inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains
Open accessAbstract
Coexisting microbial cells of the same species often exhibit genetic variation that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that uses metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compares microbial populations in a microdiversity-aware manner, greatly increasing the accuracy of genomic comparisons when benchmarked against existing methods. We use inStrain to profile >1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born by cesarean section harbor Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital rather than maternal microbiomes. Genomic loci that show diversity in individual infants include variants found between other infants, possibly reflecting inoculation from diverse hospital-associated sources. inStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The advancement of computational tools for shotgun metagenomic sequencing has enabled profiling of microbes taxonomically and quantitatively and access to genetic information at subspecies and strain resolutions.
“The advancement of computational tools for the analysis of shotgun metagenomic sequencing has enabled researchers to not only profile microbes taxonomically and quantitatively but also to access their genetic information at subspecies and strain resolutions.”
From Global genetic diversity of human gut microbiome species is related to geographic location and host health (2025) · cites this paper as [10]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works
Matplotlib: a 2D graphics environment
Hunter, J. D. (2007) · Computing in Science & Engineering · doi:10.1109/mcse.2007.55 · Cited by 39,249 · see citing works
Harris, C. R., Millman, K. J., van der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2649-2 · Cited by 23,826 · see citing works
Harris, C., Millman, K., van der Walt, S., Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., Taylor, J., Berg, S., Smith, N., et al. (2020) · RePEc: Research Papers in Economics · Cited by 17,844 · see citing works
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 12,426 · see citing works
Data Structures for Statistical Computing in Python
McKinney, W. (2010) · Proceedings of the Python in Science Conferences · doi:10.25080/majora-92bf1922-00a · Cited by 11,511 · see citing works
Circos: An information aesthetic for comparative genomicsPreprint
Krzywinski, M. I., Schein, J. E., Birol, İ., Connors, J. M., Gascoyne, R. D., Horsman, D. E., Jones, S. J. M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 10,834 · see citing works
Mathematical model for studying genetic variation in terms of restriction endonucleases.
Nei, M., & Li, W. (1979) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.76.10.5269 · Cited by 10,501 · see citing works
Biopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080 · see citing works
The Pfam protein families database in 2019
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky995 · Cited by 4,602 · see citing works
Olm, M. R., Brown, C. T., Brooks, B., & Banfield, J. F. (2017) · The ISME Journal · doi:10.1038/ismej.2017.126 · Cited by 3,031 · see citing works
Self-citationPeng, Y., Leung, H. C. M., Yiu, S., & Chin, F. Y. L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts174 · Cited by 2,997 · see citing works
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 · see citing works
The Long-Term Stability of the Human Gut Microbiota
Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058 · see citing works
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 1,823 · see citing works
Unravelling the effects of the environment and host genotype on the gut microbiome
Spor, A., Koren, O., & Ley, R. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2540 · Cited by 1,509 · see citing works
BBMerge – Accurate paired shotgun read merging via overlap
Bushnell, B., Rood, J., & Singer, E. (2017) · PLoS ONE · doi:10.1371/journal.pone.0185056 · Cited by 1,495 · see citing works
A unified catalog of 204,938 reference genomes from the human gut microbiome
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367 · see citing works
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 · see citing works
Waskom, M., Botvinnik, O. B., O'Kane, D., Hobson, P., Ostblom, J., Lukauskas, S., Gemperline, D. C., Augspurger, T., Halchenko, Y., Cole, J. B., et al. (2014) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.592845 · Cited by 1,119 · see citing works
Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth
Shao, Y., Forster, S. C., Tsaliki, E., Vervier, K., Strang, A., Simpson, N., Kumar, N., Stares, M. D., Rodger, A., Brocklehurst, P., et al. (2019) · Nature · doi:10.1038/s41586-019-1560-1 · Cited by 1,088 · see citing works
Genetic determinants of the gut microbiome in UK twins
Goodrich, J. K., Davenport, E. R., Beaumont, M., Jackson, M. A., Knight, R., Ober, C., Spector, T. D., Bell, J. T., Clark, A. G., & Ley, R. E. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.04.017 · Cited by 1,048 · see citing works
Fast algorithms for large-scale genome alignment and comparison
Delcher, A. L. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.11.2478 · Cited by 1,036 · see citing works
Temporal Stability of the Human Skin Microbiome
Oh, J., Byrd, A. L., Park, M., Kong, H. H., & Segre, J. A. (2016) · Cell · doi:10.1016/j.cell.2016.04.008 · Cited by 1,036 · see citing works
Characterization of the gut microbiome using 16S or shotgun metagenomics
Jovel, J., Patterson, J., Wang, W., Hotte, N., O'Keefe, S., Mitchel, T., Perry, T., Kao, D., Mason, A. L., Madsen, K. L., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00459 · Cited by 942 · see citing works
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 · see citing works
Dynamics and associations of microbial community types across the human body
Ding, T., & Schloss, P. D. (2014) · Nature · doi:10.1038/nature13178 · Cited by 885 · see citing works
Microbial strain-level population structure and genetic diversity from metagenomes
Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C., & Segata, N. (2017) · Genome Research · doi:10.1101/gr.216242.116 · Cited by 839 · see citing works
Yekutieli, D., & Benjamini, Y. (1999) · Journal of Statistical Planning and Inference · doi:10.1016/s0378-3758(99)00041-5 · Cited by 738 · see citing works
The dynamics of molecular evolution over 60,000 generations
Good, B. H., McDonald, M. J., Barrick, J. E., Lenski, R. E., & Desai, M. M. (2017) · Nature · doi:10.1038/nature24287 · Cited by 733 · see citing works
Using MUMmer to Identify Similar Regions in Large Sequence Sets
Delcher, A. L., Salzberg, S. L., & Phillippy, A. M. (2003) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1003s00 · Cited by 544 · see citing works
Sharon, I., Morowitz, M. J., Thomas, B. C., Costello, E. K., Relman, D. A., & Banfield, J. F. (2012) · Genome Research · doi:10.1101/gr.142315.112 · Cited by 481 · see citing works
Self-citationNayfach, S., Rodriguez-Mueller, B., Garud, N., & Pollard, K. S. (2016) · Genome Research · doi:10.1101/gr.201863.115 · Cited by 470 · see citing works
Association of host genome with intestinal microbial composition in a large healthy cohort
GEM Project Research Consortium, Turpin, W., Espin-Garcia, O., Xu, W., Silverberg, M. S., Kevans, D., Smith, M. I., Guttman, D. S., Griffiths, A., Panaccione, R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3693 · Cited by 460 · see citing works
Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life
Yassour, M., Jason, E., Hogstrom, L. J., Arthur, T. D., Tripathi, S., Siljander, H., Selvenius, J., Oikarinen, S., Hyöty, H., Virtanen, S. M., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.06.007 · Cited by 455 · see citing works
Adaptive Evolution within Gut Microbiomes of Healthy People
Zhao, S., Lieberman, T. D., Poyet, M., Kauffman, K. M., Gibbons, S. M., Groussin, M., Xavier, R. J., & Alm, E. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.007 · Cited by 434 · see citing works
Smillie, C. S., Sauk, J. S., Gevers, D., Friedman, J., Sung, J., Youngster, I., Hohmann, E. L., Staley, C. M., Khoruts, A., Sadowsky, M. J., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.01.003 · Cited by 417 · see citing works
Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data
Schirmer, M., D’Amore, R., Ijaz, U. Z., Hall, N., & Quince, C. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-0976-y · Cited by 376 · see citing works
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
Garud, N. R., Good, B. H., Hallatschek, O., & Pollard, K. S. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000102 · Cited by 347 · see citing works
The effect of heritability and host genetics on the gut microbiota and metabolic syndrome
Lim, M. Y., You, H. J., Yoon, H. S., Kwon, B., Lee, J. Y., Lee, S., Song, Y., Lee, K., Sung, J., & Ko, G. (2016) · Gut · doi:10.1136/gutjnl-2015-311326 · Cited by 340 · see citing works
Davis, S., Pettengill, J., Luo, Y., et al. (2015) · PeerJ Computer Science · doi:10.7717/peerj-cs.20 · Cited by 332 · see citing works
Selective maternal seeding and environment shape the human gut microbiomePreprint
Korpela, K., Costea, P. I., Coelho, L. P., Kandels-Lewis, S. E., Willemsen, G. A. H. M., Boomsma, D. I., Segata, N., & Peer Bork, B. (2018) · Genome Research · doi:10.1101/gr.233940.117 · Cited by 325 · see citing works
The Relationship Between the Human Genome and Microbiome Comes into View
Goodrich, J. K., Davenport, E. R., Clark, A. G., & Ley, R. E. (2017) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155532 · Cited by 311 · see citing works
Genome-Wide Association Studies of the Human Gut Microbiota
Davenport, E., Cusanovich, D. A., Michelini, K., Barreiro, L. B., Ober, C., & Gilad, Y. (2015) · PLoS ONE · doi:10.1371/journal.pone.0140301 · Cited by 253 · see citing works
Transmission of human-associated microbiota along family and social networks
Brito, I., Gurry, T., Zhao, S., Huang, K. H., Young, S., Shea, T. P., Naisilisili, W., Jenkins, A., Jupiter, S. D., Gevers, D., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0409-6 · Cited by 239 · see citing works
Royer, C. A., Tauc, P., Hervé, G., & Brochon, J. (1987) · Biochemistry · doi:10.1021/bi00394a027 · Cited by 238 · see citing works
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
Bendall, M. L., Stevens, S. L. R., Chan, L., Malfatti, S., Schwientek, P., Tremblay, J., Schackwitz, W., Martin, J., Pati, A., Bushnell, B., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2015.241 · Cited by 238 · see citing works
Brooks, B., Olm, M. R., Firek, B. A., Baker, R., Thomas, B. C., Morowitz, M. J., & Banfield, J. F. (2017) · Nature Communications · doi:10.1038/s41467-017-02018-w · Cited by 226 · see citing works
Self-citationVatanen, T., Plichta, D. R., Somani, J., Münch, P. C., Arthur, T. D., Hall, A. B., Rudolf, S., Oakeley, E. J., Ke, X., Young, R. A., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0321-5 · Cited by 216 · see citing works
pIRS: Profile-based Illumina pair-end reads simulator
Hu, X., Yuan, J., Shi, Y., Lu, J., Liu, B., Li, Z., Chen, Y., Mu, D., Zhang, H., Li, N., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts187 · Cited by 198 · see citing works
Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
Olm, M., Crits-Christoph, A., Diamond, S., Lavy, A., Carnevali, P. B. M., & Banfield, J. (2020) · mSystems · doi:10.1128/msystems.00731-19 · Cited by 195 · see citing works
Self-citationMathematical properties of the r2 measure of linkage disequilibrium.
VanLiere, J. M., & Rosenberg, N. (2008) · Theoretical Population Biology · doi:10.1016/j.tpb.2008.05.006 · Cited by 190 · see citing works
Olm, M., Bhattacharya, N., Crits-Christoph, A., Firek, B., Baker, R., Song, Y. S., Morowitz, M., & Banfield, J. (2019) · Science Advances · doi:10.1126/sciadv.aax5727 · Cited by 177 · see citing works
Self-citationNovel fold and capsid-binding properties of the lambda-phage display platform protein gpD.
Plückthun, A., Yang, F., Forrer, P., Dauter, Z., Conway, J. F., Cheng, N., Cerritelli, M. E., Steven, A. C., & Wlodawer, A. (2000) · Nature Structural Biology · doi:10.1038/73347 · Cited by 168 · see citing works
Simmons, S. L., DiBartolo, G., Denef, V. J., Goltsman, D. S. A., Thelen, M. P., & Banfield, J. F. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060177 · Cited by 152 · see citing works
Self-citationBacteriophage T4 Host Range is Expanded by Duplications of a Small Domain of the Tail Fiber Adhesin
Tétart, F., Repoila, F., Monod, C., et al. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0281 · Cited by 145 · see citing works
The first microbial environment of infants born by C-section: the operating room microbes
Shin, H., Pei, Z., Martinez, K. A., Rivera-Viñas, J. I., Méndez, K., Cavallín, H., & Domínguez-Bello, M. G. (2015) · Microbiome · doi:10.1186/s40168-015-0126-1 · Cited by 141 · see citing works
Delmont, T. O., Kiefl, E., Kilinc, O., Esen, Ö. C., Uysal, I., Rappé, M. S., Giovannoni, S. J., & Eren, A. M. (2019) · eLife · doi:10.7554/elife.46497 · Cited by 137 · see citing works
Bodelón, G., Palomino, C. M., & Fernández, L. Á. (2012) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2012.00347.x · Cited by 115 · see citing works
Dietary Patterns and Heritability of Food Choice in a UK Female Twin Cohort
Teucher, B., Skinner, J. S., Skidmore, P. M. L., Cassidy, A., Fairweather‐Tait, S. J., Hooper, L., Roe, M. A., Foxall, R., Oyston, S. L., Cherkas, L. F., et al. (2007) · Twin Research and Human Genetics · doi:10.1375/twin.10.5.734 · Cited by 114 · see citing works
Long-term stability and Red Queen-like strain dynamics in marine viruses
Ignacio‐Espinoza, J. C., Ahlgren, N. A., & Fuhrman, J. A. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0628-x · Cited by 107 · see citing works
metaSNV: A tool for metagenomic strain level analysis
Costea, P. I., Munch, R., Coelho, L. P., Paoli, L., Sunagawa, S., & Bork, P. (2017) · PLoS ONE · doi:10.1371/journal.pone.0182392 · Cited by 103 · see citing works
P1 Plasmid Partition: A Mutational Analysis of ParB
Łobocka, M. B., & Yarmolinsky, M. B. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0326 · Cited by 78 · see citing works
Crits‐Christoph, A., Olm, M. R., Diamond, S., Bouma‐Gregson, K., & Banfield, J. F. (2020) · The ISME Journal · doi:10.1038/s41396-020-0655-x · Cited by 76 · see citing works
Self-citationAcquisition, transmission and strain diversity of human gut-colonizing crAss-like phages
Siranosian, B. A., Tamburini, F. B., Sherlock, G. J., & Bhatt, A. S. (2020) · Nature Communications · doi:10.1038/s41467-019-14103-3 · Cited by 73 · see citing works
Genetic influences on ‘environmental’ factors
Vinkhuyzen, A. A. E., Van Der Sluis, S., De Geus, E. J. C., Boomsma, D. I., & Posthuma, D. (2010) · Genes, Brain and Behavior · doi:10.1111/j.1601-183x.2009.00554.x · Cited by 70 · see citing works
Genetic Exchange Across a Species Boundary in the Archaeal Genus Ferroplasma
Eppley, J. M., Tyson, G. W., Getz, W. M., & Banfield, J. F. (2007) · Genetics · doi:10.1534/genetics.107.072892 · Cited by 69 · see citing works
Self-citationTracking Strains in the Microbiome: Insights from Metagenomics and Models
Brito, I., & Alm, E. J. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00712 · Cited by 48 · see citing works
The impact of inbreeding depression on population survival depending on demographic parameters
Thévenon, S., & Couvet, D. (2002) · Animal Conservation · doi:10.1017/s1367943002001075 · Cited by 29 · see citing works
First structure of the polymyxin resistance proteins
Fu, W., Yang, F., Kang, X., et al. (2007) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2007.07.144 · Cited by 24 · see citing works
[Alcoholism and associated diseases].
Leclainche, X., & Pm, L. G. (1970) · PubMed · Cited by 4 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
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 · see citing works
Codiversification of gut microbiota with humans
Suzuki, T. A., Fitzstevens, J. L., Schmidt, V. T., Enav, H., Huus, K. E., Mbong Ngwese, M., Grießhammer, A., Pfleiderer, A., Adegbite, B. R., Zinsou, J. F., et al. (2022) · Science · doi:10.1126/science.abm7759 · Cited by 210 · see citing works
A gut microbial signature for combination immune checkpoint blockade across cancer types
Gunjur, A., Shao, Y., Rozday, T., Klein, O., Mu, A., Haak, B. W., Markman, B., Kee, D., Carlino, M. S., Underhill, C., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-02823-z · Cited by 165 · see citing works
Andreu-Sánchez, S., Blanco-Míguez, A., Wang, D., Golzato, D., Manghi, P., Heidrich, V., Fackelmann, G., Zhernakova, D. V., Kurilshikov, A., Valles-Colomer, M., et al. (2025) · Cell · doi:10.1016/j.cell.2025.04.014 · Cited by 81 · see citing works
Zhai, B., Liao, C., Jaggavarapu, S., Tang, Y., Rolling, T., Ning, Y., Sun, T., Bergin, S. A., Gjonbalaj, M., Miranda, E., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-03183-4 · Cited by 62 · see citing works
Bacterial SNPs in the human gut microbiome associate with host BMI
Zahavi, L., Lavon, A., Reicher, L., Shoer, S., Godneva, A., Leviatan, S., Rein, M., Weissbrod, O., Weinberger, A., & Segal, E. (2023) · Nature Medicine · doi:10.1038/s41591-023-02599-8 · Cited by 58 · see citing works
Integrated molecular approaches for fermented food microbiome research
Walsh, A. M., Leech, J., Huttenhower, C., Delhomme-Nguyen, H., Crispie, F., Chervaux, C., & Cotter, P. D. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad001 · Cited by 56 · see citing works
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 · see citing works
Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes
Proctor, D. M., Sansom, S. E., Deming, C., Conlan, S., Blaustein, R. A., Atkins, T. K., Program, N. C. S., Mullikin, J., Thomas, J., Young, A., et al. (2025) · Nature · doi:10.1038/s41586-025-08608-9 · Cited by 37 · see citing works
Tomofuji, Y., Kishikawa, T., Maeda, Y., Ogawa, K., Otake-Kasamoto, Y., Kawabata, S., Nii, T., Okuno, T., Oguro-Igashira, E., Kinoshita, M., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100219 · Cited by 35 · see citing works
Nori, S. R. C., Walsh, C. J., McAuliffe, F. M., Moore, R. L., Van Sinderen, D., Feehily, C., & Cotter, P. D. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00682-1 · Cited by 29 · see citing works
A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing
Andreu-Sánchez, S., Chen, L., Wang, D., Augustijn, H. E., Zhernakova, A., & Fu, J. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.648229 · Cited by 27 · see citing works
Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut
Jiang, S., Zhang, C., Han, Z., Ma, W., Wang, S., Huo, D., Cui, W., Zhai, Q., Huang, S., & Zhang, J. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00447-8 · Cited by 25 · see citing works
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes
Van Rossum, T., Costea, P. I., Paoli, L., Alves, R., Thielemann, R., Sunagawa, S., & Bork, P. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btab789 · Cited by 23 · see citing works
Gut microbiota drives structural variation of exogenous probiotics to enhance colonization
Jiang, S., Huang, S., Zhang, Z., Ma, W., Han, Z., Song, Y., Huo, D., Cui, W., & Zhang, J. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2503371 · Cited by 15 · see citing works
“Based on the correlation between strain Lp082 and gut resident microorganisms, we employed inStrain software 48 to annotate the mutation sites for a wide array of gut microbiota.”
Mah, J. C., Lohmueller, K. E., & Garud, N. R. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf010 · Cited by 11 · see citing works
- Authors
- Olm, M. R., Crits-Christoph, A., Bouma-Gregson, K., Firek, B. A., Morowitz, M. J., & Banfield, J. F.
- Affiliations
- Stanford Medicine (US)
- University of Pittsburgh (US)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Banfield, Jillian F.
- Venue
- Nature Biotechnology
- Published
- 2021-01-18
- Volume
- 39
- Issue
- 6
- Pages
- 727-736
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC9223867
- OpenAlex
- W3122118092
- Cited by
- 537
- References
- 72
- Citations by year
- 2026: 94 · 2025: 135 · 2024: 113 · 2023: 80 · 2022: 71 · 2021: 43 · 2020: 1
- FWCI
- 25.18
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (DGE 1106400, DGE1106400)
- Alfred P. Sloan Foundation (APSF-2012-10-05)
- Foundation for the National Institutes of Health (RAI092531A)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- strain comparison, fecal microbiota, preterm infants, Klebsiella, cesarean section, vaginal delivery, nucleotide diversity
- MeSH terms
- Humans, Infant, Newborn, Polymorphism, Single Nucleotide, Biodiversity, Metagenomics, Microbiota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
