Mobile genes in the human microbiome are structured from global to individual scales

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 26,312

Search and clustering orders of magnitude faster than BLAST

Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894

Prodigal: prokaryotic gene recognition and translation initiation site identification

Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,692

CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496

An obesity-associated gut microbiome with increased capacity for energy harvest

Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444

Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726

Human gut microbiome viewed across age and geography

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815

Postinfection Irritable Bowel Syndrome

Downs, I. A., Aroniadis, O. C., Kelly, L., & Brandt, L. J. (2017) · Journal of Clinical Gastroenterology · doi:10.1097/mcg.0000000000000924 · Cited by 56

The History of the Intestinal Microbiota and the Gut-Brain Axis

Lewandowska, Z., Figlerowicz, M., & Mazur‐Melewska, K. (2022) · Pathogens · doi:10.3390/pathogens11121540 · Cited by 65

Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome

Nelson, M. T., Wolter, D. J., Eng, A., Weiss, E. J., Vo, A. T., Brittnacher, M., Hayden, H. S., Ravishankar, S., Bautista, G. E., Ratjen, A., et al. (2020) · Thorax · doi:10.1136/thoraxjnl-2019-214187 · Cited by 51

Gut microbiome strain-sharing within isolated village social networks

Beghini, F., Pullman, J., Alexander, M., Shridhar, S. V., Prinster, D., Singh, A., Matute Juárez, R., Airoldi, E. M., Brito, I. L., & Christakis, N. A. (2025) · Nature · doi:10.1038/s41586-024-08222-1 · Cited by 51

Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype

Younginger, B. S., Mayba, O., Reeder, J., Nagarkar, D. R., Modrusan, Z. D., Albert, M. L., & Byrd, A. L. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.100920 · Cited by 48

Ecosystem services for human health in Oceania

McFarlane, R. A., Horwitz, P., Arabena, K., Capon, A. G., Jenkins, A., Jupiter, S. D., Negin, J., Parkes, M. W., & Saketa, S. (2019) · Ecosystem Services · doi:10.1016/j.ecoser.2019.100976 · Cited by 52

The persistence potential of transferable plasmids

Wang, T., & You, L. (2020) · Nature Communications · doi:10.1038/s41467-020-19368-7 · Cited by 47

Costs and benefits of provocation in bacterial warfare

González, D., Sabnis, A., Foster, K. R., & Mavridou, D. A. I. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1801028115 · Cited by 45

Culture-enriched human gut microbiomes reveal core and accessory resistance genes

Raymond, F., Boissinot, M., Ouameur, A. A., Déraspe, M., Plante, P.-L., Kpanou, S., Bérubé, È., Huletsky, A., Roy, P. H., Ouellette, M., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0669-7 · Cited by 44

Horizontal gene transfer enables programmable gene stability in synthetic microbiota

Wang, T., Weiss, A., Aqeel, A., Wu, F., Lopatkin, A. J., David, L. A., & You, L. (2022) · Nature Chemical Biology · doi:10.1038/s41589-022-01114-3 · Cited by 41

The rise of the opportunists: What are the drivers of the increase in infectious diseases caused by environmental and commensal bacteria?

Samsing, F., & Barnes, A. C. (2024) · Reviews in Aquaculture · doi:10.1111/raq.12922 · Cited by 44

Inflammatory Bowel Disease-Associated Gut Commensals Degrade Components of the Extracellular Matrix

Porras, A. M., Zhou, H., Shi, Q., Xiao, X., Bank, J. L. C., Longman, R., & Brito, I. (2022) · mBio · doi:10.1128/mbio.02201-22 · Cited by 39

Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem

You, L., Jin, H., Kwok, L., Lv, R., Zhao, Z., Bilige, M., Sun, Z., Liu, W., & Zhang, H. (2023) · 中国科学通报：英文版 · doi:10.1016/j.scib.2023.09.001 · Cited by 43

Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing

Chu, H. Y., Sprouffske, K., & Wagner, A. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1164-7 · Cited by 41

The internationalization of human microbiome research

Porras, A. M., & Brito, I. (2019) · Current Opinion in Microbiology · doi:10.1016/j.mib.2019.09.012 · Cited by 41

Deciphering mechanisms and implications of bacterial translocation in human health and disease

Jin, S., Wetzel, D., & Schirmer, M. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102147 · Cited by 39

Pathogen-specific antimicrobials engineered de novo through membrane-protein biomimicry

Simonson, A. W., Mongia, A., Aronson, M. R., Alumasa, J. N., Chan, D. C., Lawanprasert, A., Howe, M. D., Bolotsky, A., Mal, T. K., George, C., et al. (2021) · Nature Biomedical Engineering · doi:10.1038/s41551-020-00665-x · Cited by 39

Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes

Mahmud, B., Vargas, R. C., Sukhum, K. V., Patel, S., Liao, J., Hall, L. R., Kesaraju, A., Le, T., Kitchner, T., Kronholm, E., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01639-4 · Cited by 38

Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders

Manghi, P., Filosi, M., Zolfo, M., Casten, L. G., García-Valiente, A., Mattevi, S., Heidrich, V., Golzato, D., Perini, S., Thomas, A. M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53934-7 · Cited by 42

Microbial-driven genetic variation in holobionts

Zilber‐Rosenberg, I., & ROSENBERG, E. B. (2021) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuab022 · Cited by 38

Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes

Ravikrishnan, A., Wijaya, I., Png, E., Chng, K. R., Ho, E. X. P., Ng, A. H. Q., Naim, A. N. M., Gounot, J.-S., Guan, S. P., Lee, J. H., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52097-9 · Cited by 39

Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota

Hagbø, M. E. S., Ravi, A., Angell, I. L., Sunde, M., Ludvigsen, J., Diep, D. B., Foley, S. L., Vento, M., Collado, M. C., Pérez‐Martínez, G., et al. (2019) · Pediatric Research · doi:10.1038/s41390-019-0491-8 · Cited by 33

Global Genetic Cartography of Urban Metagenomes and Anti-Microbial ResistancePreprint

Danko, D., Bezdan, D., Afshinnekoo, E., Ahsanuddin, S., Bhattacharya, C., Butler, D., Chng, K. R., Donnellan, D., Hecht, J., Jackson, K., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/724526 · Cited by 32

A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota

Kirsch, J. M., Hryckowian, A. J., & Duerkop, B. A. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.03.005 · Cited by 32

The State of Systems Genetics in 2017

Baliga, N. S., Björkegren, J., Boeke, J. D., Boutros, M., Crawford, N. P. S., Dudley, A. M., Farber, C. R., Jones, A., Levey, A. I., Lusis, A. J., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2017.01.005 · Cited by 33

Molecular trafficking between bacteria determines the shape of gut microbial community

Boopathi, S., Liu, D., & Jia, A. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1959841 · Cited by 31

Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population

Manara, S., Selma-Royo, M., Huang, K. D., Asnicar, F., Armanini, F., Blanco-Miguez, A., Cumbo, F., Golzato, D., Manghi, P., Pinto, F., et al. (2023) · Current Biology · doi:10.1016/j.cub.2023.04.011 · Cited by 30

Unravelling plasmidome distribution and interaction with its hosting microbiome

Kav, A. B., Rozov, R., Bogumil, D. D., Sørensen, S. J., Hansen, L. H., Benhar, I., Halperin, E., Ron Shamir, A., & Mizrahi, I. (2019) · Environmental Microbiology · doi:10.1111/1462-2920.14813 · Cited by 30

Bacteria Are Smartphones and Mobile Genes Are Apps

Young, J. P. W. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2016.09.002 · Cited by 30

Latitude as a co‐driver of human gut microbial diversity?

Dikongué, E., & Ségurel, L. (2017) · BioEssays · doi:10.1002/bies.201600145 · Cited by 32

Profiling lateral gene transfer events in the human microbiome using WAAFLE

Hsu, T. Y., Nzabarushimana, É., Wong, D. H.-J., Luo, C., Beiko, R. G., Langille, M. G. I., Huttenhower, C., Nguyen, L. H., & Franzosa, E. A. (2025) · Nature Microbiology · doi:10.1038/s41564-024-01881-w · Cited by 39

Mobilome and Resistome Reconstruction from Genomes Belonging to Members of the Bifidobacterium Genus

Mancino, W., Lugli, G. A., van Sinderen, D., Ventura, M., & Turroni, F. (2019) · Microorganisms · doi:10.3390/microorganisms7120638 · Cited by 30

Segatella clades adopt distinct roles within a single individual’s gut

Xiao, X., Singh, A., Giometto, A., & Brito, I. (2024) · npj Biofilms and Microbiomes · doi:10.1038/s41522-024-00590-w · Cited by 38

Diverse functional genes harboured in extracellular vesicles from environmental and human microbiota

Zhu, L., Huang, H., Avellán‐Llaguno, R. D., Qin, Y., An, X., Su, J., Huang, Q., & Zhu, Y. (2022) · Journal of Extracellular Vesicles · doi:10.1002/jev2.12292 · Cited by 27

Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data

Lee, K., Kim, D., & Cha, C. (2021) · The Journal of Microbiology · doi:10.1007/s12275-021-0652-4 · Cited by 26

Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome

Kuthyar, S., & Reese, A. T. (2021) · mSystems · doi:10.1128/msystems.00567-21 · Cited by 28

The intricate connection between diet, microbiota, and cancer: A jigsaw puzzle

Arkan, M. C. (2017) · Seminars in Immunology · doi:10.1016/j.smim.2017.08.009 · Cited by 25

Black Queen Evolution and Trophic Interactions Determine Plasmid Survival after the Disruption of the Conjugation Network

Cairns, J., Koskinen, K., Penttinen, R. K., Patinen, T., Hartikainen, A., Jokela, R., Ruusulehto, L., Viitamäki, S., Mattila, S., Hiltunen, T., et al. (2018) · mSystems · doi:10.1128/msystems.00104-18 · Cited by 25

A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont

Sheahan, M. L., Flores, K., Coyne, M. J., García-Bayona, L., Chatzidaki‐Livanis, M., Holst, A. Q., Smith, R. C., Sundararajan, A., Barquera, B., & Comstock, L. E. (2024) · Science · doi:10.1126/science.adj9504 · Cited by 34

Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control

Bichat, A., Plassais, J., Ambroise, C., & Mariadassou, M. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00649 · Cited by 22

Distinct increase in antimicrobial resistance genes among Vibrio parahaemolyticus in recent decades worldwide

Fang, G.-Y., Liu, X., Mu, X.-J., Huang, B.-W., & Jiang, Y. (2023) · Chemosphere · doi:10.1016/j.chemosphere.2023.139905 · Cited by 23

Transmission and control strategies of antimicrobial resistance from the environment to the clinic: A holistic review

Yuan, S., Jin, G., Cui, R., Wang, X., Wang, M., & Chen, Z. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.177461 · Cited by 22

Physical Activity Shapes the Intestinal Microbiome and Immunity of Healthy Mice but Has No Protective Effects against Colitis in MUC2 −/− Mice

Estaki, M., Morck, D. W., Ghosh, S., Quin, C., Pither, J., Barnett, J. A., Gill, S. K., & Gibson, D. L. (2020) · mSystems · doi:10.1128/msystems.00515-20 · Cited by 22

Noncontact Multiphysics Probe for Spatiotemporal Resolved Single‐Cell Manipulation and Analyses

Brimmo, A. T., Menachery, A., Sukumar, P., & Qasaimeh, M. A. (2021) · Small · doi:10.1002/smll.202100801 · Cited by 22

Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes

Tso, L., Bonham, K. S., Fishbein, A., Rowland, S., & Klepac‐Ceraj, V. (2021) · Nutrients · doi:10.3390/nu13082833 · Cited by 20

A Modern-World View of Host–Microbiota–Pathogen Interactions

Tan, C. Y., Ramirez, Z. E., & Surana, N. K. (2021) · The Journal of Immunology · doi:10.4049/jimmunol.2100215 · Cited by 24

Genomic Mutations Within the Host Microbiome: Adaptive Evolution or Purifying Selection

Zhang, J., & Knight, R. D. (2022) · Engineering · doi:10.1016/j.eng.2021.11.018 · Cited by 21

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut MicrobesPreprint

Merrill, B. D., Carter, M. M., Olm, M. R., Dahan, D., Tripathi, S. M., Spencer, S. P., Yu, F. B., Jain, S., Neff, N. F., Jha, A. R., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.30.486478 · Cited by 20

Recoding the metagenome: microbiome engineering in situ

Whitfill, T. M., & Oh, J. (2019) · Current Opinion in Microbiology · doi:10.1016/j.mib.2019.09.005 · Cited by 18

Combining metagenomics and metatranscriptomics to study human, animal and environmental resistomes

Wang, Y., Hu, Y., & Gao, G. F. (2020) · Medicine in Microecology · doi:10.1016/j.medmic.2020.100014 · Cited by 20

Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking

Ogilvie, L. A., Nzakizwanayo, J., Guppy, F. M., Dedi, C., Diston, D., Taylor, H. D., Ebdon, J., & Jones, B. V. (2017) · The ISME Journal · doi:10.1038/s41396-017-0015-7 · Cited by 17

Ferric Chloride Further Simplified the Horizontal Gene Transfer Network of Antibiotic Resistance Genes in Anaerobic Digestion

Zhang, J., Lu, T., Xin, Y., & Wei, Y. (2022) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2022.157054 · Cited by 17

Peering into the Genetic Makeup of Natural Microbial Populations Using Metagenomics

Denef, V. J. (2018) · Population genomics · doi:10.1007/13836_2018_14 · Cited by 16

Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults

Rashidi, A., Gem, H., McLean, J. S., Kerns, K. A., Dean, D. R., Dey, N., & Minot, S. S. (2024) · Scientific Data · doi:10.1038/s41597-024-02916-x · Cited by 16

Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer

Peng, H., Andreu‐Sánchez, S., Ruiz-Moreno, A. J., Fernández-Pato, A., Wu, J., Gaćeša, R., Zhernakova, A., Wang, D., & Fu, J. (2025) · Nature Communications · doi:10.1038/s41467-025-66612-z · Cited by 20

Expanding germ-organ theory: Understanding non-communicable diseases through enterobacterial translocation

Boopathi, S., Priya, P. S., Haridevamuthu, B., Nayak, S. P. R. R., Chandrasekar, M., Arockiaraj, J., & Jia, A. (2023) · Pharmacological Research · doi:10.1016/j.phrs.2023.106856 · Cited by 17

Comprehensive analysis of mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene poolsPreprint

Jiang, X., Hall, A. B., Xavier, R. J., & Alm, E. J. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/214213 · Cited by 15

High conservation of the dental plaque microbiome across populations with differing subsistence strategies and levels of market integration

Velsko, I. M., Gallois, S., Stahl, R., Henry, A. G., & Warinner, C. (2023) · Molecular Ecology · doi:10.1111/mec.16988 · Cited by 13

Causal effects of gut microbiota on scoliosis: A bidirectional two-sample mendelian randomization study

Lai, B.-W., Jiang, H., Gao, Y., & Zhou, X. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e21654 · Cited by 14

Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices

Huang, K. D., Amend, L., Gálvez, E. J. C., Lesker, T.-R., de Oliveira, R., Bielecka, A., Blanco‐Míguez, A., Valles‐Colomer, M., Ruf, I., Pasolli, E., et al. (2024) · Cell Reports Medicine · doi:10.1016/j.xcrm.2024.101426 · Cited by 16

Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome

Wang, S., Jiang, Y., Che, L., Wang, R. H., & Li, S. C. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae515 · Cited by 15

Gene-specific selective sweeps are pervasive across human gut microbiomes

Wolff, R., & Garud, N. R. (2025) · Nature · doi:10.1038/s41586-025-09798-y · Cited by 28

Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities

Weiss, A., Wang, T., & You, L. (2023) · Cell Systems · doi:10.1016/j.cels.2023.09.002 · Cited by 13

Prevotella copri variants among a single host diverge in sphingolipid production

Xiao, X., Le, H. H., Lee, M.-T., Lamm, D., Johnson, E. L., & Brito, I. (2024) · mBio · doi:10.1128/mbio.02409-23 · Cited by 13

The genetic and ecological landscape of plasmids in the human gutPreprint

Yu, M., Fogarty, E. C., & Eren, A. M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.01.361691 · Cited by 13

Streptococcus abundance and oral site tropism in humans and non-human primates reflects host and lifestyle differences

Velsko, I. M., & Warinner, C. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-024-00642-1 · Cited by 12

Discovery of a widespread chemical signalling pathway in the Bacteroidota

Linares-Otoya, L., Shirkey, J. D., Chhetri, B. K., Mira, A., Biswas, A. G., Neff, S. L., Linares-Otoya, M. V., Ye, C., Florián, J. C., Ganoza-Yupanqui, M. L., et al. (2025) · Nature · doi:10.1038/s41586-025-09418-9 · Cited by 11

Global dissemination of the beta-lactam resistance gene blaTEM-1 among pathogenic bacteria

Farooq, A., Rafique, A., Han, E., & Park, S.-M. (2025) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2025.178521 · Cited by 15

Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis

Peng, H., & Fu, J. (2025) · National Science Review · doi:10.1093/nsr/nwaf128 · Cited by 11

A longitudinal study of dominant E. coli lineages and antimicrobial resistance in the gut of children living in an upper middle-income country

Calderón, D., Cárdenas, P., Prado-Vivar, B., Graham, J. P., & Trueba, G. A. (2022) · Journal of Global Antimicrobial Resistance · doi:10.1016/j.jgar.2022.03.002 · Cited by 11

Exercise and microbiome: From big data to therapy

Meng, D., Ai, S., Spanos, M., Shi, X., Li, G., Crețoiu, D., Zhou, Q., & Xiao, J. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.10.034 · Cited by 12

Application of Metagenomics to Chilean Aquaculture

Tello, M., Valdés, N., Vargas, R. A., Rojas, J., Parra, M., Gajardo, G., & González, A. (2019) · IntechOpen eBooks · doi:10.5772/intechopen.86302 · Cited by 11

Profiling novel lateral gene transfer events in the human microbiomePreprint

Hsu, T. Y., Nzabarushimana, É., Wong, D. H.-J., Luo, C., Beiko, R. G., Langille, M. G. I., Huttenhower, C., Nguyen, L. H., & Franzosa, E. A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.08.552500 · Cited by 11

Gut metagenome profile of the Nunavik Inuit youth is distinct from industrial and non-industrial counterparts

Abed, J. Y., Godon, T., Mehdaoui, F., Plante, P.-L., Boissinot, M., Bergeron, M. G., Bélanger, R. E., Muckle, G., Poliakova, N., Ayotte, P., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-04372-y · Cited by 11

Using the microbiota to study connectivity at human–animal interfaces

Muloi, D. M., Caron, A., Berkley, J. A., Hassell, J. M., Brito, I., King, K. C., Moodley, A., & Fèvre, E. M. (2025) · Trends in Microbiology · doi:10.1016/j.tim.2025.05.006 · Cited by 12

Toxin-linked mobile genetic elements in major enteric bacterial pathogens

Panwar, S., Kumari, S., Verma, J., Bakshi, S., Narendrakumar, L., Paul, D., & Das, B. (2023) · Gut Microbiome · doi:10.1017/gmb.2023.2 · Cited by 10

Mobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than Host-Specific Selective Pressures

N’Guessan, A., Brito, I., Serohijos, A. W. R., & Shapiro, B. J. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab142 · Cited by 11

A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits

Conteville, L. C., & Vicente, A. C. P. (2022) · Scientific Reports · doi:10.1038/s41598-022-16392-z · Cited by 11

Closest relatives of poxviruses replicate in the digestive system of humans and animals worldwidePreprint

Gaïa, M., Guyet, U., Ruscheweyh, H., Eren, A. M., Sunagawa, S., Koonin, E. V., Krupovìč, M., & Delmont, T. O. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.23.586382 · Cited by 10

Detecting horizontal gene transfer with metagenomics co-barcoding sequencing

Han, K., Li, J., Yang, D., Zhuang, Q., Zeng, H., Rong, C., Yue, J., Li, N., Gu, C., Chen, L., et al. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.03602-23 · Cited by 9

Decade-long warming accelerates antibiotic resistance in grassland soils

Wu, L. L., Mu, D.-S., An, J., Wang, Y., Fan, X., Lu, D., Zhang, Y., Xie, Y., Michael, J., Curtis, D., et al. (2026) · Nature · doi:10.1038/s41586-026-10413-x · Cited by 9

Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila

Wang, Y., Baumdicker, F., Schweiger, P., Küenzel, S., & Staubach, F. (2021) · BMC Biology · doi:10.1186/s12915-021-01124-y · Cited by 9

G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data

Rampelli, S., Fabbrini, M., Candela, M., Biagi, E., Brigidi, P., & Turroni, S. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.644516 · Cited by 10

Intraindividual Variation and Personal Specificity of Salivary Microbiota

Zhu, C., Yuan, C., Wei, F., Sun, X., & Zheng, S. (2020) · Journal of Dental Research · doi:10.1177/0022034520917155 · Cited by 8

Gastrointestinal Manifestations of Coronavirus Disease 2019 Across the United States: A Multicenter Cohort Study

Patel, A., Sanders, T. K., Prakash, P., Law, J., Alvencar, S., Choi, A. Y., Shah, J., Patel, K., Srivoleti, P. D., Chauhan, K., et al. (2022) · Gastro Hep Advances · doi:10.1016/j.gastha.2022.07.002 · Cited by 8

Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals

Kırdök, E., Kashuba, N., Damlien, H., Manninen, M. A., Nordqvist, B., Kjellström, A., Jakobsson, M., Lindberg, A. M., Storå, J., Persson, P., et al. (2024) · Scientific Reports · doi:10.1038/s41598-023-48762-6 · Cited by 10

A ubiquitous mobile genetic element disarms a bacterial antagonist of the gut microbiotaPreprint

Sheahan, M. L., Coyne, M. J., Flores, K., García-Bayona, L., Chatzidaki‐Livanis, M., Sundararajan, A., Holst, A. Q., Barquera, B., & Comstock, L. E. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.25.553775 · Cited by 8

Pervasive selective sweeps across human gut microbiomesPreprint

Wolff, R., & Garud, N. R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.22.573162 · Cited by 8

Emergence of alternative stable states in microbial communities undergoing horizontal gene transferPreprint

Hong, J., Xue, W., & Wang, T. (2024) · eLife · doi:10.7554/elife.99593 · Cited by 9

The role of the gut microbiota and its metabolites: a new predictor in diabetes and its complications

Wu, K., Yang, X. F., Zhang, T., Bai, Y., & Yan, M. (2025) · European journal of medical research · doi:10.1186/s40001-025-02824-9 · Cited by 11

Lessons from the model gut Bacteroidales Bacteroides fragilis and Bacteroides thetaiotaomicron and future opportunities

Comstock, L. E. (2025) · Journal of Bacteriology · doi:10.1128/jb.00346-25 · Cited by 8

Meanings, measurements, and musings on the significance of patterns in human microbiome variation

Schnorr, S. L. (2018) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2018.06.014 · Cited by 8

Segatella copri strains adopt distinct roles within a single individual's gutPreprint

Xiao, X., Singh, A., Giometto, A., & Brito, I. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.20.595015 · Cited by 7

Mobile genetic elements that shape microbial diversity and functions in thawing permafrost soilsPreprint

Guo, J., Aroney, S. T. N., Domínguez‐Huerta, G., Smith, D. A., Vik, D. R., Owusu-Ansah, C., Pratama, A. A., Solonenko, S. A., Tian, F., Howard‐Varona, C., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.12.637893 · Cited by 7

Harnessing gut microbial communities to unravel microbiome functions

Giri, S., Shi, H., Typas, A., & Huang, K. C. (2025) · Current Opinion in Microbiology · doi:10.1016/j.mib.2024.102578 · Cited by 9

Predicting plasmid persistence in microbial communities by coarse‐grained modeling

Wang, T., Weiss, A., Ha, Y., & You, L. (2021) · BioEssays · doi:10.1002/bies.202100084 · Cited by 6

A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbationsPreprint

García-Bayona, L., Said, N., Coyne, M. J., Flores, K., Elmekki, N. M., Sheahan, M. L., Gutiérrez-Camacho, A., Hutt, K., Yildiz, F. H., Kovács, Á. T., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.29.590671 · Cited by 5

The ecology of horizontal gene transfer

Etten, J. V., & Johnson, M. D. (2026) · Trends in Genetics · doi:10.1016/j.tig.2026.02.002 · Cited by 5

Evolution of Holobionts: The Hologenome Concept

ROSENBERG, E. B. (2021) · The microbiomes of humans, animals, plants, and the environment · doi:10.1007/978-3-030-65317-0_9 · Cited by 6

Bacterial plasmid-associated and chromosomal proteins have fundamentally different properties in protein interaction networks

Downing, T., & Rahm, A. D. (2022) · Scientific Reports · doi:10.1038/s41598-022-20809-0 · Cited by 5

Microbial mobilomes differ between societies

Attar, N. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.117

Mobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than Host-Specific Selective Pressures

N’Guessan, A., Brito, I., Serohijos, A. W. R., & Shapiro, B. J. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab142 · Cited by 11

The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem

Schubert, K., Shosanya, T., & García-Bayona, L. (2025) · Current Opinion in Microbiology · doi:10.1016/j.mib.2025.102675 · Cited by 5

The global human gut microbiome: genes, lifestyles, and diet

Parizadeh, M., & Arrieta, M. (2023) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2023.07.002 · Cited by 205

Probing the Mobilome: Discoveries in the Dynamic Microbiome

Carr, V. R., Shkoporov, A. N., Hill, C., Mullany, P. P., & Moyes, D. L. (2020) · Trends in Microbiology · doi:10.1016/j.tim.2020.05.003 · Cited by 86