Understanding Competition and Cooperation within the Mammalian Gut Microbiome

Diversity of the Human Intestinal Microbial Flora

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The Human Intestinal Microbiome in Health and Disease

Lynch, S. V., & Pedersen, O. (2016) · New England Journal of Medicine · doi:10.1056/nejmra1600266 · Cited by 3,637

The Competitive Exclusion Principle

Hardin, G. (1960) · Science · doi:10.1126/science.131.3409.1292 · Cited by 3,456

The ecology of the microbiome: Networks, competition, and stability

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Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

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Sparse and Compositionally Robust Inference of Microbial Ecological Networks

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Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system

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A Virulence Locus of Pseudomonas aeruginosa Encodes a Protein Secretion Apparatus

Mougous, J. D., Cuff, M. E., Raunser, S., Shen, A., Zhou, M., Gifford, C. A., Goodman, A. L., Joachimiak, G., Ordoñez, C. L., Lory, S. J., et al. (2006) · Science · doi:10.1126/science.1128393 · Cited by 1,105

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota

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Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A.-M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad0917 · Cited by 1,043

Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis

Wurster, J. I., Peterson, R. L., Brown, C. E., Penumutchu, S., Guzior, D. V., Neugebauer, K. A., Sano, W. H., Sebastian, M. M., Quinn, R. A., & Belenky, P. A. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110113 · Cited by 24

Cross-Feeding and Enzymatic Catabolism for Mannan-Oligosaccharide Utilization by the Butyrate-Producing Gut Bacterium Roseburia hominis A2-183

Bhattacharya, A., Majtorp, L., Birgersson, S., Wiemann, M., Sreenivas, K., Verbrugghe, P., Aken, O. V., van Niel, E. W. J., & Stålbrand, H. (2022) · Microorganisms · doi:10.3390/microorganisms10122496 · Cited by 23

Bioactive Polysaccharides Targeting Gut Microbiota to Modulate Host Health: A Gear Effect Theory

Sun, Y., Zhang, S., Yin, J., & Nie, S. (2025) · Food Frontiers · doi:10.1002/fft2.70048 · Cited by 24

Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research

Morgan, E. W., Perdew, G. H., & Patterson, A. D. (2022) · Toxicological Sciences · doi:10.1093/toxsci/kfac029 · Cited by 23

Effect of diet on the evolution of gut commensal bacteria

Đapa, T., & Xavier, K. B. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2369337 · Cited by 23

Freshwater transfer affected intestinal microbiota with correlation to cytokine gene expression in Asian sea bass

Morshed, S. M., Chen, Y., Lin, C., Chen, Y., & Lee, T. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1097954 · Cited by 21

Exploring the human gut microbiota targets in relation to the use of contemporary antidepressants

Lin, S.-K. K., Chen, H., Chen, C.-H., Chen, I., Lu, M., Hsu, C., Chiu, Y.-H., Wang, T.-Y., Chen, H., Chung, Y.-C. E., et al. (2023) · Journal of Affective Disorders · doi:10.1016/j.jad.2023.10.016 · Cited by 21

Impact of non-digestible carbohydrates and prebiotics on immunity, infections, inflammation and vaccine responses: a systematic review of evidence in healthy humans and a discussion of mechanistic proposals

Tunc, H. A., Calder, P. C., Cait, A., Dodd, G. F., Gasaly, N., Guillemet, D., James, D., Korzeniowski, K. J., Lubkowska, A., Meynier, A., et al. (2025) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2025.2514700 · Cited by 22

The Effects of Drug Addiction and Detoxification on the Human Oral Microbiota

Zhang, J., Liu, W., Shi, L., Liu, X., Wang, M., Li, W., Yu, D., Wang, Y., Zhang, J., Yun, K., et al. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.03961-22 · Cited by 20

Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait

Esteban-Torres, M., Ruíz, L., Rossini, V., Nally, K., & van Sinderen, D. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2235067 · Cited by 21

Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses

Hertel, J., Heinken, A., Fässler, D., & Thiele, I. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100615 · Cited by 21

Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices

Degregori, S., Wang, X., Kommala, A., Schulhof, N., Moradi, S., MacDonald, A., Eblen, K., Jukovich, S., Smith, E., Kelleher, E., et al. (2024) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.13161 · Cited by 19

Bacterial warfare is associated with virulence and antimicrobial resistance

Sharp, C., & Foster, K. R. (2025) · Nature Communications · doi:10.1038/s41467-025-64363-5 · Cited by 19

Bacillus atrophaeus NX-12 Utilizes Exosmotic Glycerol from Fusarium oxysporum f. sp. cucumerinum for Fengycin Production

Xue, J., Sun, L., Xu, H. L., Gu, Y., & Lei, P. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c01276 · Cited by 19

Ethanolamine metabolism through two genetically distinct loci enables Klebsiella pneumoniae to bypass nutritional competition in the gut

Barnes, A. J., Bennett, E. F., Vezina, B., Hudson, A. W., Hernandez, G. E., Nutter, N. A., Bray, A. S., Nagpal, R., Wyres, K. L., & Zafar, M. A. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012189 · Cited by 19

Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut

Cherrak, Y., Salazar, M. A., Näpflin, N. C., Malfertheiner, L., Herzog, M. K.-M., Schubert, C., von Mering, C., & Hardt, W. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01775-x · Cited by 18

Gut microbiome and NAFLD: impact and therapeutic potential

Li, L., Cai, F., Chen, G., Liu, Z., Qin, J., & Huang, J. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1500453 · Cited by 18

Differences in the Establishment of Gut Microbiota and Metabolome Characteristics Between Balb/c and C57BL/6J Mice After Proton Irradiation

Li, Y., Sui, L., Zhao, H., Zhang, W., Gao, L., Hu, W., Song, M. S., Liu, X., Kong, F., Gong, Y., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.874702 · Cited by 18

Disrupting the bacterial language: quorum quenching and its applications

Tu, Y., Li, H., Huo, J., Gou, L., Wen, X., Yu, X., Zhang, X., Zeng, J., & Li, Y. (2025) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2025.2466472 · Cited by 17

Single-cell analysis and spatial resolution of the gut microbiome

Madhu, B., Miller, B. M., & Levy, M. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1271092 · Cited by 18

Microbes as medicine

Daisley, B. A., & Allen‐Vercoe, E. (2024) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.15237 · Cited by 17

Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments

Pérez-Burillo, S., Hinojosa-Nogueira, D., Navajas-Porras, B., Blasco, T., Balzerani, F., Lerma-Aguilera, A. M., León, D., Pastoriza, S., Apaolaza, I., Planes, F. J., et al. (2021) · Nutrients · doi:10.3390/nu13072207 · Cited by 17

Stability of multi-layer ecosystems

Wang, Y., Yang, Y., Li, A., & Wang, L. (2023) · Journal of The Royal Society Interface · doi:10.1098/rsif.2022.0752 · Cited by 17

Early-life factors shaping the gut microbiota of Common buzzard nestlings

Pereira, H., Chakarov, N., Hoffman, J. I., Rinaud, T., Ottensmann, M., Gladow, K., Busche, T., Caspers, B. A., Maracı, Ö., & Krüger, O. (2024) · Animal Microbiome · doi:10.1186/s42523-024-00313-8 · Cited by 16

Predicting N-Strain Coexistence from Co-colonization Interactions: Epidemiology Meets Ecology and the Replicator Equation

Madec, S., & Gjini, E. (2020) · Bulletin of Mathematical Biology · doi:10.1007/s11538-020-00816-w · Cited by 19

CAZyme from gut microbiome for efficient lignocellulose degradation and biofuel production

Chettri, D., Nad, S., Konar, U., & Verma, A. K. (2022) · Frontiers in Chemical Engineering · doi:10.3389/fceng.2022.1054242 · Cited by 16

Does ecological drift explain variation in microbiome composition among groups in a social host species?

Rose, C., Lund, M., Schramm, A., Bilde, T., & Bechsgaard, J. (2023) · Journal of Evolutionary Biology · doi:10.1111/jeb.14228 · Cited by 15

Unlocking the therapeutic potential of Huoxiang Zhengqi San in cold and high humidity-induced diarrhea: Insights into intestinal microbiota modulation and digestive enzyme activity

Wu, Y., Deng, N., Liu, J., Cai, Y., Yi, X., & Tan, Z. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e32789 · Cited by 15

Gene-by-environment interactions modulate the infant gut microbiota in asthma and atopy

Stickley, S. A., Fang, Z. Y., Ambalavanan, A., Zhang, Y., Zacharias, A. M., Petersen, C., Dai, D. L., Azad, M. B., Brook, J. R., Mandhane, P. J., et al. (2025) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2025.03.018 · Cited by 16

Rehabilitation of a misbehaving microbiome: phages for the remodeling of bacterial composition and function

Baaziz, H., Baker, Z. R., Franklin, H. C., & Hsu, B. B. (2022) · iScience · doi:10.1016/j.isci.2022.104146 · Cited by 18

Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials

Quinn-Bohmann, N., Carr, A. V., & Gibbons, S. M. (2026) · PLoS Biology · doi:10.1371/journal.pbio.3003638 · Cited by 14

The faecal metabolome of black howler monkeys (Alouatta pigra) varies in response to seasonal dietary changes

Mallott, E. K., Skovmand, L. H., Garber, P. A., & Amato, K. R. (2022) · Molecular Ecology · doi:10.1111/mec.16559 · Cited by 16

Targeting the gut to prevent and counteract metabolic disorders and pathologies during aging

Milenković, D., Capel, F., Combaret, L., Comte, B., Dardevet, D. P., Evrard, B., Guillet, C., Monfoulet, L., Pinel, A., Polakof, S., et al. (2022) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2022.2089870 · Cited by 14

Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea

Feehan, B. J., Ran, Q., Dorman, V., Rumback, K., Pogranichniy, S., Ward, K., Goodband, R. D., Niederwerder, M. C., & Lee, S. T. M. (2023) · Animal Microbiome · doi:10.1186/s42523-023-00256-6 · Cited by 16

Multi-omics strategy reveals potential role of antimicrobial resistance and virulence factor genes responsible for Simmental diarrheic calves caused by Escherichia coli

Shi, Z., Lan, Y., Wang, Y., Yan, X., Ma, X., Hassan, F., Rushdi, H. E., Xu, Z., Wang, W., & Deng, T. (2024) · mSystems · doi:10.1128/msystems.01348-23 · Cited by 15

Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche

Valiei, A., Dickson, A. M., Aminian-Dehkordi, J., & Mofrad, M. R. K. (2024) · BMC Microbiology · doi:10.1186/s12866-024-03566-0 · Cited by 16

Immunomodulatory mechanisms of the gut microbiota and metabolites on regulatory T cells in rheumatoid arthritis

Xu, X., Zhou, J., Xie, H., Zhang, R., Gu, B., Liu, L., Liu, M., & Chang, X.-R. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1610254 · Cited by 14

Nutraceuticals in the Modulation of the Intestinal Microbiota: Current Status and Future Directions

Spisni, E., Turroni, S., Alvisi, P., Spigarelli, R., Azzinnari, D., Ayala, D., Imbesi, V., & Valerii, M. C. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.841782 · Cited by 14

Complexity of human death: its physiological, transcriptomic, and microbiological implications

Javan, G. T., Singh, K., Finley, S. J., Green, R. L., & Sen, C. K. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1345633 · Cited by 16

Interspecies interactions drive bacterial proteome reorganization and emergent metabolism

Kamrad, S., Aulakh, S. K., Mozzachiodi, S., Blasche, S., Scheidweiler, D., Basile, A., Guan, R., Bradley, R. E., van den Berg, N. I., Mülleder, M., et al. (2026) · Nature Ecology & Evolution · doi:10.1038/s41559-026-03030-4 · Cited by 12

Evolutionary modeling suggests that addictions may be driven by competition-induced microbiome dysbiosis

Lewin‐Epstein, O., Jaques, Y., Feldman, M. W., Kaufer, D., & Hadany, L. (2023) · Communications Biology · doi:10.1038/s42003-023-05099-0 · Cited by 13

Effects of antibiotic and disinfectant exposure on the mouse gut microbiome and immune function

Xu, W.-B., Wang, Y.-F., Meng, S.-Y., Zhang, X., Wang, Y., & Liu, Z. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.00611-24 · Cited by 12

Interspecies and intraspecies ‘Talk’ shape the bacterial biofilms

Yiyang, L., Liu, Z., Zhang, Q., Zhang, L., Liao, X., Yang, T., Liu, D., Lu, X., Ahn, J., Ding, T., et al. (2025) · Food Quality and Safety · doi:10.1093/fqsafe/fyaf008 · Cited by 12

The ratio of single to co‐colonization is key to complexity in interacting systems with multiple strains

Gjini, E., & Madec, S. (2021) · Ecology and Evolution · doi:10.1002/ece3.7259 · Cited by 14

Bacterial community of reindeer lichens differs between northern and southern lichen woodlands

Alonso, M., & Villarreal, J. C. (2022) · Canadian Journal of Forest Research · doi:10.1139/cjfr-2021-0272 · Cited by 13

Ribosome-binding antibiotics increase bacterial longevity and growth efficiency

Wood, E., Schulenburg, H., Rosenstiel, P. C., Bergmiller, T., Ankrett, D. N., Gudelj, I., & Beardmore, R. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2221507120 · Cited by 11

Effect of stress urinary incontinence on vaginal microbial communities

Zhang, M., Zhou, Y., Yao, S., Zhao, Y., Batool, S. S., Huang, J., Jiang, L., Yan, D., Yan, W., & Yu, Z. P. (2024) · BMC Microbiology · doi:10.1186/s12866-024-03237-0 · Cited by 11

A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability

Lim, B., Xu, J., Wierzbicki, I. H., Gonzalez, C. G., Chen, Z., Gonzalez, D. J., Gao, X., & Goodman, A. L. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.01.008 · Cited by 12

Separation of Donor and Recipient Microbial Diversity Allows Determination of Taxonomic and Functional Features of Gut Microbiota Restructuring following Fecal Transplantation

Olekhnovich, E. I., Ivanov, A. B., Игоревич, У. В., & Ilina, E. N. (2021) · mSystems · doi:10.1128/msystems.00811-21 · Cited by 12

Gonadal bacterial community composition is associated with sex-specific differences in swamp eels (Monopterus albus)

Meng, K., Lin, X., Liu, H., Chen, H., Liu, F., Xu, Z., Sun, Y., & Luo, D. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.938326 · Cited by 11

Evolutionary implications of host genetic control for engineering beneficial microbiomes

Henry, L. P., & Bergelson, J. M. (2023) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2023.100455 · Cited by 11

Glycan-related genes in human gut microbiota exhibit differential distribution and diversity in carbohydrate degradation and glycan synthesis

Takihara, H., & Okuda, S. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1137303 · Cited by 11

Queuine Salvaging in the Human Parasite Entamoeba histolytica

Sarid, L., Sun, J., Chittrakanwong, J., Trebicz‐Geffen, M., Ye, J., Dedon, P. C., & Ankri, S. (2022) · Cells · doi:10.3390/cells11162509 · Cited by 11

Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogensPreprint

Mortzfeld, B. M., Bhattarai, S. K., & Bucci, V. (2024) · eLife · doi:10.7554/elife.102912 · Cited by 11

Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity

Midani, F. S., & David, L. A. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.910390 · Cited by 10

Exploring Microbial Signatures in Endometrial Tissues with Endometriosis

Guo, W., Xu, Z., Hu, S., & Shen, Y. (2025) · International Immunopharmacology · doi:10.1016/j.intimp.2025.114072 · Cited by 11

Commensal resilience: ancient ecological lessons for the modern microbiota

Rose, A. E., Fansler, R. T., & Zhu, W. (2025) · Infection and Immunity · doi:10.1128/iai.00502-24 · Cited by 12

Molecular Mechanisms of the Microbiota–Gut–Brain Axis in the Onset and Progression of Stroke

Caballero‐Villarraso, J., Pons-Villarta, S., Cruces-Párraga, J., Navarrete-Pérez, A., Camargo, A., Moreno, J. A., Túnez, I., & Agüera, E. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms262010071 · Cited by 11

High-order correlations in species interactions lead to complex diversity-stability relationships for ecosystems

Korkmazhan, E., & Dunn, A. R. (2022) · Physical review. E · doi:10.1103/physreve.105.014406 · Cited by 10

Synthesis of queuine by colonic gut microbiome via cross‐feeding

Yan, F., Xiang, S., Shi, L., & Zhu, X. (2023) · Food Frontiers · doi:10.1002/fft2.307 · Cited by 10

Inflammatory bowel disease biomarkers revealed by the human gut microbiome network

Hu, M., Caldarelli, G., & Gili, T. (2023) · Scientific Reports · doi:10.1038/s41598-023-46184-y · Cited by 10

Microbial metabolites as engines of behavioral variation across animals

Ntiri, E. S., & Wong, A. C.-N. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2501191 · Cited by 10

Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies

Zhang, D., Hu, Q., Zhou, Y., Yu, H., Cong, W., Cheng, M., Wang, J., Liu, X., Zou, K., Long, S., et al. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00836-1 · Cited by 9

Friend or foe? Contextualizing Bacteroides through the lens of niche remodeling

Fansler, R. T., Wu, Y., & Zhu, W. (2025) · Trends in Microbiology · doi:10.1016/j.tim.2025.11.005 · Cited by 9

Microbiome–induced increases and decreases in bone matrix strength can be initiated after skeletal maturity

Liu, C., Cyphert, E. L., Stephen, S. J., Wang, B., Morales, A. L., Nixon, J. C., Natsoulas, N. R., Garcia, M., Blázquez-Carmona, P., Vill, A. C., et al. (2024) · Journal of Bone and Mineral Research · doi:10.1093/jbmr/zjae157 · Cited by 9

A single system detects and protects the beneficial oral bacterium Streptococcus sp. A12 from a spectrum of antimicrobial peptides

Lee, K., Kaspar, J., Rojas-Carreño, G., Walker, A., & Burne, R. (2021) · Molecular Microbiology · doi:10.1111/mmi.14703 · Cited by 8

A mucin-responsive hybrid two-component system controls Bacteroides thetaiotaomicron colonization and gut homeostasis

Lee, J.-H., Kwon, S.-J., Han, J., Cho, S., Cho, Y., & Park, J. (2022) · The Journal of Microbiology · doi:10.1007/s12275-022-1649-3 · Cited by 9

Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea

Xu, T., Novotny, A., Zamora‐Terol, S., Hambäck, P. A., & Winder, M. (2024) · Microbial Ecology · doi:10.1007/s00248-024-02362-7 · Cited by 8

The potential of live biotherapeutic products in allergic disease: current findings and future directions

Tarrant, I., & Finlay, B. B. (2024) · Frontiers in Microbiomes · doi:10.3389/frmbi.2024.1418633 · Cited by 8

Fermentation of Alginate and Its Oligosaccharides by the Human Gut Microbiota: Structure–Property Relationships and New Findings Focusing on Bacteroides xylanisolvens

Li, J., Lv, Y., Shao, M., Lv, D., Fu, Z., Guo, P., Li, Q., & Shang, Q. (2025) · Nutrients · doi:10.3390/nu17091424 · Cited by 8

Function, Evolution, and Ecology of Type VI Secretion Systems of Plant-Associated Bacteria

Scouten, J. M., Hsieh, S.-C., Sung, L., Wen, Y. V., Kuo, C., Lai, E., & Chang, J. H. (2025) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-121423-084620 · Cited by 8

Working together: gut microbe-microbe interactions shape host inflammation

Lawing, A., & Bleich, R. M. (2025) · Infection and Immunity · doi:10.1128/iai.00512-24 · Cited by 8

Gut microbiota: emerging biomarkers and potential therapeutics for premature ovarian failure

Liu, Z., Wang, M., Lei, Y., Xu, K., & Fan, L. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1606001 · Cited by 8

Why Do Filamentous Actinomycetota Produce Such a Vast Array of Specialized Metabolites?

Morin, L. M. C., Dekoninck, K., Sridhar, V., Disney-McKeethen, S., Proctor, T., Eng, A. Y., & Traxler, M. F. (2025) · Annual Review of Microbiology · doi:10.1146/annurev-micro-060424-051257 · Cited by 8

Pathogenesis of Bovine Mastitis and Influence of the Gut Microbiota: A Review

Zhu, S., Bian, S., Lu, J., Wang, Y., Iqbal, M., Kiani, F. A., Dong, H., Zhang, X., Yuan, Z., Liu, F., et al. (2026) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.5c13667 · Cited by 8

Gut-Microbiome Interactions: Characterization, Therapeutic Implications and Machine Learning

Ayivi-Tosuh, S. M., Dofuor, A. K., Yamoah, J. A. A., Gayi, B. K., Aiduenu, A. F., Akomea, A., Anovunga, S. A., Ekloh, W., & Basing, L. A. (2026) · Sage Open Pathology · doi:10.1177/30502098251415109 · Cited by 8

Metagenomic signatures of balancing selection in the human gut

Moeller, A. H. (2022) · Molecular Ecology · doi:10.1111/mec.16474 · Cited by 8

Food and drug design for gut microbiota-directed regulation: Current experimental landscape and future innovation

Gao, X., Zhao, J., Chen, W., & Zhai, Q. (2023) · Pharmacological Research · doi:10.1016/j.phrs.2023.106867 · Cited by 8

A single intranasal dose of essential oil spray confers modulation of the nasopharyngeal microbiota and short-term inhibition of Mannheimia in feedlot cattle: a pilot study

Magossi, G., Schmidt, K. N., Winders, T., Carlson, Z. E., Holman, D. B., Underdahl, S. R. R., Swanson, K. C., & Amat, S. (2024) · Scientific Reports · doi:10.1038/s41598-023-50704-1 · Cited by 8

Increase of intestinal bacterial sialidase activity exacerbates acute colitis in mice

Hasler, T., Tavares-Gomes, L., Gut, S., Swayambhu, M., Gysi, M., Hausmann, M., Arora, N., & Hennet, T. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.1075459 · Cited by 8

A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin

Bowran, K., Garrett, S., van Vliet, A. H. M., & Palmer, T. (2023) · Microbial Genomics · doi:10.1099/mgen.0.001036 · Cited by 8

Rapidly evolving orphan immunity genes protect human gut bacteria from intoxication by the type VI secretion systemPreprint

Azhieh, A., Hernandez, P., Anderson, A. C., Sychantha, D., Verster, A. J., Whitney, J. C. C., & Ross, B. D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.03.651265 · Cited by 8

Culex pipiens and Culex restuans larval interactions shape the bacterial communities in container aquatic habitats

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Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial

Wong, M. K., Armstrong, E., Heirali, A., Schneeberger, P. H. H., Chen, H., Cochrane, K., Sherriff, K., Allen‐Vercoe, E., Siu, L. L., Spreafico, A., et al. (2025) · mBio · doi:10.1128/mbio.01904-25 · Cited by 7

Approaches to dissect the vitamin biosynthetic network of the gut microbiota

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Bidirectional microbial regulation by tyrosine metabolism enhances palmatine-mediated colitis protection

Sun, D., Hua, Z., Xiao, Y., He, D., Wu, H., Lin, X., Chen, Q., Li, Z., & Hou, Y. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2596405 · Cited by 7

The Role of Indirect Effects in Coevolution along the Mutualism-Antagonism Continuum

Pedraza, F., Liu, H., Gawecka, K. A., & Bascompte, J. (2023) · The American Naturalist · doi:10.1086/727472 · Cited by 7

Harnessing gut microbial communities to unravel microbiome functions

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

Gut microbiota responses to dietary fibre sources in rats fed starch-based or quasi-human background diets

Paturi, G., Mishra, S. S., HEDDERLEY, D. I., & Monro, J. A. (2021) · Journal of Functional Foods · doi:10.1016/j.jff.2021.104565 · Cited by 7

Predicted Adsorption Affinity for Enteric Microbial Metabolites to Metal and Carbon Nanomaterials

Brinkmann, B. W., Singhal, A., Sevink, G. J. A., Neeft, L., Vijver, M. G., & Peijnenburg, W. J. G. M. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00492 · Cited by 9

Effects of dietary restriction and one-carbon metabolite supplementation during the first 63 days of gestation on the maternal gut, vaginal, and blood microbiota in cattle

Luecke, S. M., Aryee, G., Holman, D. B., Schmidt, K. N., King, L. E., Crouse, M. S., Ward, A. K. K., Dahlen, C. R., Caton, J. S. S., & Amat, S. (2024) · Animal Microbiome · doi:10.1186/s42523-024-00335-2 · Cited by 7

Effect of walnut peptide‐ZnO nanocomposites on the colon adhesion behavior of Lactobacillus rhamnosus LRa05

Liang, M., Wang, M., Zhou, M., Nie, S., Xu, Y., Yang, X., Yuan, E., & Ren, J. (2023) · Food Frontiers · doi:10.1002/fft2.253 · Cited by 6

Gut microbes predominantly act as living beneficial partners rather than raw nutrients

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Determination of the virulence status of Clostridium perfringens strains using a chicken intestinal ligated loop model is important for understanding the pathogenesis of necrotic

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Community ecological succession of endophytic fungi associates with medicinal compound accumulation in Sophora alopecuroides

Ju, M., Zhang, Q., Wang, R., Yan, S., Zhang, Q., Li, P., Hao, F., & Gu, P. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.03076-23 · Cited by 6

Bacillus subtilis Intraspecies Interactions Shape Probiotic Activity Against Salmonella Typhimurium

Kovačec, E., Kraigher, B., Podnar, E., Lories, B., Steenackers, H. P. L., & Mandić-Mulec, I. (2024) · Microbial Biotechnology · doi:10.1111/1751-7915.70065 · Cited by 6

Diversity–Function Relationships and the Underlying Ecological Mechanisms in Host-Associated Microbial Communities

Cuellar‐Gempeler, C. (2021) · Advances in environmental microbiology · doi:10.1007/978-3-030-63512-1_17 · Cited by 6

Taxonomy, not locality, influences the cloacal microbiota of two nearctic colubrids: a preliminary analysis

Dallas, J. W., Meshaka, W. E., Zeglin, L. H., & Warne, R. W. (2021) · Molecular Biology Reports · doi:10.1007/s11033-021-06645-x · Cited by 6

A resource for the comparison and integration of heterogeneous microbiome networksPreprint

Hu, Z., Kishore, D., Wang, Y., Bîrzu, G., DeLisi, C., Korolev, K. S., & Segrè, D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.07.503059 · Cited by 6

Fecal Microbiota Transplantation for Inflammatory Bowel Disease: Where We Stand and What Is Next

Ishikawa, D., Zhang, X., Nomura, K., & Nagahara, A. (2025) · Inflammatory Intestinal Diseases · doi:10.1159/000549227 · Cited by 5

Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem

Wang, S., Mu, L., Yu, C. H. A., He, Y., Hu, X., Jiao, Y., Xu, Z., You, S., Liu, S.-L., & Bao, H. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2296603 · Cited by 94

Cross-feeding in the gut microbiome: Ecology and mechanisms

Culp, E. J., & Goodman, A. L. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.03.016 · Cited by 562

Health-associated key gut microbiota drives the variation in community metabolic interactions in non-human primates

Gao, S., Lan, L., Li, Y., Chen, T., & Fan, P. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116477 · Cited by 3

Commensal inter-bacterial interactions shaping the microbiota

Kern, L., Abdeen, S. K., Kolodziejczyk, A. A., & Elinav, E. (2021) · Current Opinion in Microbiology · doi:10.1016/j.mib.2021.07.011 · Cited by 82

Interbacterial warfare in the human gut: insights from Bacteroidales’ perspective

Jiang, K., Pang, X., Li, W., Xu, X., Yang, Y., Shang, C., & Gao, X. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2473522 · Cited by 30