Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome
Open accessAbstract
Background: Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods. Results: We combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10–70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice. Conclusions: Collectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans.
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?
In a previous study, probiotic strain Lp082 rapidly acquired adaptive mutations within the gut, significantly enhanced its carbon utilization and acid tolerance.
“In our previous study, we first demonstrated that a probiotic strain, Lactiplantibacillus plantarum HNU082 (Lp082), rapidly acquired adaptive mutations within the gut, significantly enhanced its carbon utilization and acid tolerance.25”
From Gut microbiota drives structural variation of exogenous probiotics to enhance colonization (2025) · cites this paper as [25]
The method for isolating and identifying Lp082 from feces has been established in previous research.
“The method for isolating and identifying Lp082 from feces has been established in previous research.25”
From Gut microbiota drives structural variation of exogenous probiotics to enhance colonization (2025) · cites this paper as [25]
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
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
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 25,691 · see citing works
Hill (2014) · doi:10.1038/nrgastro.2014.66 · Cited by 9,592 · see citing works
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · see citing works
Improved metagenomic analysis with Kraken 2
Wood, D. E., Lu, J., & Langmead, B. (2019) · Genome biology · doi:10.1186/s13059-019-1891-0 · Cited by 7,173 · see citing works
Gibson, G. R., Hutkins, R., Sanders, M. E., Prescott, S. L., Reimer, R. A., Salminen, S. J., Scott, K., Stanton, C., Swanson, K. S., Cani, P. D., et al. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.75 · Cited by 5,634 · see citing works
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012) · GigaScience · doi:10.1186/2047-217x-1-18 · Cited by 5,274 · see citing works
Self-citationLetunic, I., & Bork, P. (2016) · Nucleic Acids Res. · doi:10.1093/nar/gkw290 · Cited by 4,851 · see citing works
Environment dominates over host genetics in shaping human gut microbiota
Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D., Costea, P. I., Godneva, A., Kalka, I. N., Bar, N., et al. (2018) · Nature · doi:10.1038/nature25973 · Cited by 2,859 · see citing works
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
Schubert, M., Lindgreen, S., & Orlando, L. (2016) · BMC Research Notes · doi:10.1186/s13104-016-1900-2 · Cited by 2,091 · see citing works
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
Kurtz, Z. D., Müller, C. L., Miraldi, E. R., Littman, D. R., Blaser, M. J., & Bonneau, R. A. (2015) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004226 · Cited by 1,799 · see citing works
Species-level functional profiling of metagenomes and metatranscriptomes
Franzosa, E. A., McIver, L. J., Rahnavard, G., Thompson, L. R., Schirmer, M., Weingart, G., Lipson, K. S., Knight, R., Caporaso, J. G., Segata, N., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0176-y · Cited by 1,693 · see citing works
Self-citationConsumption of fermented milk product with probiotic modulates brain activity
Tillisch, K., Labus, J., Kilpatrick, L., Jiang, Z., Stains, J., Ebrat, B., Guyonnet, D., Legrain–Raspaud, S., Trotin, B., Naliboff, B., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.02.043 · Cited by 1,192 · see citing works
Suez, J., Zmora, N., Zilberman-Schapira, G., Mor, U., Dori-Bachash, M., Bashiardes, S., Zur, M., Regev-Lehavi, D., Ben-Zeev Brik, R., Federici, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.047 · Cited by 1,184 · see citing works
Newberry, S. J. (2012) · JAMA · doi:10.1001/jama.2012.3507 · Cited by 870 · see citing works
Safety assessment of probiotics for human use
Sanders, M. E., Akkermans, L. M. A., Haller, D., Hammerman, C., Heimbach, J. T., Hörmannsperger, G., & Huys, G. (2010) · Gut Microbes · doi:10.4161/gmic.1.3.12127 · Cited by 816 · see citing works
Storelli, G., Defaye, A., Erkoşar, B., Pascal Hols, A., Royet, J., & Leulier, F. (2011) · Cell Metabolism · doi:10.1016/j.cmet.2011.07.012 · Cited by 804 · see citing works
Our gut microbiome: The evolving inner self
Kundu, P., Blacher, E., Elinav, E., & Pettersson, S. (2017) · Cell · doi:10.1016/j.cell.2017.11.024 · Cited by 633 · see citing works
Establishing microbial composition measurement standards with reference frames
Morton, J. T., Marotz, C., Washburne, A., Silverman, J., Zaramela, L. S., Edlund, A., Zengler, K., & Knight, R. (2019) · Nature Communications · doi:10.1038/s41467-019-10656-5 · Cited by 613 · see citing works
Self-citationFate, activity, and impact of ingested bacteria within the human gut microbiota
Derrien, M., & van Hylckama Vlieg, J. E. T. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.03.002 · Cited by 605 · see citing works
Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition
Schwarzer, M., Makki, K., Storelli, G., Machuca‐Gayet, I., Šrůtková, D., Hermanová, P. P., Martino, M. E., Balmand, S., Hudcovic, T., Heddi, A., et al. (2016) · Science · doi:10.1126/science.aad8588 · Cited by 590 · see citing works
McNulty, N. P., Yatsunenko, T., Hsiao, A., Faith, J. J., Muegge, B. D., Goodman, A. L., Henrissat, B., Oozeer, R., Cools-Portier, S., Gobert, G., et al. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3002701 · Cited by 544 · see citing works
Self-citationMaldonado-Gómez, M. X., Martínez, I., Bottacini, F., O’Callaghan, A., Ventura, M., van Sinderen, D., Hillmann, B., Vangay, P., Knights, D., Hutkins, R. W., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.09.001 · Cited by 517 · see citing works
Fucose sensing regulates bacterial intestinal colonization
Pacheco, A. R., Curtis, M. M., Ritchie, J. M., Munera, D., Waldor, M. K., Moreira, C. G., & Sperandio, V. (2012) · Nature · doi:10.1038/nature11623 · Cited by 499 · see citing works
Exploring host–microbiota interactions in animal models and humansPreprint
Kostic, A. D., Howitt, M. R., & Garrett, W. S. (2013) · Genes & Development · doi:10.1101/gad.212522.112 · Cited by 491 · see citing works
Microbial Invasions: The Process, Patterns, and Mechanisms
Mallon, C. A., van Elsas, J. D., & Salles, J. F. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.07.013 · Cited by 488 · see citing works
Nayfach, S., Rodriguez-Mueller, B., Garud, N., & Pollard, K. S. (2016) · Genome Research · doi:10.1101/gr.201863.115 · Cited by 470 · see citing works
Temporal variability is a personalized feature of the human microbiome
Flores, G. E., Caporaso, J. G., Henley, J. B., Rideout, J. R., Domogala, D., Chase, J., Leff, J. W., Vázquez-Baeza, Y., Gonzalez, A., Knight, R., et al. (2014) · Genome Biology · doi:10.1186/s13059-014-0531-y · Cited by 446 · see citing works
Self-citationAdaptive 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
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
Yelin, I., Flett, K. B., Merakou, C., Mehrotra, P., Stam, J., Snesrud, E., Hinkle, M., Lesho, E., McGann, P., McAdam, A. J., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0626-9 · Cited by 315 · see citing works
Leatham, M. P., Banerjee, S., Autieri, S. M., Mercado–Lubo, R., Conway, T., & Cohen, P. S. (2009) · Infection and Immunity · doi:10.1128/iai.00059-09 · Cited by 233 · see citing works
Sánchez, Á., & Gore, J. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001547 · Cited by 216 · see citing works
Walter, J., Maldonado-Gómez, M. X., & Martínez, I. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.08.008 · Cited by 198 · see citing works
Martino, M. E., Joncour, P., Leenay, R. T., Gervais, H., Shah, M., Hughes, S., Gillet, B., Beisel, C. L., & Leulier, F. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.06.001 · Cited by 149 · see citing works
Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut
Crook, N., Ferreiro, A. L., Gasparrini, A. J., Pesesky, M. W., Gibson, M. K., Wang, B., Sun, X., Condiotte, Z. J., Dobrowolski, S., Peterson, D. A., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.02.005 · Cited by 133 · see citing works
Multiscale Evolutionary Dynamics of Host-Associated Microbiomes
Ferreiro, A., Crook, N., Gasparrini, A. J., & Dantas, G. (2018) · Cell · doi:10.1016/j.cell.2018.02.015 · Cited by 127 · see citing works
Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice
Marco, M. L., de Vries, M. C., Wels, M., Douwe Molenaar, B., Mangell, P., Ahrné, S., de Vos, W. M., Vaughan, E. E., & Kleerebezem, M. (2010) · The ISME Journal · doi:10.1038/ismej.2010.61 · Cited by 105 · see citing works
Zhang, J., Wang, X., Huo, D., Li, W., Hu, Q., Xu, C., Liu, S., & Li, C. (2016) · Scientific Reports · doi:10.1038/srep32524 · Cited by 102 · see citing works
Self-citationSchröder, G., & Lanka, E. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.15.4371-4381.2003 · Cited by 86 · see citing works
Shao, Y., Huo, D., Peng, Q., Pan, Y., Jiang, S., Liu, B., & Zhang, J. (2017) · Food & Function · doi:10.1039/c7fo00902j · Cited by 72 · see citing works
Self-citationSucci, M., Tremonte, P., Pannella, G., Tipaldi, L., Cozzolino, A., Romaniello, R., Sorrentino, E., & Coppola, R. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01067 · Cited by 43 · see citing works
Kwok, L., Guo, Z., Zhang, J., Wang, L., Qiao, J., Hou, Q., Zheng, Y., & Zhang, H. (2015) · Beneficial Microbes · doi:10.3920/bm2014.0063 · Cited by 38 · see citing works
Self-citationGenomic Variations in Probiotic Lactobacillus plantarum P-8 in the Human and Rat Gut
Song, Y., He, Q., Zhang, J., Qiao, J., Xu, H., Zhong, Z., Zhang, W., Sun, Z., Yang, R., Cui, Y., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00893 · Cited by 28 · see citing works
Self-citationMethod for the simulation of blood platelet shape and its evolution during activation
Moskalensky, A. E., Yurkin, M. A., Muliukov, A. R., Litvinenko, A. L., Nekrasov, V. M., Chernyshev, A. V., & Maltsev, V. P. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005899 · Cited by 22 · see citing works
SAMSVM: A tool for misalignment filtration of SAM-format sequences with support vector machine
Yang, J., Ding, X., Sun, X., Tsang, S., & Xue, H. (2015) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720015500250 · Cited by 19 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Wu, Y., Jha, R., Li, A., Liu, H., Zhang, Z., Zhang, C., Zhai, Q., & Zhang, J. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.01651-22 · Cited by 243 · see citing works
Self-citationA novel approach to Lactiplantibacillus plantarum: From probiotic properties to the omics insights
Echegaray, N., Yılmaz, B., Sharma, H., Kumar, M., Pateiro, M., Özoğul, F., & Lorenzo, J. M. (2022) · Microbiological Research · doi:10.1016/j.micres.2022.127289 · Cited by 215 · see citing works
Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes
Russell, B. J., Brown, S. D., Siguenza, N., Mai, I., Saran, A. R., Lingaraju, A., Maissy, E. S., Dantas Machado, A. C., Pinto, A. F. M., Sanchez, C., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.050 · Cited by 151 · see citing works
Self-citationIntrahost evolution of the gut microbiota
Barreto, H. C., & Gordo, I. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00890-6 · Cited by 81 · see citing works
Wu, Y., Li, A., Liu, H., Zhang, Z., Zhang, C., Ma, C., Zhang, L., & Zhang, J. (2022) · Food & Function · doi:10.1039/d2fo02303b · Cited by 67 · see citing works
Self-citationFang, X., Liu, H., Du, Y., Jiang, L., Gao, F., Wang, Z., Chi, Z., Shi, B., & Zhao, X. (2024) · Research · doi:10.34133/research.0415 · Cited by 56 · see citing works
Jiang, Y., Liang, M., Yang, Y.-H., Xue, J., & Suo, H. (2023) · Aquaculture · doi:10.1016/j.aquaculture.2023.740506 · Cited by 45 · see citing works
Data-driven prediction of colonization outcomes for complex microbial communities
Wu, L., Wang, X.-W., Tao, Z., Wang, T., Zuo, W., Zeng, Y., Liu, Y.-Y., & Dai, L. (2024) · Nature Communications · doi:10.1038/s41467-024-46766-y · Cited by 44 · see citing works
Self-citationmetaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model
Wu, S., Feng, T., Tang, W., Qi, C., Gao, J., He, X., Wang, J., Zhou, H., & Fang, Z. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae085 · Cited by 43 · see citing works
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 45 · see citing works
Probiotics: insights and new opportunities for Clostridioides difficile intervention
Pal, R., Athamneh, A. I. M., Deshpande, R., Ramirez, J. A. R., Adu, K. T., Muthuirulan, P., Pawar, S., Biazzo, M., Apidianakis, Y., Sundekilde, U. K., et al. (2022) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2022.2072705 · Cited by 42 · see citing works
Licitra, R., Fronte, B., Verri, T., Marchese, M., Sangiacomo, C., & Santorelli, F. M. (2024) · Biology · doi:10.3390/biology13040209 · Cited by 36 · see citing works
Saeed, M., Al-Khalaifah, H. S., Al-Nasser, A. Y., & Al-Surrayai, T. (2025) · Poultry Science · doi:10.1016/j.psj.2025.105130 · Cited by 35 · see citing works
Precise probiotic therapy: Advances, bottlenecks, and the road to microbiome-informed nutrition
Jiang, Y., Jiang, S., Wang, Z., Zhu, P., Zhang, J., Teng, F., & Huang, S. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2623359 · Cited by 39 · see citing works
Self-citationNative 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
Self-citationLeeflang, J., Wright, J. A., Worthley, D. L., Din, M. O., & Woods, S. L. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00734-6 · Cited by 24 · see citing works
Ma, C., Zhang, C., Chen, D., Jiang, S., Shen, S., Huo, D., Huang, S. W., Zhai, Q., & Zhang, J. (2021) · Communications Biology · doi:10.1038/s42003-021-02724-8 · Cited by 24 · see citing works
Self-citationMiao, Z., Chen, L., Zhang, Y., Zhang, J., & Zhang, H. (2023) · mSystems · doi:10.1128/msystems.01013-23 · Cited by 27 · see citing works
Self-citationAdvances in adaptive laboratory evolution applications for Escherichia coli
Peng, W., Zhang, X., Qi, Q., & Liang, Q. (2025) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2025.07.011 · Cited by 20 · see citing works
Genomic Mutations Within the Host Microbiome: Adaptive Evolution or Purifying Selection
Zhang, J., & Knight, R. D. (2022) · Engineering · doi:10.1016/j.eng.2021.11.018 · Cited by 21 · see citing works
Self-citationTuerhong, N., Wang, L., Cui, J., Shataer, D., Yan, H., Dong, X., Gao, Z., Zhang, M., Qin, Y., & Lu, J. (2024) · Foods · doi:10.3390/foods13223569 · Cited by 17 · see citing works
Mendoza, R. M., Kim, S. H., Vasquez, R., Hwang, I., Park, Y., Paik, H., Moon, G., & Kang, D. (2022) · Food Science and Biotechnology · doi:10.1007/s10068-022-01142-8 · Cited by 17 · see citing works
The Impact of Diet on the Colonization of Beneficial Microbes from an Ecological Perspective
Chen, Z., Xiao, C., Zhang, J., Jian, S., Li, P., Lin, J., He, C., Chen, Z., Qi, Y., Shi, J., et al. (2025) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.5c02086 · Cited by 17 · see citing works
Self-citationGut 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
“20,25 This study identified two parallel evolutionary genes in clade-1 isolates, while 56 were identified in clade-2 isolates.”
Self-citationWu, Y., Li, A., Cheng, L., Chen, Q., Li, J., Xu, Y., & Huo, D. (2022) · Food & Function · doi:10.1039/d2fo02501a · Cited by 15 · see citing works
Self-citationMaritan, E., Gallo, M., Šrůtková, D., Jelinkova, A., Benada, O., Kofroňová, O., Silva-Soares, N. F., Hudcovic, T., Gifford, I., Barrick, J. E., et al. (2022) · BMC Biology · doi:10.1186/s12915-022-01477-y · Cited by 11 · see citing works
He, B., Hu, T., & Wu, H. (2023) · Food Bioscience · doi:10.1016/j.fbio.2023.102949 · Cited by 11 · see citing works
Vasudha, M., & Gayathri, D. (2024) · The Microbe · doi:10.1016/j.microb.2024.100173 · Cited by 11 · see citing works
Xiong, D., Sun, T., Liu, M., Wang, B., Guan, T., Song, L., Jiao, X., & Yang, Z. (2024) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-024-10440-y · Cited by 11 · see citing works
Li, W., Xu, M. Y., Liu, Y., Zhang, S., Wang, J., Zhang, Z., Xiao, G., Wang, R., Zhang, J., & Xue, H. (2025) · Foods · doi:10.3390/foods14050813 · Cited by 11 · see citing works
Self-citationWu, Q., Li, W., Kwok, L.-Y., Lv, H., Sun, J., & Sun, Z. (2024) · Food Research International · doi:10.1016/j.foodres.2024.114840 · Cited by 9 · see citing works
Jiang, S., Zhang, Z., Shen, S., Li, J., Su, S., Du, L., Ma, W., & Zhang, J. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2447819 · Cited by 9 · see citing works
Self-citationLiu, P., Ouyang, Y., Gao, Z., Tan, J., Chen, X., Xiao, Y., Wang, Y., Liu, J., Liu, B., Gao, B., et al. (2025) · Journal of Functional Foods · doi:10.1016/j.jff.2025.107029 · Cited by 10 · see citing works
Ma, C., Zhang, Y., Jiang, S., Teng, F., Huang, S. W., & Zhang, J. (2023) · mSystems · doi:10.1128/msystems.00828-23 · Cited by 8 · see citing works
Self-citationHan, X., Shi, C., Wei, Z., Lu, Z., Chai, L., Xu, H.-Y., Shi, J., Zhang, X., & Xu, Z. (2025) · LWT · doi:10.1016/j.lwt.2025.118148 · Cited by 7 · see citing works
Dobloug, M. S., Skagen-Sandvik, C., Evensen, Ø., Gadan, K., Bakke, M. J., Sørum, H. R., & Salonius, K. (2023) · Applied Microbiology · doi:10.3390/applmicrobiol3040090 · Cited by 7 · see citing works
Wang, X., Xie, W., Zhang, S., Shao, Y., Cai, J., Cai, L., Wang, X., Shan, Z., Zhou, H., Li, J., et al. (2022) · Foods · doi:10.3390/foods11203169 · Cited by 7 · see citing works
Gut microbiome evolution impacts the clinical outcomes of diseases
Sun, L., Li, J., Feng, Y., & Sun, Y. (2023) · HepatoBiliary Surgery and Nutrition · doi:10.21037/hbsn-23-127 · Cited by 7 · see citing works
Madison, J. D., Osborne, O. G., Ellison, A., Garvey, C. N., Gentry, L. K., Gross, H., Gratwicke, B., Grayfer, L., & Muletz‐Wolz, C. R. (2025) · Infection and Immunity · doi:10.1128/iai.00569-24 · Cited by 6 · see citing works
Wang, Z., Feng, Y., Han, J., Lu, C., Zhou, J. Y., Wang, Z., & Su, X. (2023) · Food Bioscience · doi:10.1016/j.fbio.2023.102694 · Cited by 6 · see citing works
Different intestinal ecological niches drive the divergent evolution of probiotics in the gut
Han, Z., Huang, D., Liu, X., Ma, W., Cui, W., Jiang, S., Zheng, D., & Zhang, J. (2025) · ISME Communications · doi:10.1093/ismeco/ycaf023 · Cited by 5 · see citing works
Self-citationAdaptive responses and molecular mechanisms of Lactiplantibacillus plantarum to citric acid stress
Han, X., Zhang, W., Shi, C., Liu, R., Lu, Z., Chai, L., Xu, H., Shi, J., Zhang, X., & Xu, Z. (2025) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2025.111340 · Cited by 4 · see citing works
The Effects of Social Experience on Host Gut Microbiome in Male Zebrafish ( Danio rerio )
Scott, E., Brewer, M. S., Peralta, A. L., & Issa, F. A. (2023) · Biological Bulletin · doi:10.1086/729377 · Cited by 3 · see citing works
Biodiversity responses of gut mycobiota and bacteriophages induced by probiotic consumption
Li, J., Ma, C., Liu, X., Jiang, S., Huo, D., Cai, K., & Zhang, J. (2023) · Journal of Functional Foods · doi:10.1016/j.jff.2023.105615 · Cited by 4 · see citing works
Self-citationZhang, Z., Lv, Y., Guo, Z., Liu, L., Chen, X., Han, W., Wei, J., Guo, S., Sun, Y., & Wang, S. (2025) · Poultry Science · doi:10.1016/j.psj.2025.106274 · Cited by 3 · see citing works
Dobloug, M. S., Iakhno, S., Nørstebø, S. F., Evensen, Ø., & Sørum, H. R. (2025) · Aquaculture · doi:10.1016/j.aquaculture.2025.743518 · Cited by 2 · see citing works
Competition and compromise between exogenous probiotics and native microbiota
Han, Z., Sun, Z., Zhao, Q., Du, L., Zhen, D., Liu, X., Jiang, S., Liu, Y., & Zhang, J. (2026) · Cell Systems · doi:10.1016/j.cels.2025.101516 · Cited by 2 · see citing works
Self-citationWang, Z., Zhang, Z., Shi, Q., Liu, S., Wu, Q., Wang, Z., Saiding, E., Han, J., Zhou, J., Wang, R., et al. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1295058 · Cited by 2 · see citing works
Ma, C., Zhang, Y., Jiang, S., Teng, F., Huang, S. W., & Zhang, J. (2022) · Research Square · doi:10.21203/rs.3.rs-1747065/v1 · Cited by 2 · see citing works
Self-citationEspiritu, H. M., & Parayao, A. M. (2026) · DNA · doi:10.3390/dna6020018 · Cited by 1 · see citing works
Bujdoš, D., Walter, J., & O’Toole, P. W. (2026) · The ISME Journal · doi:10.1093/ismejo/wrag198 · Cited by 1 · see citing works
de Almeida, M. E., Sodré, M. M. D., Oliveira, S. S., de Carvalho, L. D., Apolônio, A. C. M., Rocha, V. N., Rezende, R. P., & Romano, C. C. (2024) · Research Square · doi:10.21203/rs.3.rs-4978949/v1 · Cited by 1 · see citing works
Maritan, E., Gallo, M., Šrůtková, D., Jelinkova, A., Benada, O., Kofroňová, O., Silva-Soares, N. F., Hudcovic, T., Gifford, I., Barrick, J. E., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.04.482961
Host, pathogenic fungi and the microbiome: A genetic triangle in infection
Gago, S., Mandarano, M., Floridi, C., & Zelante, T. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1078014
Smith, T. J., & Guillemin, K. J. (2024) · Science · doi:10.1126/science.adt8031
Meta-analysis of postbiotics on evaluating health benefits and mechanisms
Barathikannan, K., Chelliah, R., David, H. A., Kulandairaj, E. P., Vijayalakshmi, S., Rubab, M., & Oh, D.-H. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-22188-0.00019-x
Ma, W., Han, Z., Liu, X., Cui, W., Zheng, D., Zhou, X., Song, Y., & Jiang, S. (2025) · Microorganisms · doi:10.3390/microorganisms13040731
Self-citationDeng, J., Chen, Z., Chen, X., Shi, X., Fan, J., Lv, X., & Kuang, Y. (2026) · Aquaculture Reports · doi:10.1016/j.aqrep.2026.103452
Wang, P., Zhang, S., Qü, Z., Zhang, S., Wu, Y., Wang, Y., & Li, G. (2026) · Food Bioscience · doi:10.1016/j.fbio.2026.109278
Huan, R. H., Feng, X., Gu, Y., Li, J., Cai, J. Q., Zhai, Z., & Hao, Y. (2026) · Applied and Environmental Microbiology · doi:10.1128/aem.00639-26
Munir, A., Javed, S., Javed, G. A., Mushtaq, M., Shahzad, B., Hameed, M., Asif, S., Saif, A., & Arshad, N. (2026) · BMC Microbiology · doi:10.1186/s12866-026-05309-9
- Authors
- Huang, S., Jiang, S., Huo, D., Allaband, C., Estaki, M., Cantu, V., Belda-Ferre, P., Vázquez-Baeza, Y., Zhu, Q., Ma, C., Li, C., Zarrinpar, A., Liu, Y.-Y., Knight, R., & Zhang, J.
- Affiliations
- Hainan University (CN)
- University of California San Diego (US)
- UC San Diego Health System (US)
- Brigham and Women's Hospital (US)
- Corresponding author
- Knight, Rob
- Zhang, Jiachao
- ORCID
- Venue
- Microbiome
- Published
- 2021-06-30
- Volume
- 9
- Issue
- 1
- Pages
- 151-151
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC8247228
- OpenAlex
- W3177468406
- Cited by
- 61
- References
- 47
- Citations by year
- 2026: 8 · 2025: 16 · 2024: 11 · 2023: 13 · 2022: 12 · 2021: 1
- FWCI
- 5.52
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Microbiome (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Natural Science Foundation of China (31701577)
- National Institutes of Health (T32 OD017863, K08 DK102902, R01AI141529, R01HD093761, R01AG067744)
- NIDDK (P30 DK120515, P30 DK063491, and UL1 TR001442)
- National Center for Complementary and Integrative Health (DP1-AT010885)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Immunology and Microbiology › Immunology › Aquaculture disease management and microbiota
- Keywords
- Lactobacillus plantarum, point mutations, genetic stability, host-specific adaptation, human gut microbiome, mouse gut microbiome, Bacteroides, Bifidobacterium, carbohydrate utilization, acid resistance, probiotic engineering
- MeSH terms
- Gastrointestinal Microbiome, Animals, Bifidobacterium, Humans, Zebrafish, Probiotics, Mice, 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
