under the candlestick - healthy urogenital tract as a source of UTI-related Escherichia coli lineages
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    biorxiv.org/content/10.1101/2021.08.06.455400v1
  41. www.biorxiv.org www.biorxiv.org
    Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth
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    biorxiv.org/content/10.1101/2023.01.13.523991v2
  42. www.biorxiv.org www.biorxiv.org
    SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)
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    biorxiv.org/content/10.1101/2021.08.16.456517v1
  43. www.biorxiv.org www.biorxiv.org
    Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults
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    biorxiv.org/content/10.1101/2021.03.12.435204v2
  44. www.biorxiv.org www.biorxiv.org
    Critical Assessment of Metagenome Interpretation - the second round of challenges
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    biorxiv.org/content/10.1101/2021.07.12.451567v1
  45. www.biorxiv.org www.biorxiv.org
    New submission 11/09/2023, 11:48:00
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    biorxiv.org/content/10.1101/2022.02.16.480740v1