An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

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Items 301–400 of 455

1. In Vivo Expression of Chicken Gut Anaerobes Identifies Carbohydrate- or Amino Acid-Utilising, Motile or Type VI Secretion System-Expressing Bacteria
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2. Meanings, measurements, and musings on the significance of patterns in human microbiome variation
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3. Exact variance component tests for longitudinal microbiome studies
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4. Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes
   Zhemin Zhou, Nina Luhmann, Nabil-Fareed Alikhan, Christopher Quince, Mark Achtman · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
5. Systematic dissection of a complex gut bacterial community
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6. Validation of Core and Whole-Genome Multi-Locus Sequence Typing Schemes for Shiga-Toxin-Producing E. coli (STEC) Outbreak Detection in a National Surveillance Network, PulseNet 2.0, USA
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7. Strains Colonizing Different Intestinal Sites within an Individual Are Derived from a Single Founder Population
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8. SNV-FEAST: microbial source tracking with single nucleotide variants
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9. A bacterial sensor taxonomy across earth ecosystems for machine learning applications
   Helen Park, Marcin P. Joachimiak, Sean P. Jungbluth, Ziming Yang, William J. Riehl, Richard Shane Canon, Adam P. Arkin, Paramvir Dehal · 2023 · mSystems
10. kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes
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11. Intraspecies associations from strain-rich metagenome samples
    Evan B. Qu, Jacob S. Baker, Laura Markey, Veda D. Khadka, Christopher P. Mancuso, Arielle D. Tripp, Tami D. Lieberman · 2025 · Cell Reports
12. Metagenomic sequencing reveals altered gut microbiota of sojourners at high altitude: a longitudinal study
    Brij Bhushan, Malleswara Rao Eslavath, A. P. Yadav, Ashish Kumar Srivastava, M. Prasanna Kumar Reddy, Tsering Norboo, Bhuvnesh Kumar, Shailza Singh, Lilly Ganju · 2021 · Journal of Proteins and Proteomics
13. Amplicon Sequencing of Single-Copy Protein-Coding Genes Reveals Accurate Diversity for Sequence-Discrete Microbiome Populations
    Chengfeng Yang, Qinzhi Su, Min Tang, Shiqi Luo, Hao Zheng, Xue Zhang, Xin Yu Zhou · 2022 · Microbiology Spectrum
14. CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection
    Lingdi Zhang, Jahan A. Rahman, Matthew C. Chung, Lauren P. Lashua, Aubree L. Gordon, Ángel Balmaseda, Guillermina M. Kuan, Richard Bonneau, Elodie Ghedin · 2023 · Microbiome
15. An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data
    Boyan Zhou, Chan Wang, Gregory Putzel, Jiyuan Hu, Menghan Liu, Fen Wu, Yu Chen, Alejandro Pironti, Huilin Li · 2024 · Microbiology Spectrum
16. Genetic Diversity and Anatoxin Profiles of Freshwater Benthic Cyanobacteria From Nova Scotia (Canada)
    Cecilio Valadez‐Cano, Nicolas Tromas, Adrián Reyes‐Prieto, Lindsay Johnston, Yannan Huang, Hannah Morris, Lydia Zamlynny, Daniel G. Beach, Rob Jamieson, Janice E. Lawrence · 2025 · Environmental Microbiology
17. Dysbiosis of Oral Microbiota and Its Effect on Epithelial-Mesenchymal Transition: a Review
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18. On a Non-Discrete Concept of Prokaryotic Species
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19. Panoramic Insights into Microevolution and Macroevolution of a Prevotella Copri -Containing Lineage in Primate Guts
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20. Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data
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21. A diet-dependent enzyme from the human gut microbiome promotes Th17 cell accumulation and colitis
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22. SynTracker: a synteny based tool for tracking microbial strains
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23. Development of colorectal cancer detection and prediction based on gut microbiome big-data
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24. Aerosol-based exposure to opportunistic pathogens originating from hospital sink drains
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25. Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population
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26. Genetic diversity and antimicrobial resistance of clinical Klebsiella pneumoniae isolates: An ISSR-PCR analysis
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27. Prolonged Streptococcus gallolyticus subsp. pasteurianus gut colonization in healthcare workers and potential transmission role in neonatal sepsis
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28. The effect of host admixture on wild house mouse gut microbiota is weak when accounting for spatial autocorrelation
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29. Integrating phylogenetic and functional data in microbiome studies
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30. Comparative Metagenomics
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31. Low Intrahost and Interhost Genetic Diversity of Carnivore Protoparvovirus 1 in Domestic Cats during a Feline Panleukopenia Outbreak
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32. MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun meta-genomic data
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33. Implicating or exonerating the gut microbiome in blood-borne infection
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34. The Tempo and Mode of Adaptation in a Complex Natural Population: the Microbiome
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35. Quantitative insights into the efficacy of genome-resolved surveys of microbial communities through ribosomal protein phylogeography and EcoPhylo
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36. The planktonic microbiome of the Great Barrier Reef
    Steven J. Robbins, Marko Terzin, Katherine E. Dougan, Julian Zaugg, Sara C. Bell, Patrick W. Laffy, Joan Pamela Engelberts, Kim‐Anh Lê Cao, Renee K. Gruber, Nicole S. Webster et al. · 2026 · Nature
37. Prevalence, Risk Factors, and Human Health Implications of Salmonella enterica and Campylobacter spp. in Vermont Backyard Poultry
    Chelsey A. Patch, Katalin M. Larsen, Cheryl M. Armstrong, Siddhartha Kanrar, A Michaelides, P. Chakraborty, Kelcey Harper, Valarie Devlin, L. Michele Martin, Alia Lunna et al. · 2025 · Zoonoses and Public Health
38. Microbiome establishment and maturation: early life environmental factors
    Alyson L. Yee, Promi Das, Mariana C. Salas Garcia, Mary M. Buschmann, Jack A. Gilbert · 2020 · Elsevier eBooks
39. Divergence of gut bacteria through the selection of genomic variants implicated in the metabolism of sugars, amino acids, and purines by small extracellular vesicles in milk
    Fang Zhou, Peerzada Tajamul Mumtaz, Haluk Dogan, Roland Madadjim, Juan Cui, Janos Zempleni · 2025 · Gut Microbes
40. Multimodal metagenomic analysis reveals microbial InDels as superior biomarkers for pediatric Crohn’s disease
    Mengping Shen, Sheng Gao, Ruixin Zhu, Wei J. Wang, Wenxing Gao, Liwen Tao, Wanning Chen, Xinyue Zhu, Yuwei Yang, Tingjun Xu et al. · 2025 · Journal of Crohn s and Colitis
41. Metagenomic Strain-Typing Combined with Isolate Sequencing Provides Increased Resolution of the Genetic Diversity of Campylobacter jejuni Carriage in Wild Birds
    Malte Herold, Louise Hock, Christian Penny, Cécile Walczak, Fatu Djabi, Henry‐Michel Cauchie, Catherine Ragimbeau · 2023 · Microorganisms
42. Pangenomics of plant growth-promoting microorganisms for gene variations and environmental response
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43. Uniform bacterial genetic diversity along the gut
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44. Sepia, a taxonomy oriented read classifier in Rust
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45. Progress and Challenges in Studying the Ecophysiology of Archaea
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46. Strain-resolved metagenomic analysis of the premature infant microbiome and other natural microbial communities
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47. Rapid Mycobacterium tuberculosis spoligotyping from uncorrected long reads using Galru
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48. Target-enriched sequencing enables genomic characterization within diverse microbial populations – a preprint
    Enrique Doster, Lee J. Pinnell, Cory A. Wolfe, Noelle Robertson Noyes, Robert J. Valeris-Chacin, William B. Crosby, Michael L. Clawson, Amelia R. Woolums, Paul S. Morley · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
49. Experimental systems are essential for strengthening ecological modeling of microbiomes beyond observational data
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50. Application of Whole‐Genome Sequencing and Metagenomic Sequencing in Microbial Analysis of Milk Powder and Its Processing Environment: Current Findings and Challenges
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51. Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro
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52. SMS: A Novel Approach for Bacterial Strain Analysis in Multiple Samples
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53. Vive la Persistence: Engineering Human Microbiomes in the 21st Century
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54. phylogenize : correcting for phylogeny reveals genes associated with microbial distributions
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55. Genome-Enabled Molecular Subtyping and Serotyping for Shiga Toxin-Producing Escherichia coli
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56. The perfect condition for the rising of superbugs: person-to-person contagion and antibiotic use are the key factors responsible for the positive correlation between antibiotic resistance gene diversity and virulence gene diversity in human metagenomes
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57. Extensive inheritance of gut microbial communities in a superorganismal termite
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58. Bioinformatic methods for genome-centric metagenomics
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59. Community coalescence reveals strong selection and coexistence within species in complex microbial communities
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60. Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrābād, Iran
    Conor Rossi, Gabriela Ruß-Popa, Valeria Mattiangeli, Fionnuala McDaid, Andrew J. Hare, Hossein Davoudi, Haeedeh Laleh, Zahra Lorzadeh, Roya Khazaeli, Homa Fathi et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
61. Comparison between Ribosomal Assembly and Machine Learning Tools for Microbial Identification of Organisms with Different Characteristics
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62. Spatial Distribution of Microbes in the Apartment Transition Spaces and Exposure Risks Along Resident Flow Paths
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63. SourceApp: A Novel Metagenomic Source Tracking Tool that can Distinguish between Fecal Microbiomes Using Genome-To-Source Associations Benchmarked Against Mixed Input Spike-In Mesocosms
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64. Applicability of synthetic communities of the infant gut microbiota to understand microbial dynamics in an interchanging glycan landscape
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65. Gut microbiome–mediated bioactive ingredients and health benefits of medicinal and edible fermented products: A comprehensive review
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66. Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling
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67. Interaction Between Climatic Variation and Pathogen Diversity Shape Endemic Disease Dynamics in the Agricultural Settings
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68. How the social lives of bacteria affect their pangenome
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69. Recombination shapes the dynamics of selective constraint in global populations of human gut bacteria
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70. Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables
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71. Microsynteny is a powerful front for microbial strain tracking
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72. Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses
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73. Metagenomic Approaches Highlight the Organization and Dynamics of Plankton at the Species Level
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74. High-resolution sweep metagenomics using fast probabilistic inference
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75. Development of anaerobic culturing methods to study the evolution and of the human intestinal microbiota
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76. Author response: SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations
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77. It takes a village : Exploring the effect of antibiotics and other modulators on raising the infant gut microbiota
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78. Longitudinal dynamics of ethanol-resistant microbes and sporulation in the human gut
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79. ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics
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80. Mining the Microbiome for Drug Targets
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81. The development of early life gut microbiota in health and allergic disease
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82. Taxonomic Classification at the Strain Level using a Species-of-Interest $\boldsymbol{k}$-mer Database
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83. Reconstruction of Bacterial Strain Genomes from Shotgun Metagenomic Reads
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84. Intestinal microbiota assembly and dynamics in health and disease
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85. Геномика древних патогенов: первые успехи и перспективы
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86. Faculty Opinions recommendation of Precision identification of diverse bloodstream pathogens in the gut microbiome.
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87. Avian Pathogens: Editorial and the Perspectives of Research
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88. A microbiome record for life
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89. Faculty Opinions recommendation of Selective maternal seeding and environment shape the human gut microbiome.
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90. Faculty Opinions recommendation of Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth.
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91. Faculty Opinions recommendation of Discordant transmission of bacteria and viruses from mothers to babies at birth.
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92. Faculty Opinions recommendation of Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.
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93. Faculty Opinions recommendation of New insights from uncultivated genomes of the global human gut microbiome.
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94. Extensive inheritance of gut microbial communities in a superorganismal termite
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95. Editor's evaluation: Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome
    Sara Mitri · 2022 · eLife
96. Decision letter: SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations
    2022 · eLife
97. Additional file 2 of CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection
    Lingdi Zhang, Jahan A. Rahman, Matthew C. Chung, Lauren P. Lashua, Aubree L. Gordon, Ángel Balmaseda, Guillermina M. Kuan, Richard Bonneau, Elodie Ghedin · 2023 · Figshare
98. Additional file 6 of Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts
    Yujie Meng, Shuang Li, Chong Zhang, Hao Zheng · 2022 · Figshare
99. Additional file 5 of Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts
    Yujie Meng, Shuang Li, Chong Zhang, Hao Zheng · 2022 · Figshare
100. Additional file 4 of Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts
     Yujie Meng, Shuang Li, Chong Zhang, Hao Zheng · 2022 · Figshare