Genome-scale resources in the infant gut symbiont Bifidobacterium breve reveal genetic determinants of colonization and host-microbe interactions
Open accessAbstract
Bifidobacteria represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest in bifidobacteria as a live biotic therapy, our understanding of colonization, host-microbe interactions, and the health-promoting effects of bifidobacteria is limited. To address these major knowledge gaps, we used a large-scale genetic approach to create a mutant fitness compendium in Bifidobacterium breve. First, we generated a high-density randomly barcoded transposon insertion pool and used it to determine fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. Second, to enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1,462 genes. We leveraged these tools to reveal community- and diet-specific requirements for colonization and to connect the production of immunomodulatory molecules to growth benefits. These resources will catalyze future investigations of this important beneficial microbe.
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?
B. bifidum is characteristic of the bifidobacterial communities residing in the infant gut and contributes to early microbial colonization, alongside B. breve.
“B. bifidum is characteristic of the bifidobacterial communities residing in the infant gut and contributes to early microbial colonization, alongside Bifidobacterium breve [6-10] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [7]
The Introduction describes bifidobacteria as early colonizers of the human gut and identifies B. breve as preferentially associated with infants. The Methods list B. bifidum among human-residential species, but the cited passages do not establish that B. bifidum specifically is characteristic of infant gut communities or contributes to early colonization. No page numbers are available in our copy. (LLM, conf=0.86)
Experimental — accuracy not yet measured
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
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698 · see citing works
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0209-9 · Cited by 23,742 · see citing works
Mootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. (2003) · Nature Genetics · doi:10.1038/ng1180 · Cited by 10,197 · see citing works
KEGG: new perspectives on genomes, pathways, diseases and drugs
Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., & Morishima, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1092 · Cited by 8,865 · see citing works
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 · see citing works
A medium for the cultivation of lactobacilli
De MAN, J. C., ROGOSA, M., & SHARPE, M. E. (1960) · Journal of Applied Bacteriology · doi:10.1111/j.1365-2672.1960.tb00188.x · Cited by 5,311 · see citing works
Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002601107 · Cited by 4,774 · see citing works
Gut microbiota in human metabolic health and disease
Fan, Y., & Pedersen, O. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0433-9 · Cited by 4,724 · see citing works
Peptidoglycan types of bacterial cell walls and their taxonomic implications
SCHLEIFER, K. H., & Kandler, O. (1972) · Bacteriological Reviews · doi:10.1128/br.36.4.407-477.1972 · Cited by 4,203 · see citing works
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis
Tsugawa, H., Čajka, T., Kind, T., Ma, Y., Higgins, B. T., Ikeda, K., Kanazawa, M., VanderGheynst, J. S., Fiehn, O., & Arita, M. (2015) · Nature Methods · doi:10.1038/nmeth.3393 · Cited by 3,423 · see citing works
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.004 · Cited by 3,315 · see citing works
Database resources of the national center for biotechnology information
Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1112 · Cited by 2,812 · see citing works
Zelante, T., Iannitti, R. G., Cunha, C., De Luca, A., Giovannini, G., Pieraccini, G., Zecchi, R., D’Angelo, C., Massi-Benedetti, C., Fallarino, F., et al. (2013) · Immunity · doi:10.1016/j.immuni.2013.08.003 · Cited by 2,614 · see citing works
MUMmer4: A fast and versatile genome alignment system
Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L., & Zimin, A. (2018) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005944 · Cited by 2,484 · see citing works
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Overbeek, R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki866 · Cited by 2,019 · see citing works
Temporal development of the gut microbiome in early childhood from the TEDDY study
Stewart, C. J., Ajami, N. J., O’Brien, J. L., Hutchinson, D. S., Smith, D. P., Wong, M. C., Ross, M. C., Lloyd, R. E., Doddapaneni, H., Metcalf, G., et al. (2018) · Nature · doi:10.1038/s41586-018-0617-x · Cited by 1,996 · see citing works
Extensive impact of non-antibiotic drugs on human gut bacteria
Maier, L., Pruteanu, M., Kuhn, M., Zeller, G., Telzerow, A., Anderson, E. E., Brochado, A. R., Fernandez, K. C., Dose, H., Mori, H., et al. (2018) · Nature · doi:10.1038/nature25979 · Cited by 1,905 · see citing works
Diet-induced extinctions in the gut microbiota compound over generations
Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016) · Nature · doi:10.1038/nature16504 · Cited by 1,730 · see citing works
Self-citationComputer Control of Microscopes Using µManager
Edelstein, A., Amodaj, N., Hoover, K., Vale, R. D., & Stuurman, N. (2010) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb1420s92 · Cited by 1,678 · see citing works
Antibiotics, birth mode, and diet shape microbiome maturation during early life
Bokulich, N. A., Chung, J., Battaglia, T., Henderson, N., Jay, M., Li, H., D. Lieber, A., Wu, F., Perez-Perez, G. I., Chen, Y., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad7121 · Cited by 1,469 · see citing works
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
Ebrahim, A., Lerman, J. A., Palsson, B. O., & Hyduke, D. R. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-74 · Cited by 1,378 · see citing works
Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., Broadbelt, L. J., Vassily Hatzimanikatis, A., & Palsson, B. Ø. (2007) · Molecular Systems Biology · doi:10.1038/msb4100155 · Cited by 1,367 · see citing works
The microbiome and human cancer
Sepich-Poore, G. D., Zitvogel, L., Straussman, R., Hasty, J., Wargo, J. A., & Knight, R. (2021) · Science · doi:10.1126/science.abc4552 · Cited by 1,332 · 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
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A., Haraldsdóttir, H. S., Wachowiak, J., Keating, S., Vlasov, V., et al. (2019) · Nature Protocols · doi:10.1038/s41596-018-0098-2 · Cited by 1,253 · see citing works
Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., Holland, T. A., Keseler, I. M., Kothari, A., Kubo, A., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1103 · Cited by 1,204 · see citing works
Interaction between drugs and the gut microbiome
Weersma, R. K., Zhernakova, A., & Fu, J. (2020) · Gut · doi:10.1136/gutjnl-2019-320204 · Cited by 988 · see citing works
Tsugawa, H., Ikeda, K., Takahashi, M., Satoh, A., Mori, Y., Uchino, H., Okahashi, N., Yamada, Y., Tada, I., Bonini, P., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0531-2 · Cited by 895 · see citing works
Bifidobacteria-mediated immune system imprinting early in life
Henrick, B. M., Rodriguez, L., Lakshmikanth, T., Pou, C., Henckel, E., Arzoomand, A., Olin, A., Wang, J., Mikeš, J., Tan, Z., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.030 · Cited by 808 · see citing works
Graph Clustering Via a Discrete Uncoupling Process
van Dongen, S. (2008) · SIAM Journal on Matrix Analysis and Applications · doi:10.1137/040608635 · Cited by 726 · see citing works
Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat
Goodman, A. L., McNulty, N. P., Zhao, Y., Leip, D., Mitra, R. D., Lozupone, C., Knight, R. D., & Gordon, J. I. (2009) · Cell Host & Microbe · doi:10.1016/j.chom.2009.08.003 · Cited by 713 · see citing works
Phenotypic Landscape of a Bacterial Cell
Nichols, R. J., Sen, Ś., Choo, Y. J., Beltrão, P., Zietek, M., Chaba, R., Lee, S., Kazmierczak, K. M., Lee, K. J., Wong, A., et al. (2010) · Cell · doi:10.1016/j.cell.2010.11.052 · Cited by 702 · see citing works
The Genera of Lactic Acid Bacteria
(1995) · doi:10.1007/978-1-4615-5817-0 · Cited by 685 · see citing works
Early life dynamics of the human gut virome and bacterial microbiome in infants
Lim, E. S., Zhou, Y., Zhao, G., Bauer, I. K., Droit, L., Ndao, I. M., Warner, B. B., Tarr, P. I., Wang, D., & Holtz, L. R. (2015) · Nature Medicine · doi:10.1038/nm.3950 · Cited by 644 · see citing works
Laursen, M. F., Sakanaka, M., von Burg, N., Mörbe, U., Andersen, D., Moll, J. M., Pekmez, C. T., Rivollier, A., Michaelsen, K. F., Mølgaard, C., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00970-4 · Cited by 596 · see citing works
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis
Koo, B., Kritikos, G., Farelli, J. D., Todor, H., Tong, K., Kimsey, H. H., Wapinski, I. N., Galardini, M., Cabal, A., Peters, J. M., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2016.12.013 · Cited by 584 · see citing works
Mutant phenotypes for thousands of bacterial genes of unknown function
Price, M. N., Wetmore, K. M., Waters, R. J., Callaghan, M., Ray, J., Liu, H., Kuehl, J. V., Melnyk, R. A., Lamson, J. S., Suh, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0124-0 · Cited by 576 · see citing works
Self-citationVan Valen, D. A., Kudo, T., Lane, K. M., Macklin, D. N., Quach, N. T., DeFelice, M. M., Maayan, I., Tanouchi, Y., Ashley, E. A., & Covert, M. W. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005177 · Cited by 557 · see citing works
Feedback control of AHR signalling regulates intestinal immunity
Schiering, C., Wincent, E., Metidji, A., Iseppon, A., Li, Y., Potocnik, A. J., Omenetti, S., Henderson, C. J., Wolf, C. R., Nebert, D. W., et al. (2017) · Nature · doi:10.1038/nature21080 · Cited by 537 · see citing works
Yoshioka, H., Iseki, K.-I., & Fujita, K. (1983) · PEDIATRICS · doi:10.1542/peds.72.3.317 · Cited by 516 · see citing works
MEMOTE for standardized genome-scale metabolic model testing
Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0446-y · Cited by 509 · see citing works
Wetmore, K. M., Price, M. N., Waters, R. J., Lamson, J. S., He, J., Hoover, C. A., Blow, M. J., Bristow, J. D., Butland, G. P., Arkin, A. P., et al. (2015) · mBio · doi:10.1128/mbio.00306-15 · Cited by 474 · see citing works
Self-citationBurroughs, A. M., Allen, K. N., Dunaway‐Mariano, D., & Aravind, L. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.06.049 · Cited by 461 · 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
A metabolomics pipeline for the mechanistic interrogation of the gut microbiome
Han, S., Treuren, W. V., Fischer, C. R., Merrill, B. D., DeFelice, B. C., Sánchez, J. M., Higginbottom, S. K., Guthrie, L., Fall, L. A., Dodd, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03707-9 · Cited by 400 · see citing works
Self-citationBioModels—15 years of sharing computational models in life science
Malik-Sheriff, R. S., Glont, M., Nguyen, T. V. N., Tiwari, K., Roberts, M. G., Xavier, A., Vu, M. T., Men, J., Maire, M., Kananathan, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1055 · Cited by 361 · see citing works
Vanderpool, C. K., & Gottesman, S. (2004) · Molecular Microbiology · doi:10.1111/j.1365-2958.2004.04348.x · Cited by 353 · see citing works
CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering
Vo, P. L. H., Ronda, C., Klompe, S. E., Chen, E. E., Acree, C., Wang, H. H., & Sternberg, S. H. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-00745-y · Cited by 346 · see citing works
Probiotic Bifidobacterium breve Induces IL-10-Producing Tr1 Cells in the Colon
Jeon, S. G., Kayama, H., Ueda, Y., Takahashi, T., Asahara, T., Tsuji, H., Tsuji, N. M., Kiyono, H., Ma, J. S., Kusu, T., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002714 · Cited by 343 · see citing works
Meng, D., Sommella, E., Salviati, E., Campiglia, P., Ganguli, K. A., Djebali, K., Zhu, W., & Walker, W. A. (2020) · Pediatric Research · doi:10.1038/s41390-019-0740-x · Cited by 338 · see citing works
The essential genome of a bacterium
Christen, B., Abeliuk, E., Collier, J. M., Kalogeraki, V. S., Passarelli, B., Coller, J. A., Fero, M. J., McAdams, H. H., & Shapiro, L. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.58 · Cited by 336 · see citing works
The Essential Genome of Escherichia coli K-12
Goodall, E. C. A., Robinson, A., Johnston, I. G., Jabbari, S., Turner, K. A., Cunningham, A. F., Lund, P. A., Cole, J. A., & Henderson, I. R. (2018) · mBio · doi:10.1128/mbio.02096-17 · Cited by 324 · see citing works
Ehrlich, A. M., Pacheco, A. R., Henrick, B. M., Taft, D. H., Xu, G., Huda, M. N., Mishchuk, D. O., Goodson, M. L., Slupsky, C. M., Barile, D., et al. (2020) · BMC Microbiology · doi:10.1186/s12866-020-02023-y · Cited by 314 · see citing works
A strategy for extracting and analyzing large-scale quantitative epistatic interaction data
Collins, S. R., Schuldiner, M., Krogan, N. J., & Weissman, J. S. (2006) · Genome biology · doi:10.1186/gb-2006-7-7-r63 · Cited by 300 · see citing works
Conjugated linoleic acid biosynthesis by human-derived Bifidobacterium species
Coakley, M., Ross, R. P., Nordgren, M., Fitzgerald, G., Devery, R., & Stanton, C. (2003) · Journal of Applied Microbiology · doi:10.1046/j.1365-2672.2003.01814.x · Cited by 299 · see citing works
Microbes vs. chemistry in the origin of the anaerobic gut lumen
Friedman, E. S., Bittinger, K. L., Esipova, T. V., Hou, L., Chau, L., Jiang, J., Mesaros, C., Lund, P. J., Liang, X., FitzGerald, G. A., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1718635115 · Cited by 272 · see citing works
Exploring Vertical Transmission of Bifidobacteria from Mother to Child
Milani, C., Mancabelli, L., Lugli, G. A., Duranti, S., Turroni, F., Ferrario, C., Mangifesta, M., Viappiani, A., Ferretti, P., Gorfer, V., et al. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.02037-15 · Cited by 259 · see citing works
Sgorbati, B., Biavati, B., & Palenzona, D. L. (1995) · Springer eBooks · doi:10.1007/978-1-4615-5817-0_8 · Cited by 248 · see citing works
Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides
Wu, M., McNulty, N. P., Rodionov, D. A., Khoroshkin, M., Griffin, N. W., Cheng, J., Latreille, P., Kerstetter, R. A., Terrapon, N., Henrissat, B., et al. (2015) · Science · doi:10.1126/science.aac5992 · Cited by 245 · see citing works
Tunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome
Whitaker, W. R., Shepherd, E. S., & Sonnenburg, J. L. (2017) · Cell · doi:10.1016/j.cell.2017.03.041 · Cited by 244 · see citing works
Self-citationThe TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
Barquist, L., Mayho, M., Cummins, C. A., Cain, A. K., Boinett, C. J., Page, A. J., Langridge, G. C., Quail, M. A., Keane, J. A., & Parkhill, J. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw022 · Cited by 230 · see citing works
Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut
Lim, B., Zimmermann, M., Barry, N. A., & Goodman, A. L. (2017) · Cell · doi:10.1016/j.cell.2017.03.045 · Cited by 218 · see citing works
Robust variation in infant gut microbiome assembly across a spectrum of lifestyles
Olm, M. R., Dahan, D., Carter, M. M., Merrill, B. D., Yu, F. B., Jain, S., Meng, X., Tripathi, S. M., Wastyk, H. C., Neff, N. F., et al. (2022) · Science · doi:10.1126/science.abj2972 · Cited by 210 · see citing works
Self-citationEgan, M., Motherway, M. O., Kilcoyne, M., Kane, M., Joshi, L., Ventura, M., & van Sinderen, D. (2014) · BMC Microbiology · doi:10.1186/s12866-014-0282-7 · Cited by 192 · see citing works
Samara, J., Moossavi, S., Alshaikh, B., Ortega, V. A., Pettersen, V. K., Ferdous, T., Hoops, S. L., Soraisham, A., Vayalumkal, J., Dersch-Mills, D., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.005 · Cited by 191 · see citing works
High-throughput analysis of gene essentiality and sporulation in Clostridium difficile
Dembek, M., Barquist, L., Boinett, C. J., Cain, A. K., Mayho, M., Lawley, T. D., Fairweather, N. F., & Fagan, R. P. (2015) · mBio · doi:10.1128/mbio.02383-14 · Cited by 185 · see citing works
Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome
Jin, W., Li, T., Huo, D., Qu, S., Li, X. V., Arifuzzaman, M., Lima, S. F., Shi, H., Wang, A., Putzel, G., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.035 · Cited by 178 · see citing works
Depletion of microbiome-derived molecules in the host using Clostridium genetics
Guo, C., Allen, B. M., Hiam-Galvez, K. J., Dodd, D., Treuren, W. V., Higginbottom, S. K., Nagashima, K., Fischer, C. R., Sonnenburg, J. L., Spitzer, M. H., et al. (2019) · Science · doi:10.1126/science.aav1282 · Cited by 175 · see citing works
Self-citationThe dihydroorotate dehydrogenases: Past and present
Reis, R. A. G., Calil, F. A., Feliciano, P. R., Pinheiro, M. P., & Nonato, M. C. (2017) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2017.06.019 · Cited by 169 · see citing works
Barratt, M. J., Nuzhat, S., Ahsan, K., Frese, S. A., Arzamasov, A. A., Sarker, S. A., Islam, M. M., Palit, P., Islam, M. R., Hibberd, M. C., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abk1107 · Cited by 169 · see citing works
Peters, A., Krumbholz, P., Jäger, E., Heintz‐Buschart, A., Çakır, M. V., Rothemund, S., Gaudl, A., Ceglarek, U., Schöneberg, T., & Stäubert, C. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008145 · Cited by 168 · see citing works
Beck, L. C., Masi, A. C., Young, G. R., Vatanen, T., Lamb, C. A., Smith, R., Coxhead, J. M., Butler, A., Marsland, B. J., Embleton, N. D., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01213-w · Cited by 165 · see citing works
Liu, H., Shiver, A. L., Price, M. N., Carlson, H. K., Trotter, V. V., Chen, Y., Escalante, V., Ray, J., Hern, K. E., Petzold, C. J., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108789 · Cited by 161 · see citing works
Self-citationJames, K., Motherway, M. O., Bottacini, F., & van Sinderen, D. (2016) · Scientific Reports · doi:10.1038/srep38560 · Cited by 153 · see citing works
Self-citationMoritz, B., Striegel, K., de Graaf, A. A., & Sahm, H. (2000) · European Journal of Biochemistry · doi:10.1046/j.1432-1327.2000.01354.x · Cited by 150 · see citing works
Poupard, J. A., Husain, I., & Norris, R. F. (1973) · Bacteriological Reviews · doi:10.1128/br.37.2.136-165.1973 · Cited by 150 · see citing works
Bennel, R., & Nord, C. E. (1987) · Infection · doi:10.1007/bf01647733 · Cited by 148 · see citing works
Metabolism of Sialic Acid by Bifidobacterium breve UCC2003
Egan, M., Motherway, M. O., Ventura, M., & van Sinderen, D. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.01114-14 · Cited by 148 · see citing works
A Gram-negative-selective antibiotic that spares the gut microbiome
Muñoz, K. A., Ulrich, R. J., Vasan, A. K., Sinclair, M., Wen, P., Holmes, J. R., Lee, H. Y., Hung, C., Fields, C. J., Tajkhorshid, E., et al. (2024) · Nature · doi:10.1038/s41586-024-07502-0 · Cited by 142 · see citing works
Pathway of Glucose Fermentation in Relation to the Taxonomy of Bifidobacteria
de Vries, W., & Stouthamer, A. H. (1967) · Journal of Bacteriology · doi:10.1128/jb.93.2.574-576.1967 · Cited by 136 · see citing works
Ursell, T. S., Lee, T. K., Shiomi, D., Shi, H., Tropini, C., Monds, R. D., Colavin, A., Billings, G., Bhaya-Grossman, I., Broxton, M. J., et al. (2017) · BMC Biology · doi:10.1186/s12915-017-0348-8 · Cited by 136 · see citing works
Self-citationPaperBLAST: Text Mining Papers for Information about Homologs
Price, M. N., & Arkin, A. P. (2017) · mSystems · doi:10.1128/msystems.00039-17 · Cited by 136 · see citing works
Conjugated linoleic acid (CLA) as a functional food: Is it beneficial or not?
Badawy, S., Liu, Y., Guo, M., Liu, Z., Xie, C., Marawan, M. A., Arés, I., López-Torres, B., Martínez, M., Maximiliano, J.-E., et al. (2023) · Food Research International · doi:10.1016/j.foodres.2023.113158 · Cited by 135 · see citing works
The Gram-positive Non-spore-bearing Anaerobic Bacilli of Human Feces
Eggerth, A. H. (1935) · Journal of Bacteriology · doi:10.1128/jb.30.3.277-299.1935 · Cited by 134 · see citing works
Zhang, G., Mills, D. A., & Block, D. E. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.01416-08 · Cited by 132 · see citing works
Production of Indole-3-Lactic Acid by Bifidobacterium Strains Isolated fromHuman Infants
Sakurai, T., Odamaki, T., & Xiao, J.-Z. (2019) · Microorganisms · doi:10.3390/microorganisms7090340 · Cited by 129 · see citing works
From cells to muropeptide structures in 24 h: Peptidoglycan mapping by UPLC-MS
Kühner, D., Stahl, M., Demircioğlu, D. D., & Bertsche, U. (2014) · Scientific Reports · doi:10.1038/srep07494 · Cited by 124 · see citing works
Comparative genomics of the genus Bifidobacterium
Bottacini, F., Medini, D., Pavesi, A., Turroni, F., Foroni, E., Riley, D. R. J., Giubellini, V., Tettelin, H., van Sinderen, D., & Ventura, M. (2010) · Microbiology · doi:10.1099/mic.0.039545-0 · Cited by 120 · see citing works
Self-citationAdministration of Folate-Producing Bifidobacteria Enhances Folate Status in Wistar Rats ,
Pompei, A., Cordisco, L., Amaretti, A., Zanoni, S., Raimondi, S., Matteuzzi, D., & Rossi, M. (2007) · Journal of Nutrition · doi:10.1093/jn/137.12.2742 · Cited by 120 · see citing works
Some Important Metabolites Produced by Lactic Acid Bacteria Originated from Kimchi
Lee, S.-J., Jeon, H. S., Yoo, J., & Kim, J.-H. (2021) · Foods · doi:10.3390/foods10092148 · Cited by 120 · see citing works
Motherway, M. O., O’Driscoll, J., Fitzgerald, G. F., & van Sinderen, D. (2008) · Microbial Biotechnology · doi:10.1111/j.1751-7915.2008.00071.x · Cited by 117 · see citing works
Improvement and Optimization of Two Engineered Phage Resistance Mechanisms in Lactococcus lactis
McGrath, S., Fitzgerald, G. F., & van Sinderen, D. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.2.608-616.2001 · Cited by 115 · see citing works
Motherway, M. O., Fitzgerald, G. F., Neirynck, S., Ryan, S. M., Steidler, L., & van Sinderen, D. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.01169-08 · Cited by 112 · see citing works
Properties of Escherichia coli Mutants Deficient in Enzymes of Glycolysis
Irani, M. H., & Maitra, P. K. (1977) · Journal of Bacteriology · doi:10.1128/jb.132.2.398-410.1977 · Cited by 101 · see citing works
Álvarez, L., Hernández, S. B., de Pedro, M. A., & Cava, F. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3676-2_2 · Cited by 98 · see citing works
Self-citationSmith, L. C., Ravel, J. M., Lax, S. R., & Shive, W. (1962) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)70858-8 · Cited by 97 · see citing works
Motherway, M. O., Kinsella, M., Fitzgerald, G. F., & van Sinderen, D. (2012) · Microbial Biotechnology · doi:10.1111/1751-7915.12011 · Cited by 87 · see citing works
Mazé, A., Motherway, M. O., Fitzgerald, G. F., Deutscher, J., & van Sinderen, D. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.01496-06 · Cited by 86 · see citing works
Cellodextrin Utilization by Bifidobacterium breve UCC2003
Pokusaeva, K., Motherway, M. O., Zomer, A., MacSharry, J. A., Fitzgerald, G. F., & van Sinderen, D. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.01786-10 · Cited by 85 · see citing works
Obesogenic diets alter metabolism in mice
Showalter, M. R., Nonnecke, E. B., Linderholm, A., Čajka, T., Michael, R., Lönnerdal, B. L., Kenyon, N. J., & Fiehn, O. (2018) · PLoS ONE · doi:10.1371/journal.pone.0190632 · Cited by 74 · see citing works
GapMind: Automated Annotation of Amino Acid Biosynthesis
Price, M. N., Deutschbauer, A. M., & Arkin, A. P. (2020) · mSystems · doi:10.1128/msystems.00291-20 · Cited by 74 · see citing works
Self-citationFeehily, C., O’Neill, I. J., Walsh, C. J., Moore, R., Killeen, S. L., Geraghty, A. A., Lawton, E. M., Byrne, D. F., Sánchez-Gallardo, R., Nori, S. R. C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38694-0 · Cited by 73 · see citing works
NIELSEN, F. S., Andersen, P. S., & Jensen, K. F. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.46.29359 · Cited by 70 · see citing works
Taft, D. H., Lewis, Z. T., Nguyen, N., Ho, S., Masarweh, C. F., Dunne-Castagna, V. P., Tancredi, D. J., Huda, M. N., Stephensen, C. B., Hinde, K., et al. (2022) · Nutrients · doi:10.3390/nu14071423 · Cited by 68 · see citing works
In vitro fermentation of raffinose to unravel its potential as prebiotic ingredient
Amorim, C., Silvério, S. C., Cardoso, B. B., Alves, J. I., Pereira, M. A., & Rodrigues, L. R. (2020) · LWT · doi:10.1016/j.lwt.2020.109322 · Cited by 66 · see citing works
Cheng, C. C., Duar, R. M., Lin, X. B., Pérez-Muñoz, M. E., Tollenaar, S. L., Oh, J., van Pijkeren, J., Li, F., van Sinderen, D., Gänzle, M. G., et al. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.00190-20 · Cited by 65 · see citing works
Metabolism of Four α-Glycosidic Linkage-Containing Oligosaccharides by Bifidobacterium breve UCC2003
O’Connell, K. J., Motherway, M. O., O’Callaghan, J., Fitzgerald, G. F., Ross, R. P., Ventura, M., Stanton, C., & van Sinderen, D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01775-13 · Cited by 63 · see citing works
Ribose utilization by the human commensal Bifidobacterium breve UCC2003
Pokusaeva, K., Neves, A. R., Zomer, A., Motherway, M. O., MacSharry, J. A., Curley, P., Fitzgerald, G. F., & van Sinderen, D. (2009) · Microbial Biotechnology · doi:10.1111/j.1751-7915.2009.00152.x · Cited by 63 · see citing works
Hagen, K. D., & Meeks, J. C. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m010472200 · Cited by 59 · see citing works
Quantifying rapid bacterial evolution and transmission within the mouse intestine
Vasquez, K. S., Willis, L., Cira, N., Ng, K. M., Pedro, M. F., Aranda-Díaz, A., Rajendram, M., Yu, F. B., Higginbottom, S. K., Neff, N. F., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.08.003 · Cited by 55 · see citing works
Self-citationStructural Snapshots of Escherichia coli Histidinol Phosphate Phosphatase along the Reaction Pathway
Rangarajan, E. S., Proteau, A., Wagner, J., Hung, M., Matte, A., & Cygler, M. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m604916200 · Cited by 48 · see citing works
Ruíz, L., Motherway, M. O., Lanigan, N., & van Sinderen, D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064699 · Cited by 47 · see citing works
Shi, H., Colavin, A., Lee, T. K., & Huang, K. C. (2017) · Nature Protocols · doi:10.1038/nprot.2016.181 · Cited by 47 · see citing works
Self-citationSchöpping, M., Gaspar, P., Neves, A. R., Franzén, C. J., & Zeidan, A. A. (2021) · npj Systems Biology and Applications · doi:10.1038/s41540-021-00207-4 · Cited by 46 · see citing works
Gut Microbial Dynamics during Conventionalization of Germfree Chicken
Thomas, M., Wongkuna, S., Ghimire, S., Kumar, R., Antony, L., Doerner, K. C., Singery, A., Nelson, E. A., Woyengo, T. A., Chankhamhaengdecha, S., et al. (2019) · mSphere · doi:10.1128/msphere.00035-19 · Cited by 45 · see citing works
Self-citation[8] Dihydroorotate dehdydrogenase (Escherichia coli)
Karibian, D. (1978) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(78)51010-0 · Cited by 41 · see citing works
Sun, Y., & Vanderpool, C. K. (2010) · Journal of Bacteriology · doi:10.1128/jb.01008-10 · Cited by 41 · see citing works
Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria
Shiver, A. L., Culver, R. N., Deutschbauer, A. M., & Huang, K. C. (2021) · Nature Protocols · doi:10.1038/s41596-021-00531-3 · Cited by 40 · see citing works
Self-citationENZYMES OF THE PYRIMIDINE PATHWAY IN ESCHERICHIA COLI II
Taylor, W. H., & Taylor, M. L. (1964) · Journal of Bacteriology · doi:10.1128/jb.88.1.105-110.1964 · Cited by 38 · see citing works
O’Connell, K. J., Motherway, M. O., Liedtke, A., Fitzgerald, G. F., Ross, R. P., Stanton, C., Zomer, A., & van Sinderen, D. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00130-14 · Cited by 37 · see citing works
Accessing the Inaccessible: Molecular Tools for Bifidobacteria
Sun, Z., Baur, A., Zhurina, D. S., Yuan, J., & Riedel, C. U. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.00551-12 · Cited by 36 · see citing works
The essential genomic landscape of the commensal Bifidobacterium breve UCC2003
Ruíz, L., Bottacini, F., Boinett, C. J., Cain, A. K., Motherway, M. O., Lawley, T. D., & van Sinderen, D. (2017) · Scientific Reports · doi:10.1038/s41598-017-05795-y · Cited by 35 · see citing works
Self-citationCharacterization of GH2 and GH42 β-galactosidases derived from bifidobacterial infant isolates
Ambrogi, V., Bottacini, F., O’Sullivan, J., Motherway, M. O., Cao, L., Schoemaker, B., Schoterman, M. H. C., & van Sinderen, D. (2019) · AMB Express · doi:10.1186/s13568-019-0735-3 · Cited by 33 · see citing works
Self-citationPeters, A., Rabe, P., Liebing, A., Krumbholz, P., Nordström, A., Jäger, E., Kraft, R., & Stäubert, C. (2021) · Pharmacological Research · doi:10.1016/j.phrs.2021.106047 · Cited by 33 · see citing works
Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization
Kennedy, M. S., Zhang, M., DeLeon, O., Bissell, J., Trigodet, F., Lolans, K., Temelkova, S., Carroll, K., Fiebig, A., Deutschbauer, A. M., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113009 · Cited by 32 · see citing works
Self-citationArjes, H. A., Sun, J., Liu, H., Nguyen, T. H., Culver, R. N., Celis, A. I., Walton, S. J., Vasquez, K. S., Yu, F. B., Xue, K. S., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01481-2 · Cited by 28 · see citing works
Self-citationTripathi, S. M., Voogdt, C. G. P., Bassler, S. O., Anderson, M. E., Huang, P., Sakenova, N., Capraz, T., Jain, S., Koumoutsi, A., Bravo, A. M., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113517 · Cited by 26 · see citing works
Self-citationThe intestinal flora of infants and young children
Logan, W. R. (1913) · The Journal of Pathology and Bacteriology · doi:10.1002/path.1700180154 · Cited by 25 · see citing works
<i>Bacillus bifidus</i>: its Characters and Isolation from the Intestine of Infants.
Cruickshank, R. (1925) · Epidemiology and Infection · doi:10.1017/s0022172400008718 · Cited by 24 · see citing works
Kahler, A. E., NIELSEN, F. S., & Switzer, R. L. (1999) · Archives of Biochemistry and Biophysics · doi:10.1006/abbi.1999.1455 · Cited by 22 · see citing works
Koperniku, A., Garcia, A. A., & Mochly‐Rosen, D. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c01577 · Cited by 22 · see citing works
Broad Purpose Vector for Site-Directed Insertional Mutagenesis in Bifidobacterium breve
Hoedt, E. C., Bottacini, F., Cash, N., Bongers, R. S., van Limpt, K., Amor, K. B., Knol, J., MacSharry, J. A., & van Sinderen, D. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.636822 · Cited by 21 · see citing works
Self-citationAdams, A. N. D., Azam, M. S., Costliow, Z. A., Ma, X., Degnan, P. H., & Vanderpool, C. K. (2021) · Journal of Bacteriology · doi:10.1128/jb.00217-21 · Cited by 21 · see citing works
Production of Hydroxycarboxylic Acid Receptor 3 (HCA3) Ligands by Bifidobacterium
Sakurai, T., Horigome, A., Odamaki, T., Shimizu, T., & Xiao, J. (2021) · Microorganisms · doi:10.3390/microorganisms9112397 · Cited by 21 · see citing works
Voogdt, C. G. P., Tripathi, S. M., Bassler, S. O., McKeithen-Mead, S. A., Guiberson, E. R., Koumoutsi, A., Bravo, A. M., Buie, C., Zimmermann, M., Sonnenburg, J. L., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113519 · Cited by 21 · see citing works
Self-citationWatanabe, S. (2020) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)49890-5 · Cited by 16 · see citing works
Watanabe, S. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.011854 · Cited by 11 · see citing works
Determinants of raffinose family oligosaccharide use in Bacteroides speciesPreprint
Basu, A., Adams, A. N. D., Degnan, P. H., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.07.597959 · Cited by 1 · see citing works
Flagged first, then by citations
Research works printed but not linked: 4
- [37]Meng D, Sommella E, Salviati E, Campiglia P, Ganguli K, Djebali K, Zhu W, and Walker WA (2020). Indole-3-lactic acid, a metabolite of tryptophan, secreted by Bifidobacterium longum subspecies infantis is anti-inflammatory in the immature intestine. Pediatr Res 88, 209– 217. 10.1038/s41390-019-0740-x. 31945773 PMC7363505 · DOI
- [41]Wetmore Kelly M., Price Morgan N., Waters Robert J., Lamson Jacob S., He J, Hoover Cindi A., Blow Matthew J., Bristow J, Butland G, Arkin Adam P., and Deutschbauer A (2015). Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons. mBio 6, e00306–00315. 10.1128/mBio.00306-15. PMC4436071 25968644 · DOI
- [64]Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, and Gordon JI (2009). Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 6, 279– 289. 10.1016/j.chom.2009.08.003. 19748469 PMC2895552 · DOI
- [146]Wetmore KM, Price MN, Waters RJ, Lamson JS, He J, Hoover CA, Blow MJ, Bristow J, Butland G, Arkin AP, and Deutschbauer A (2015). Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. mBio 6, e00306– 00315. 10.1128/mBio.00306-15. 25968644 PMC4436071 · DOI
Cited by
Sorted by citations
Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering
Bakkeren, E., Piskovsky, V., & Foster, K. R. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.05.013 · Cited by 91 · see citing works
Arzamasov, A. A., Rodionov, D. A., Hibberd, M. C., Guruge, J. L., Kent, J. E., Kazanov, M. D., Leyn, S. A., Elane, M. L., Sejane, K., Fürst, A., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02056-x · Cited by 49 · see citing works
Manzanera, M. (2025) · Biology · doi:10.3390/biology14091203 · Cited by 16 · see citing works
“These interactions drive evolutionary outcomes such as host–microbe co-speciation (parallel divergence of gut microbiomes and hominid lineages) and local adaptation (geographic Bifidobacterium strains matching lactase persistence genotypes) [64].”
Bacterial fitness for plant colonization is influenced by plant growth substrate
Torres, M., Price, M. N., Khasanova, A., Kosina, S. M., Zhalnina, K. V., Northen, T. R., & Deutschbauer, A. M. (2025) · New Phytologist · doi:10.1111/nph.70617 · Cited by 9 · see citing works
Self-citationBifidobacterium as Keystone Species Driving Microbial Interactions in the Infant Digestive Tract
Vásquez-Dean, J., Canales, A., Orellana, C. A., & Garrido, D. (2026) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-052924-065321 · Cited by 7 · see citing works
Bacteriocin gene-mediated ecological adaptation of Bifidobacterium breve in the adult human gut
Wang, J., Qian, X., Li, Q., Jin, Z., Liu, N., Zhao, J., Chen, W., Wang, S., & Tian, P. (2026) · Cell Genomics · doi:10.1016/j.xgen.2025.101106 · Cited by 5 · see citing works
“Although broad-spectrum carbohydrate metabolism, mediated by glycoside hydrolase families such as GH36, 19 has been presumed to underlie its adaptability, our comparative genomic analysis of infant-and adult-derived B . breve strains revealed a high level of conservation in core genome architecture…”
Yang, P., Xiao, C.-Y., Wang, J., Yan, C.-H., Li, Q.-Y., Li, S.-Y., Li, J., Zhang, L.-J., & Dai, C. (2026) · World Journal of Gastroenterology · doi:10.3748/wjg.v32.i6.113010 · Cited by 4 · see citing works
The phenotypic landscape of the mycobacterial cellPreprint
Herrera, N., Todor, H., Kim, L. M., Burkhart, H. N., Billings, E., Fay, A., Warner, T. C., Lee, S. Y., Sayegh, N. Y., Bosch, B., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.14.688347 · Cited by 4 · see citing works
“Moreover, even in the distantly related actinobacterium Bifidobacterium breve , TnSeq experiments show a substantial similarity between the phenotypes of the UPF0182-family homolog and the YccA homolog (r = 0.62, reciprocal top hits 46 ) (Figure 5A).”
InfluentialHe, T., Chen, J., Zheng, J., Li, H., Ma, D., Wang, L., Mao, J., Luo, J., & Yang, Z. (2026) · Food & Function · doi:10.1039/d5fo05140a · Cited by 3 · see citing works
An exciting future for microbial molecular biology and physiology
Bridges, A. A., Guthrie, L. T. C., Lehman, M. K., Kellogg, E. H., Miranda, S. W., Pountain, A. W., Shiver, A. L., Varble, A., Kaplan, H. B., Shank, E. A., et al. (2025) · mBio · doi:10.1128/mbio.00694-25 · Cited by 2 · see citing works
Self-citationLi, H., Han, J. J., Li, Y., Yang, T., Liu, K. Z., Zhang, L., Fu, T., & Su, C. Y. (2025) · animal · doi:10.1016/j.animal.2025.101741 · Cited by 2 · see citing works
Morozova, A., Golovneva, N. A., Kurchenko, V., Evdokimov, I., Lodygin, A., Nagdalian, A., & Ulrih, N. P. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.152774 · Cited by 2 · see citing works
Li, Y., Li, H., Zhang, Q., Cui, S., Zhai, Q., Stanton, C., Ross, P. M., Zhao, J., Chen, W., & Yang, B. (2026) · Food & Function · doi:10.1039/d5fo05688h · Cited by 1 · see citing works
Friess, L., McAuliffe, F. M., Cotter, P. D., Shiver, A. L., Huang, K. C., de Jong, A., & van Sinderen, D. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2647591 · Cited by 1 · see citing works
“64 Furthermore, the ability to utilize arabinose and xylose could be exploited to develop prebiotics to specifically enrich B. longum subsp. longum , similar to a recent finding that an arabinoxylan-rich diet increased the relative abundance of B. longum subsp. longum.”
Self-citationPlenge, T. G., Pedersen, M., & Laursen, M. F. (2026) · Applied and Environmental Microbiology · doi:10.1128/aem.02511-25 · Cited by 1 · see citing works
“In”
Ennis, D., Andreu‐Sánchez, S., Jayaprakash, Y. K., Sinha, T., Peng, H., Goldberger, O., Docherty, J. A. D., Kuzub, N., Fernández-Pato, A., Zhao, S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.23.661074 · Cited by 1 · see citing works
Selleri, E., Longhi, G., Tarracchini, C., Carolis, E. D., Petraro, S., Mancabelli, L., Milani, C., Turroni, F., Ventura, M., & Lugli, G. A. (2026) · Microbiome Research Reports · doi:10.20517/mrr.2026.19
Spark the immunization by seeding bifidobacteria in early life
Zeng, S., Mu, D., & Wang, S. (2025) · 中国科学通报:英文版 · doi:10.1016/j.scib.2025.07.038
Gao, Z., & Feng, L. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1653505
Machine Learning Reveals Quantitative Amino Acid Preferences in Bifidobacterium longum Growth
Kaneko, H., Kadowaki, K., Yoshimoto, S., Odamaki, T., & Ying, B. (2026) · Microbial Biotechnology · doi:10.1111/1751-7915.70367
“In B. breve , aromatic lactic acid production produced from aromatic amino acids provides a direct fitness advantage that markedly promotes growth (Shiver et al. 2025).”
Tong, X., Liang, H., Tian, Y., Yang, X., Wang, Y., Wang, H., Gu, Y., Ma, Z., Su, W., Liu, Y., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.21.726744
Dietary fiber selectively regulates intestinal persistence of probiotic bifidobacteriaPreprint
Choi, G., Chatterjee, S., Shah, U., Won, T. H., Skouris, A., Kim, J. Y., Mujib, W., Sun, H., Fontaine, M. A., Messyasz, A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.06.730603
Gu, Z., Xie, Z., Lu, Z., Xu, S., Huang, Q., Zhao, L., Liu, F., & Zhang, B. (2026) · Food Bioscience · doi:10.1016/j.fbio.2026.109712
Lee, J., Glazier, J., Weichselbaum, R. R., & Mimee, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.12.744520
“Previous transposon mutagenesis studies in B. breve have enabled genome-wide analysis of native gene functions 46 , but their reliance on disruptive insertions limits functional analysis to mutants that can be recovered and does not allow specific genes to be selectively repressed 47 .”
Grinberg, L., Sirhan, W., Kurtz, M., Assa, M., Malka, A., Perez, S., Katina, C., Levin, Y., & Piran, R. (2026) · Experimental and Molecular Medicine · doi:10.1038/s12276-026-01826-9
Bifidobacteria: biogeography, host adaptation and ecological functions
Tarracchini, C., Milani, C., Jones, C. N. L., Turroni, F., Burgess, G., Mahony, J., Hall, L. J., Ventura, M., & van Sinderen, D. (2026) · Nature Reviews Microbiology · doi:10.1038/s41579-026-01367-y
Chen, S., Wang, L., Zhang, S., Zhang, J., Yan, X., & Wu, Z. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1931902
“The gut microbiota is in fl uenced by multiple factors such as host genetic background, dietary structure, antibiotic use history, and age (162 – 165).”
- Authors
- Shiver, A. L., Sun, J., Culver, R., Violette, A., Wynter, C., Nieckarz, M., Mattiello, S. P., Sekhon, P. K., Bottacini, F., Friess, L., Carlson, H. K., Wong, D. P. G. H., Higginbottom, S., Weglarz, M., Wang, W., Knapp, B. D., Guiberson, E., Sanchez, J., Huang, P.-H., Garcia, P. A., Buie, C. R., Good, B. H., DeFelice, B., Cava, F., Scaria, J., Sonnenburg, J. L., Van Sinderen, D., Deutschbauer, A. M., & Huang, K. C.
- Affiliations
- Stanford University (US)
- Science for Life Laboratory (SE)
- South Dakota State University (US)
- Oklahoma State University (US)
- University College Cork (IE)
- Lawrence Berkeley National Laboratory (US)
- Stanford Medicine (US)
- Middlebury College (US)
- Massachusetts Institute of Technology (US)
- Chan Zuckerberg Biohub San Francisco (US)
- Corresponding author
- Huang, Kerwyn Casey
- ORCID
- Shiver, Anthony L.
- Sun, Jiawei
- Culver, Rebecca
- Violette, Arvie
- Nieckarz, Marta
- Mattiello, Samara Paula
- Sekhon, Prabhjot Kaur
- Bottacini, Francesca
- Friess, Lisa
- Carlson, Hans K.
- Wong, Daniel P.G.H.
- Higginbottom, Steven
- Weglarz, Meredith
- Wang, Weigao
- Knapp, Benjamin D.
- Guiberson, Emma
- Huang, Po-Hsun
- Buie, Cullen R.
- Good, Benjamin H.
- DeFelice, Brian
- Cava, Felipe
- Scaria, Joy
- Sonnenburg, Justin L.
- Deutschbauer, Adam M.
- Huang, Kerwyn Casey
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2025-04
- Volume
- 188
- Issue
- 7
- Pages
- 2003-2021.e19
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC13403077
- OpenAlex
- W4408290372
- Cited by
- 27
- References
- 141
- Citations by year
- 2026: 16 · 2025: 11
- FWCI
- 8.12
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 367 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion)
- Funders
- NIH National Institute of General Medical Sciences (RM1 GM135102, R35 GM146949)
- National Science Foundation (EF-2125383, IOS-2032985)
- Svenska Sällskapet för Medicinsk Forskning
- Vetenskapsrådet
- Science Foundation Ireland (SFI/12/RC/2273-P2, SFI/12/RC/2273-P1)
- Knut och Alice Wallenbergs Stiftelse
- National Defense Science and Engineering Graduate
- National Institutes of Health
- Kempe Foundation
- National Institute of Allergy and Infectious Diseases Division of Intramural Research (R01 AI147023)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Keywords
- Bifidobacterium breve, infant gut microbiota, intestinal colonization, host-microbe interactions, transposon mutant library, germ-free mice, chickens, diet, immunomodulatory molecules, probiotics
- MeSH terms
- Gastrointestinal Microbiome, Bifidobacterium breve, Host Microbial Interactions, Animals, Chickens, DNA Transposable Elements, Female, Germ-Free Life, Humans, Infant, Mice, Inbred C57BL, Symbiosis, Genome, Bacterial, Mice
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