On the Road to Strain-Resolved Comparative Metagenomics

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Li, D., Liu, C.-M., Luo, R., Sadakane, K., & Lam, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv033 · Cited by 10,133

metaSPAdes: a new versatile metagenomic assembler

Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496

Shotgun metagenomics, from sampling to analysis

Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

Scher, J. U., Sczesnak, A., Longman, R. S., Segata, N., Ubeda, C., Bielski, C., Rostron, T., Cerundolo, V., Pamer, E. G., Abramson, S. B., et al. (2013) · eLife · doi:10.7554/elife.01202 · Cited by 2,047

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

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Anvi’o: an advanced analysis and visualization platform for ‘omics data

Eren, A. M., Esen, Ö. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., & Delmont, T. O. (2015) · PeerJ · doi:10.7717/peerj.1319 · Cited by 1,869

Infection with Helicobacter pylori strains possessing cagA is associated with an increased risk of developing adenocarcinoma of the stomach.

Blaser, M. J., Perez-Perez, G. I., Kleanthous, H., Cover, T. L., Peek, R. M., Chyou, P.-H., Stemmermann, G. N., & Nomura, A. M. Y. (1995) · PubMed · Cited by 1,608

Epidemic Profile of Shiga-Toxin–Producing Escherichia coli O104:H4 Outbreak in Germany

Frank, C., Werber, D., Cramer, J. P., Askar, M., Faber, M., an der Heiden, M., Bernard, H., Fruth, A., Prager, R., Spode, A., et al. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1106483 · Cited by 1,139

Genomic variation landscape of the human gut microbiome

Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907

Microbiome definition re-visited: old concepts and new challenges

Berg, G., Rybakova, D., Fischer, D., Cernava, T., Vergès, M.-C. C., Charles, T., Chen, X., Cocolin, L., Eversole, K., Corral, G. H., et al. (2020) · Microbiome · doi:10.1186/s40168-020-00875-0 · Cited by 2,275

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

Ferretti, P., Pasolli, E., Tett, A., Asnicar, F., Gorfer, V., Fedi, S., Armanini, F., Truong, D. T., Manara, S., Zolfo, M., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.06.005 · Cited by 1,292

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

Thomas, A. M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0405-7 · Cited by 1,030

Host-microbiota interactions: from holobiont theory to analysis

Simon, J., Marchesi, J. R., Mougel, C., & Selosse, M. (2019) · Microbiome · doi:10.1186/s40168-019-0619-4 · Cited by 544

The person-to-person transmission landscape of the gut and oral microbiomes

Valles-Colomer, M., Blanco-Míguez, A., Manghi, P., Asnicar, F., Dubois, L., Golzato, D., Armanini, F., Cumbo, F., Huang, K. D., Manara, S., et al. (2023) · Nature · doi:10.1038/s41586-022-05620-1 · Cited by 449

Diversity within Species: Interpreting Strains in Microbiomes

Van Rossum, T., Ferretti, P., Maistrenko, O. M., & Bork, P. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0368-1 · Cited by 441

The Healthy Microbiome—What Is the Definition of a Healthy Gut Microbiome?

Shanahan, F., Ghosh, T. S., & O’Toole, P. W. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.09.057 · Cited by 383

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

Ianiro, G., Punčochář, M., Karcher, N., Porcari, S., Armanini, F., Asnicar, F., Beghini, F., Blanco-Míguez, A., Cumbo, F., Manghi, P., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01964-3 · Cited by 366

Critical Assessment of Metagenome Interpretation: the second round of challenges

Meyer, F., Fritz, A., Deng, Z.-L., Koslicki, D., Lesker, T. R., Gurevich, A. A., Robertson, G., Alser, M., Antipov, D., Beghini, F., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01431-4 · Cited by 394

A predictive index for health status using species-level gut microbiome profiling

Gupta, V. K., Kim, M., Bakshi, U., Cunningham, K. Y., Davis, J. M., Lazaridis, K. N., Nelson, H., Chia, N., & Sung, J. (2020) · Nature Communications · doi:10.1038/s41467-020-18476-8 · Cited by 338

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic

Porcari, S., Benech, N., Valles-Colomer, M., Segata, N., Gasbarrini, A., Cammarota, G., Sokol, H., & Ianiro, G. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.03.020 · Cited by 331

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

Pérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000409 · Cited by 314

Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity

Brown, E., Kenny, D. J., & Xavier, R. J. (2019) · Annual Review of Immunology · doi:10.1146/annurev-immunol-042718-041841 · Cited by 318

The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303

Metagenomics-enabled microbial surveillance

Ko, K. K. K., Chng, K. R., & Nagarajan, N. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01089-w · Cited by 287

A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina

Ma, B., France, M., Crabtree, J., Holm, J. B., Humphrys, M. S., Brotman, R. M., & Ravel, J. (2020) · Nature Communications · doi:10.1038/s41467-020-14677-3 · Cited by 170

Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin

Zhou, W. L., Spoto, M., Hardy, R., Guan, C., Fleming, E. S., Larson, P. J., Brown, J. S., & Oh, J. (2020) · Cell · doi:10.1016/j.cell.2020.01.006 · Cited by 169

Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice

Smith, B. J., Miller, R. A., & Schmidt, T. M. (2021) · mSphere · doi:10.1128/msphere.00851-21 · Cited by 158

Developing standards for the microbiome field

Amos, G. C. A., Logan, A., Anwar, S., Fritzsche, M., Mate, R., Bleazard, T., & Rijpkema, S. G. T. (2020) · Microbiome · doi:10.1186/s40168-020-00856-3 · Cited by 154

Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data

Anyansi, C., Straub, T. J., Manson, A. L., Earl, A. M., & Abeel, T. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01925 · Cited by 122

STRONG: metagenomics strain resolution on assembly graphs

Quince, C., Nurk, S., Raguideau, S., James, R., Soyer, O. S., Summers, J., Limasset, A., Eren, A. M., Chikhi, R., & Darling, A. (2021) · Genome Biology · doi:10.1186/s13059-021-02419-7 · Cited by 94

Metagenomics: a path to understanding the gut microbiome

Yen, S., & Johnson, J. S. (2021) · Mammalian Genome · doi:10.1007/s00335-021-09889-x · Cited by 101

Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

Guerin, E., Shkoporov, A. N., Stockdale, S. R., Colom, J., Khokhlova, E. V., Clooney, A. G., Daly, K. M., Draper, L. A., Stephens, N., Scholz, D., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01036-7 · Cited by 86

Metagenome-assembled genomes: concepts, analogies, and challenges

Setúbal, J. C. (2021) · Biophysical Reviews · doi:10.1007/s12551-021-00865-y · Cited by 87

Microbiome dynamics and genomic determinants of bovine mastitis

Hoque, M. N., Istiaq, A., Rahman, M. S., Islam, M. R., Anwar, A., Siddiki, A. Z., Sultana, M., Crandall, K. A., & Hossain, M. A. (2020) · Genomics · doi:10.1016/j.ygeno.2020.09.039 · Cited by 88

Changes in human gut microbiota composition are linked to the energy metabolic switch during 10 d of Buchinger fasting

Mesnage, R., Grundler, F., Schwiertz, A., Maho, Y. L., & de Toledo, F. W. (2019) · Journal of Nutritional Science · doi:10.1017/jns.2019.33 · Cited by 79

Listeria monocytogenes faecal carriage is common and depends on the gut microbiota

Hafner, L., Pichon, M., Burucoa, C., Nusser, S. H. A., Moura, A., Garcia‐Garcerà, M., & Lecuit, M. (2021) · Nature Communications · doi:10.1038/s41467-021-27069-y · Cited by 80

Systematic processing of ribosomal RNA gene amplicon sequencing data

Tremblay, J., & Yergeau, É. (2019) · GigaScience · doi:10.1093/gigascience/giz146 · Cited by 75

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit

Meyer, F., Lesker, T.-R., Koslicki, D., Fritz, A., Gurevich, A. A., Darling, A. E., Sczyrba, A., Bremges, A., & McHardy, A. C. (2021) · Nature Protocols · doi:10.1038/s41596-020-00480-3 · Cited by 74

Strainberry: automated strain separation in low-complexity metagenomes using long reads

Vicedomini, R., Quince, C., Darling, A. E., & Chikhi, R. (2021) · Nature Communications · doi:10.1038/s41467-021-24515-9 · Cited by 59

Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses

Fernández-Pato, A., Sinha, T., Gaćeša, R., Andreu‐Sánchez, S., Gois, M. F. B., Gelderloos-Arends, J., Jansen, D. B. H., Kruk, M., Jaeger, M., Joosten, L. A. B., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-54353-w · Cited by 56

Host determinants of among-species variation in microbiome composition in drosophilid flies

Adair, K. L., Bost, A., Bueno, E., Kaunisto, S., Kortet, R., Peters-Schulze, G., Martinson, V. G., & Douglas, A. E. (2019) · The ISME Journal · doi:10.1038/s41396-019-0532-7 · Cited by 54

Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures

Wang, S., Zeng, S., Egan, M., Cherry, P., Strain, C., Morais, E. D. S., Boyaval, P., Ryan, C. A., Dempsey, E. M., Ross, R. P., et al. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1911571 · Cited by 53

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

Oral-gut microbiome interactions in advanced cirrhosis: characterisation of pathogenic enterotypes and salivatypes, virulence factors and antimicrobial resistance

Lee, S., Arefaine, B., Begum, N., Stamouli, M., Witherden, E. A., Mohamad, M., Harzandi, A., Zamalloa, A., Cai, H., Williams, R. L., et al. (2024) · Journal of Hepatology · doi:10.1016/j.jhep.2024.09.046 · Cited by 56

Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes

Poulsen, C. S., Ekstrøm, C. T., Aarestrup, F. M., & Pamp, S. J. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00090-22 · Cited by 50

Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers

Sato, N., Kakuta, M., Hasegawa, T., Yamaguchi, R., Uchino, E., Kobayashi, W., Sawada, K., Tamura, Y., Tokuda, I., Murashita, K., et al. (2020) · npj Biofilms and Microbiomes · doi:10.1038/s41522-020-0121-6 · Cited by 48

Human microbiome acquisition and transmission

Heidrich, V., Valles‐Colomer, M., & Segata, N. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01166-x · Cited by 50

Critical Assessment of Metagenome Interpretation - the second round of challengesPreprint

Meyer, F., Fritz, A., Deng, Z.-L., Koslicki, D., Gurevich, A. A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.12.451567 · Cited by 42

Individualized recovery of gut microbial strains post antibiotics

Koo, H., Hakim, J. A., Crossman, D. K., Kumar, R., Lefkowitz, E. J., & Morrow, C. D. (2019) · npj Biofilms and Microbiomes · doi:10.1038/s41522-019-0103-8 · Cited by 38

Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization

Bayjanov, J. R., Baan, J., Rogers, M. R. C., Troelstra, A., Willems, R. J. L., & van Schaik, W. (2019) · Microbial Genomics · doi:10.1099/mgen.0.000277 · Cited by 40

Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples

Li, F., Liu, J., Maldonado-Gómez, M. X., Frese, S. A., Gänzle, M. G., & Walter, J. (2024) · Microbiome · doi:10.1186/s40168-024-01881-2 · Cited by 40

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must

Sirén, K., Mak, S. S. T., Melkonian, C., Carøe, C., Swiegers, J. H., Douwe Molenaar, B., Fischer, U., & Gilbert, M. T. P. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00697 · Cited by 36

Bioinformatic approaches for studying the microbiome of fermented food

Walsh, L. H., Coakley, M., Walsh, A. M., O’Toole, P. W., & Cotter, P. D. (2022) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2022.2132850 · Cited by 38

Host traits, lifestyle and environment are associated with human skin bacteria

Moitinho‐Silva, L., Boraczynski, N., Emmert, H., Baurecht, H., Szymczak, S., Schulz, H., Haller, D., Linseisen, J., Gieger, C., Peters, A., et al. (2021) · British Journal of Dermatology · doi:10.1111/bjd.20072 · Cited by 39

Specific metagenomic asset drives the spontaneous fermentation of Italian sausages

Franciosa, I., Ferrocino, I., Giordano, M., Mounier, J., Rantsiou, K., & Cocolin, L. (2021) · Food Research International · doi:10.1016/j.foodres.2021.110379 · Cited by 40

Probing periodontal microbial dark matter using metataxonomics and metagenomics

Kumar, P., Dabdoub, S. M., & Ganesan, S. M. (2020) · Periodontology 2000 · doi:10.1111/prd.12349 · Cited by 35

Evaluating the prebiotic effect of oligosaccharides on gut microbiome wellness using in vitro fecal fermentation

Lee, D. H., Seong, H., Chang, D., Gupta, V. K., Kim, J., Cheon, S., Kim, G., Sung, J., & Han, N. S. (2023) · npj Science of Food · doi:10.1038/s41538-023-00195-1 · Cited by 35

Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer

Casimiro‐Soriguer, C. S., Loucera, C., Peña-Chilet, M., & Dopazo, J. (2022) · Scientific Reports · doi:10.1038/s41598-021-04182-y · Cited by 38

Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing

Cerk, K., Ugalde‐Salas, P., Nedjad, C. G., Lecomte, M., Muller, C., Sherman, D. J., Hildebrand, F., Labarthe, S., & Frioux, C. (2024) · Microbial Biotechnology · doi:10.1111/1751-7915.14396 · Cited by 39

Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome

Hu, D., Fuller, N. R., Caterson, I. D., Holmes, A. J., & Reeves, P. R. (2022) · Cell Reports · doi:10.1016/j.celrep.2021.110239 · Cited by 30

Thank you for biting: dispersal of beneficial microbiota through 'antagonistic' interactions

Grupstra, C. G. B., Lemoine, N. P., Cook, C. N., & Correa, A. M. S. (2022) · Trends in Microbiology · doi:10.1016/j.tim.2022.03.006 · Cited by 30

Sharing of gut microbial strains between selected individual sets of twins cohabitating for decades

Koo, H., Hakim, J. A., Crossman, D. K., Lefkowitz, E. J., & Morrow, C. D. (2019) · PLoS ONE · doi:10.1371/journal.pone.0226111 · Cited by 29

An individualized mosaic of maternal microbial strains is transmitted to the infant gut microbial community

Koo, H., McFarland, B. C., Hakim, J. A., Crossman, D. K., Crowley, M. R., Rodriguez, J. M., Benveniste, E. N., & Morrow, C. D. (2020) · Royal Society Open Science · doi:10.1098/rsos.192200 · Cited by 28

Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease

Bacci, G., Taccetti, G., Dolce, D., Armanini, F., Segata, N., Cesare, F. D., Lucidi, V., Fiscarelli, E. V., Morelli, P., Casciaro, R., et al. (2020) · Microorganisms · doi:10.3390/microorganisms8071003 · Cited by 30

A Metagenomics Investigation of Intergenerational Effects of Non-nutritive Sweeteners on Gut Microbiome

Wang, W., Nettleton, J. E., Gänzle, M. G., & Reimer, R. A. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2021.795848 · Cited by 29

Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility

Ventura, E. F., Esteban-Torres, M., Gueimonde, M., van Sinderen, D., Koren, O., Hall, L. J., Segata, N., Valles‐Colomer, M., & Collado, M. C. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00720-y · Cited by 27

Reduced metagenome sequencing for strain-resolution taxonomic profiles

Snipen, L. G., Angell, I.-L., Rognes, T., & Rudi, K. (2021) · Microbiome · doi:10.1186/s40168-021-01019-8 · Cited by 26

Genome‐resolved metagenomics to study co‐occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations

Newberry, E. A., Bhandari, R., Kemble, J. M., Sikora, E. J., & Potnis, N. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.14989 · Cited by 25

Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms

Lindner, B. G., Suttner, B., Zhu, K. J., Conrad, R. E., Rodriguez‐R, L. M., Hatt, J. K., Brown, J. M., & Konstantinidis, K. T. (2021) · Water Research · doi:10.1016/j.watres.2021.117993 · Cited by 25

The gut microbiota perspective for interventions in MS

Żołędziewska, M. (2019) · Autoimmunity Reviews · doi:10.1016/j.autrev.2019.03.016 · Cited by 25

Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense

Dunn, K. A., MacDonald, T., Rodrigues, G. J., Forbrigger, Z., Bielawski, J. P., Langille, M. G. I., Limbergen, J. V., & Kulkarni, K. P. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.924707 · Cited by 21

On the complexity of haplotyping a microbial community

Nicholls, S. M., Aubrey, W., Grave, K. D., Schietgat, L., Creevey, C. J., & Clare, A. J. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa977 · Cited by 20

Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

Koo, H., & Morrow, C. D. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02312-0 · Cited by 16

Strain-Level Diversity in the Gut: The P. copri Case

Metwaly, A., & Haller, D. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.02.006 · Cited by 15

Toward accurate diagnosis and surveillance of bacterial infections using enhanced strain-level metagenomic next-generation sequencing of infected body fluids

Ruan, Z., Zou, S., Wang, Z., Zhang, L., Chen, H., Wu, Y., Jia, H., Draz, M. S., & Feng, Y. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac004 · Cited by 15

Bacterial dispersal and biogeography as underappreciated influences on phytobiomes

Baltrus, D. A. (2020) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2020.02.010 · Cited by 14

Computational genomic discovery of diverse gene clusters harbouring Fe-S flavoenzymes in anaerobic gut microbiota

Andreu, V. P., Fischbach, M. A., & Medema, M. H. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000373 · Cited by 13

Strain Tracking to Identify Individualized Patterns of Microbial Strain Stability in the Developing Infant Gut Ecosystem

Koo, H., Crossman, D. K., & Morrow, C. D. (2020) · Frontiers in Pediatrics · doi:10.3389/fped.2020.549844 · Cited by 13

StrainPanDA: Linked reconstruction of strain composition and gene content profiles via pangenome‐based decomposition of metagenomic data

Hu, H., Tan, Y., Li, C., Chen, J., Kou, Y., Xu, Z. Z., Liu, Y., Tan, Y. Q., & Dai, L. (2022) · iMeta · doi:10.1002/imt2.41 · Cited by 12

A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Sanders, J. G., Yan, W., Mjungu, D. C., Lonsdorf, E. V., Hart, J. A. L., Sanz, C., Morgan, D., Peeters, M., Hahn, B. H., & Moeller, A. H. (2022) · Genome biology · doi:10.1186/s13059-022-02777-w · Cited by 11

Perturbation of the human gastrointestinal tract microbial ecosystem by oral drugs to treat chronic disease results in a spectrum of individual specific patterns of extinction and persistence of dominant microbial strains

Koo, H., & Morrow, C. D. (2020) · PLoS ONE · doi:10.1371/journal.pone.0242021 · Cited by 13

New microbe genomic variants in patients fecal community following surgical disruption of the upper human gastrointestinal tract

Kumar, R., Grams, J. M., Chu, D. I., Crossman, D. K., Stahl, R. D., Eipers, P. G., Goldsmith, K., Crowley, M., Lefkowitz, E. J., & Morrow, C. D. (2018) · Human Microbiome Journal · doi:10.1016/j.humic.2018.10.002 · Cited by 12

CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis

Lam, T. J., & Ye, Y. (2019) · The CRISPR Journal · doi:10.1089/crispr.2018.0046 · Cited by 12

Alteration in gut microbiota after colonoscopy: proposed mechanisms and the role of probiotic interventions

Jo, H. H., Lee, M. Y., Ha, S. E., Yeom, D. H., & Kim, Y. S. (2024) · Clinical Endoscopy · doi:10.5946/ce.2024.147 · Cited by 13

Metaomics in Clinical Laboratory: Potential Driving Force for Innovative Disease Diagnosis

Wang, L., Li, F., Gu, B., Qu, P., Liu, Q., Wang, J., Tang, J., Cai, S., Zhao, Q., & Ming, Z. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.883734 · Cited by 10

Metagenomics Strain Resolution on Assembly GraphsPreprint

Quince, C., Nurk, S., Raguideau, S., James, R., Soyer, O. S., Summers, J., Limasset, A., Eren, A., Chikhi, R., & Darling, A. E. (2020) · bioRxiv · doi:10.1101/2020.09.06.284828 · Cited by 37

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes

Defazio, G., Tangaro, M. A., Pesole, G., & Fosso, B. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae680 · Cited by 7

High strain-level diversity of Bradyrhizobium across Australian soils

de Mesquita, C. P. B., Olm, M. R., Bissett, A. B., & Fierer, N. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf222 · Cited by 6

Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community

Pavloudi, C., & Zafeiropoulos, H. (2022) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiac141 · Cited by 6

Impact of evolution on lifestyle in microbiome

González, A., Fullaondo, A., & Odriozola, A. (2024) · Advances in genetics · doi:10.1016/bs.adgen.2024.02.003 · Cited by 4

Less Is More: Genome Reduction and the Emergence of Cooperation—Implications into the Coevolution of Microbial Communities

Bosi, E., & Mascagni, F. (2019) · International Journal of Genomics · doi:10.1155/2019/2659175 · Cited by 4

Do we need to change our perspective about gut biomarkers? A public data mining approach to identify differentially abundant bacteria in intestinal inflammatory diseases

Vega, L., Bohórquez, L., Ramírez, J. D., & Muñoz, M. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.918237 · Cited by 4

Strain-Level Profiling of Oral Microbiota with Targeted Sequencing

Mukherjee, C., & Leys, E. J. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1518-8_14 · Cited by 4

Quantification of discrete gut bacterial strains following fecal transplantation for recurrent Clostridioides difficile infection demonstrates long-term stable engraftment in non-relapsing recipientsPreprint

Aggarwala, V., Mogno, I., Li, Z., Yang, C., Britton, G. J., Chen-Liaw, A., Mitcham, J., Bongers, G., Gevers, D., Clemente, J. C., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.10.292136 · Cited by 4

Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains

Koo, H., & Morrow, C. D. (2022) · PLoS ONE · doi:10.1371/journal.pone.0274633 · Cited by 3

Identifying causes and consequences of rhizosphere microbiome heritability

Wagner, M. R. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002604 · Cited by 3

Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosaPreprint

Bacci, G., Taccetti, G., Dolce, D., Armanini, F., Segata, N., Cesare, F. D., Lucidi, V., Fiscarelli, E. V., Morelli, P., Casciaro, R., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/609057 · Cited by 3

Mora: abundance aware metagenomic read re-assignment for disentangling similar strains

Zheng, A., Shaw, J., & Yu, Y. W. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05768-9 · Cited by 4

UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog

Liu, S., Feng, B., Zhang, Z., Miao, J., Lai, X., Zhao, W., Xie, Q., Ye, X., Cao, C., Yu, P., et al. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00828-1 · Cited by 9

Identification of donor Bacteroides vulgatus genes encoding proteins that correlate with early colonization following fecal transplant of patients with recurrent Clostridium difficile

Koo, H., & Morrow, C. D. (2023) · Scientific Reports · doi:10.1038/s41598-023-41128-y · Cited by 2

Bioinformatic methods for genome-centric metagenomics

Newell, R. (2023) · Queensland University of Technology · doi:10.5204/thesis.eprints.237953 · Cited by 3

Expansion, restructuring and characterization of the Legionellaceae familyPreprint

Gabrielli, M., Cavallaro, A., & Hammes, F. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.21.619444 · Cited by 2

Assessing the performance of current strain resolution tools on long-read metagenomesPreprint

Afolayan, A. O., Ayala-Montaño, S., Akintayo, I. J., Santos, L., & Reuter, S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.20.624313 · Cited by 2

Comparison between Ribosomal Assembly and Machine Learning Tools for Microbial Identification of Organisms with Different Characteristics

Chau, S., Rojas, C., Jetcheva, J. G., Markart, M., Vijayakumar, S., Yuan, S., Stowbunenko, V., Shelton, A. N., & Andreopoulos, W. (2024) · Current Bioinformatics · doi:10.2174/0115748936299440240709070105 · Cited by 1

The plant microbiome: From ecological foundations to precision microbial engineering for sustainable agriculture

Wei, M., Lian, T., Chen, L., Wang, L., Ye, J., Yao, X., Duan, S., Lu, Z., Jinji, T. U., Li, H., et al. (2026) · iMeta · doi:10.1002/imt2.70152 · Cited by 3

Early indicators of microbial strain dysbiosis in the human gastrointestinal microbial community of certain healthy humans and hospitalized COVID-19 patients

Koo, H., & Morrow, C. D. (2022) · Scientific Reports · doi:10.1038/s41598-022-10472-w · Cited by 1

Molecular epidemiology of Staphylococcus epidermidis in prosthetic joint infections

Månsson, E. (2019) · KTH Publication Database DiVA (KTH Royal Institute of Technology)

Bioinformatic Platforms for Metagenomics

Eckenberger, J., Walker, S. P., & Claesson, M. J. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-816395-5.00009-5

Novel municipal sewage-associated bacterial genomes and their potential in source trackingPreprint

Lindner, B. G., Suttner, B., Conrad, R. E., Rodriguez‐R, L. M., Hatt, J. K., Zhu, K. J., Brown, J. M., & Konstantinidis, K. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.15.452399

Integrating strain‑level metagenomics in human and food microbiomes

Pasolli, E. (2026) · IMAGINE - Repository of the Institute of molecular genetics and genetic engineering (University of Belgrade)

Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges

Park, H., Kim, J. S., Kim, D. J., & Suk, K. T. (2026) · Microorganisms · doi:10.3390/microorganisms14030720 · Cited by 5

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGCPreprint

Smith, B. J., Zhao, C., Dubinkina, V. B., Jin, X., Zahavi, L., Shoer, S., Anderson, J. M., Segal, E., & Pollard, K. S. (2025) · Genome Research · doi:10.1101/gr.279543.124 · Cited by 11

Strain Identification and Quantitative Analysis in Microbial Communities

Ghazi, A. R., Münch, P. C., Chen, D., Jensen, J., & Huttenhower, C. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167582 · Cited by 44

Toward hypothesis-driven, personalized microbiome screening

Sedrani, C., & Wilmes, P. (2022) · Cell Reports Methods · doi:10.1016/j.crmeth.2021.100139 · Cited by 5