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

Cited by (455)

Items 401–455 of 455

1. Additional file 3 of Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome
   Shi Wei Huang, Shuaiming Jiang, Dongxue Huo, Celeste Allaband, Mehrbod Estaki, Victor Cantu, Pedro Belda‐Ferre, Yoshiki Vázquez‐Baeza, Qiyun Zhu, Chenchen Ma et al. · 2021 · Figshare
2. Additional file 2 of Strain-level analysis reveals the vertical microbial transmission during the life cycle of bumblebee
   Qinzhi Su, Wang, Qinglin, Xiaohuan Mu, Chen, Hao, Yujie Meng, Xue Zhang, Zheng Li, Hu, Xiaosong, Yifan Zhai, Hao Zheng · 2021 · Figshare
3. Additional file 1 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
4. Microbiome in multiple sclerosis
   Sergio E. Baranzini · 2024 · Elsevier eBooks
5. stana: an R package for metagenotyping analysis and interactive application based on clinical data
   Noriaki Sato, Kotoe Katayama, Daichi Miyaoka, Miho Uematsu, Ayumu Saito, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto · 2025 · NAR Genomics and Bioinformatics
6. More questions than answers? Predicting faecal microbiota transplantation outcomes for recurrent Clostridioides difficile infection
   Georgiana-Emmanuela Gîlcă-Blanariu, Sepideh Pakpour, Dina H. Kao · 2025 · Clinical Microbiology and Infection
7. Pipelines and Databases—Microbiome Analysis
   Jonathan Sanders, Lin Huang, Qiyun Zhu, James T. Morton · 2025 · Wiley eBooks
8. Association Between Ocular Microbiomes of Children and Their Siblings and Parents
   Xiangtian Ling, Yuzhou Zhang, Christine H. T. Bui, Hei-Nga Chan, Pancy O. S. Tam, Peng Yu, Xiu Juan Zhang, Charlene C. Yim, Ka Wai Kam, Wai Kit Chu et al. · 2025 · Investigative Ophthalmology & Visual Science
9. Additional file 2 of In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision
   Jonathan L. Golob, Samuel S. Minot · 2020 · Figshare
10. Additional file 3 of Strain-level analysis reveals the vertical microbial transmission during the life cycle of bumblebee
    Qinzhi Su, Wang, Qinglin, Xiaohuan Mu, Chen, Hao, Meng, Yujie, Zhang, Xue, Zheng, Li, Hu, Xiaosong, Yifan Zhai, Zheng, Hao · 2021 · Figshare
11. Additional file 20 of Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
    Olga M. Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Moreno, Elisa, Alessandra Giani, Laísa Corrêa Braga Marques, Nathalie Y. Fortin, B. Jesse Shapiro · 2021 · Figshare
12. Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrābād, Iran
    Conor Rossi, Ruß-Popa, Gabriela, Valeria Mattiangeli, McDaid, Fionnuala, Andrew J. Hare, Hossein Davoudi, Laleh, Haeedeh, Lorzadeh, Zahra, Khazaeli, Roya, Fathi, Homa et al. · 2021 · Apollo (University of Cambridge)
13. Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrābād, Iran.
    Rossi, Conor, Ruß-Popa, Gabriela, Mattiangeli, Valeria, McDaid, Fionnuala, Hare, Andrew J, Davoudi, Hossein, Laleh, Haeedeh, Lorzadeh, Zahra, Khazaeli, Roya, Fathi, Homa et al. · 2021 · Apollo (University of Cambridge)
14. Additional file 2 of Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome
    Huang, Shi, Shuaiming Jiang, Dongxue Huo, Celeste Allaband, Mehrbod Estaki, Victor Cantu, Pedro Belda‐Ferre, Vázquez-Baeza, Yoshiki, Qiyun Zhu, Ma, Chenchen et al. · 2021 · Figshare
15. Additional file 3 of Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis
    Meng, Yujie, Xue Zhang, Yifan Zhai, Li, Yuan, Zenghua Shao, Liu, Shanshan, Zhang, Chong, Xing, Xin-Hui, Zheng, Hao · 2024 · Figshare
16. Additional file 7 of Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
    Utter, Daniel R., Gary G. Borisy, Eren, A. Murat, Colleen M. Cavanaugh, Mark Welch, Jessica L. · 2020 · Figshare
17. Additional file 1 of StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
    Lucas R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber, Christine Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson et al. · 2022 · Figshare
18. Additional file 1 of High-resolution strain-level microbiome composition analysis from short reads
    Liao, Herui, Yongxin Ji, Sun, Yanni · 2023 · Figshare
19. Additional file 1 of Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis
    Meng, Yujie, Xue Zhang, Yifan Zhai, Li, Yuan, Zenghua Shao, Liu, Shanshan, Zhang, Chong, Xing, Xin-Hui, Zheng, Hao · 2024 · Figshare
20. Additional file 3 of Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle
    Browne, Hilary P., Alexandre Almeida, Kumar, Nitin, Kévin Vervier, Anne Adoum, Viciani, Elisa, Nicholas J. R. Dawson, Forster, Samuel C., Claire Cormie, Goulding, David et al. · 2021 · Figshare
21. Additional file 1 of Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts
    Meng, Yujie, Li, Shuang, Zhang, Chong, Zheng, Hao · 2022 · Figshare
22. Additional file 1 of Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle
    Claire N. Freeman, Emily K. Herman, Jennifer N Abi Younes, Dana E. Ramsay, Nathan Erickson, Stothard, Paul, Links, Matthew G., Simon J. G. Otto, Cheryl Waldner · 2022 · Figshare
23. Additional file 13 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
    Alon Shaiber, Amy D. Willis, Tom O. Delmont, Simon Roux, Chen, Lin-Xing, Abigail C. Schmid, Yousef, Mahmoud, Watson, Andrea R., Karen Lolans, Özcan C. Esen et al. · 2020 · Figshare
24. Additional file 8 of Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
    Utter, Daniel R., Gary G. Borisy, Eren, A. Murat, Colleen M. Cavanaugh, Mark Welch, Jessica L. · 2020 · Figshare
25. Additional file 8 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
    Alon Shaiber, Amy D. Willis, Tom O. Delmont, Simon Roux, Chen, Lin-Xing, Abigail C. Schmid, Yousef, Mahmoud, Watson, Andrea R., Karen Lolans, Özcan C. Esen et al. · 2020 · Figshare
26. Additional file 1 of Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium
    Sato, Yui, Juliane Wippler, Cecilia Wentrup, Rebecca Ansorge, Miriam Sadowski, Harald R. Gruber‐Vodicka, Nicole Dubilier, Manuel Kleiner · 2022 · Figshare
27. Additional file 4 of StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
    Lucas R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber, Christine Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson et al. · 2022 · Figshare
28. Additional file 2 of Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity
    Brown, C. Titus, Moritz, Dominik, Michael P. O’Brien, Felix Reidl, Reiter, Taylor, Blair D. Sullivan · 2020 · Figshare
29. Additional file 2 of Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis
    Meng, Yujie, Xue Zhang, Yifan Zhai, Li, Yuan, Zenghua Shao, Liu, Shanshan, Zhang, Chong, Xing, Xin-Hui, Zheng, Hao · 2024 · Figshare
30. Additional file 4 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
    Alon Shaiber, Amy D. Willis, Tom O. Delmont, Simon Roux, Chen, Lin-Xing, Abigail C. Schmid, Yousef, Mahmoud, Watson, Andrea R., Karen Lolans, Özcan C. Esen et al. · 2020 · Figshare
31. Additional file 1 of Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle
    Hilary P. Browne, Alexandre Almeida, Kumar, Nitin, Kévin Vervier, Anne Adoum, Viciani, Elisa, Nicholas J. R. Dawson, Forster, Samuel C., Claire Cormie, Goulding, David et al. · 2021 · Figshare
32. Additional file 2 of Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle
    Claire N. Freeman, Emily K. Herman, Jennifer N Abi Younes, Dana E. Ramsay, Nathan Erickson, Stothard, Paul, Links, Matthew G., Simon J. G. Otto, Cheryl Waldner · 2022 · Figshare
33. Additional file 1 of Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
    Utter, Daniel R., Gary G. Borisy, Eren, A. Murat, Colleen M. Cavanaugh, Mark Welch, Jessica L. · 2020 · Figshare
34. Additional file 1 of SNV-FEAST: microbial source tracking with single nucleotide variants
    Leah Briscoe, Halperin, Eran, Nandita R. Garud · 2024 · Figshare
35. Additional file 2 of Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
    Olga M. Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Moreno, Elisa, Alessandra Giani, Laísa Corrêa Braga Marques, Nathalie Y. Fortin, B. Jesse Shapiro · 2021 · Figshare
36. Additional file 1 of Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity
    Brown, C. Titus, Moritz, Dominik, Michael P. O’Brien, Felix Reidl, Reiter, Taylor, Blair D. Sullivan · 2020 · Figshare
37. Additional file 2 of SNV-FEAST: microbial source tracking with single nucleotide variants
    Leah Briscoe, Halperin, Eran, Nandita R. Garud · 2024 · Figshare
38. Additional file 5 of Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
    Olga M. Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laísa Corrêa Braga Marques, Nathalie Y. Fortin, B. Jesse Shapiro · 2021 · Figshare
39. Extensive recombination, selection, and asexual blooms shape the diversity of the dominant clade of Prochlorococcus
    Alana Papula, Gabriel Bîrzu, Daniel S. Fisher · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
40. Data Diversity and Sequence Length: Key Levers for Powerful Biological AI
    Liam Kozma, Adrienne Hoarfrost · 2026 · NATO science for peace and security series. A, Chemistry and biology
41. Salivary microbiome diversity is associated with oral health and disease
    David L Lin, Madisyn D Augustine, David M. Ojcius · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
42. Gut Microbiome as a Source and Propagator of Multidrug‐Resistance: Mechanisms and Therapeutic Strategies
    Meghana Shashikanth, D. B. M. Virupakshaiah · 2026 · Advanced Gut & Microbiome Research
43. Reconstitution de pan-génomes microbiens par séquençage métagénomique aléatoire : Application à l’étude du microbiote intestinal humain
    Florian Plaza Oñate · 2018
44. Étude des bases moléculaires de l’adaptation et de l’acclimatation aux changements environnementaux chez les picocyanobactéries marines, des organismes clés du phytoplancton
    Ulysse Guyet · 2020
45. Analyses de variations génomiques liées à la biogéographie des picoalgues Mamiellales
    Jade Leconte · 2020
46. Exploration du microbiote digestif humain par les approches de microscomics, culturomique et de metagenomiques
    Edmond Kuete Yimagou · 2020
47. Identification of key players in the gut microbiota based on a unified reference for a standardized quantitative metagenomics and metabolic analysis framework
    Marianne Borderes · 2021 · theses.fr (ABES)
48. PopMAG: a Nextflow pipeline for population genetics analysis based on metagenome-assembled genomes
    Daniel Sabogal-Rodriguez, Alejandro Caro‐Quintero · 2026 · Bioinformatics Advances
49. Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes
    Peter J. Laurin, Nandita R. Garud · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
50. Environmental monitoring for antimicrobial resistance in a metropolitan watershed
    David Holcomb, Molly E. Cantrell, Dorian J. Feistel, Michael Meyer, Jessica Sterling, Jessica C. Chen, Krittika Krishnan, Sung B. Im, Jason P. Folster, Justin Kim et al. · 2026 · Journal of Water and Health
51. Growth capacity and mortality burden shape microbial persistence under osmotic stress in Bacteroides thetaiotaomicron
    Hans Ghezzi, Ricky Wolff, Asmita Jain, Juan C. Burckhardt, Michael Hunter, Katharine M. Ng, Shaqed Carasso, Naama Geva‐Zatorsky, Nandita R. Garud, Carolina Tropini · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
52. Neurolinking the microbiome: The gut–bladder–vaginal axis in urogenital dysbiosis and precision therapeutics
    Saleem Ahmad, Muhammad Nauman Aftab, Muhammad Ghalib, Muhammad Shahbaz Alsam · 2026 · Gut Microbiome and Health
53. Genomically and ecologically cohesive subspecies as biologically meaningful units in the global ocean microbiome
    Lucas Paoli, Taylor Priest, Adrián Davín, Melanie L. Stäubli, Dominic Eriksson, Hans‐Joachim Ruscheweyh, Martin F. Polz, Shinichi Sunagawa · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
54. Shotgun metagenomics reveals the microbiome and resistome of water harvesting ponds used by Kenyan rural smallholders
    Benjamin H. Gregson, Alessia Bani, Laurel Steinfield, Diane Holt, Ecaterina Edith Vamos, Rowan Connell, Corinne B. Whitby, Robert Ferguson · 2026 · Environmental Microbiome
55. Strain resolution and wide relative abundance quantification of bacterial microbiomes with nanopore sequencing of the ribosomal RNA operon
    C.J. Woodruff, Terence Paul Speed · 2026 · bioRxiv (Cold Spring Harbor Laboratory)