Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection

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Investigating the composition and recruitment of the mycobacterial ImuA′–ImuB–DnaE2 mutasome

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Complex Microbiota in Laboratory Rodents: Management Considerations

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Antimicrobial Resistance Transmission in Environmental Matrices: Current Prospects and Future Directions

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Impact of dietary carbohydrate, fat or protein restriction on the human gut microbiome: a systematic review

Schoonakker, M. P., van Peet, P. G., van den Burg, E. L., Numans, M. E., Ducarmon, Q. R., Pijl, H., & Wiese, M. (2024) · Nutrition Research Reviews · doi:10.1017/s0954422424000131 · Cited by 16

The social microbiome: The missing mechanism mediating the sociality-fitness nexus?

Baniel, A., & Charpentier, M. J. E. (2024) · iScience · doi:10.1016/j.isci.2024.109806 · Cited by 14

Listeria monocytogenes gut interactions and listeriosis: Gut modulation and pathogenicity

Oliveira, M., Barbosa, J. B., & Teixeira, P. (2025) · Microbiological Research · doi:10.1016/j.micres.2025.128187 · Cited by 15

Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing

Qin, P., Chen, Y., Ding, L., Zhao, Z., Yan, P., Storey, K. B., Shi, H., & Hong, M. (2020) · PeerJ · doi:10.7717/peerj.8501 · Cited by 15

Milk phospholipid supplementation mediates colonization resistance of mice against Salmonella infection in association with modification of gut microbiota

Xiu, W., Kong, X., Qin, Y., Zhu, X., Qu, D., & Han, J. (2020) · Food & Function · doi:10.1039/d0fo00883d · Cited by 14

Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples

Baumgartner, M., Pfrunder‐Cardozo, K. R., & Hall, A. R. (2021) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2020.3106 · Cited by 16

Targeting Enterococcus faecalis HMG-CoA reductase with a non-statin inhibitor

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The Gut Microbiota Contributes to Systemic Responses and Liver Injury in Gut-Derived Sepsis

Zhao, M., Ma, J., Liu, H., Luo, Y., Deng, H., Wang, D., Wang, F., & Zhang, P. (2023) · Microorganisms · doi:10.3390/microorganisms11071741 · Cited by 13

Risk Factors for Carbapenem-Resistant Enterobacteriaceae Colonization and the Effect on Clinical Outcomes and Prognosis in Allogeneic Hematopoietic Stem Cell Transplanted Patients

Wu, W.-Q., Zhang, Y., Xu, J., Tang, Z., Li, S.-J., Wei, X.-Y., Li, L., Wu, H., Ma, X., Liu, J.-S., et al. (2023) · Infection and Drug Resistance · doi:10.2147/idr.s424048 · Cited by 13

Animal and In Vitro Models as Powerful Tools to Decipher the Effects of Enteric Pathogens on the Human Gut Microbiota

Calvigioni, M., Mazzantini, D., Celandroni, F., & Ghelardi, E. (2023) · Microorganisms · doi:10.3390/microorganisms12010067 · Cited by 13

Targeted Screening of Fiber Degrading Bacteria with Probiotic Function in Herbivore Feces

Chen, B., Zeng, Y., Wang, J., Lei, M., Gan, B., Wan, Z., Wu, L., Luo, G., Cao, S., An, T., et al. (2024) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-024-10215-5 · Cited by 13

Lactobacillus agilis SNF7 Presents Excellent Antibacteria and Anti-Inflammation Properties in Mouse Diarrhea Induced by Escherichia coli

Feng, M., Cheng, J., Su, Y., Tong, J., Wen, X., Jin, T., Ren, M., Song, D., Song, J., Li, X., et al. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252413660 · Cited by 13

Toll-Like Receptor 4 Signaling in the Ileum and Colon of Gnotobiotic Piglets Infected with Salmonella Typhimurium or Its Isogenic ∆rfa Mutants

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Intestinal loads of OXA-48-producing Klebsiella pneumoniae in colonized patients determined from surveillance rectal swabs

Lázaro-Perona, F., Rodríguez-Tejedor, M., Carrascoso, G. R., Díaz‐Pollán, B., Loeches, B., Ramos, J. C. R., & Mingorance, J. (2020) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2020.09.054 · Cited by 13

Identification of Valerate as Carrying Capacity Modulator by Analyzing Lactiplantibacillus plantarum Colonization of Colonic Microbiota in vitro

Isenring, J., Stevens, M. J. A., Jans, C., Lacroix, C., & Geirnaert, A. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.910609 · Cited by 13

Intestinal stem cells and gut microbiota therapeutics: hype or hope?

Sophien, A. N. A., Jusop, A. S., Tye, G. J., Tan, Y.-F., Zaman, W. S. W. K., & Nordin, F. (2023) · Frontiers in Medicine · doi:10.3389/fmed.2023.1195374 · Cited by 14

Factors influencing gut microbial colonization: A host-microbe-environment interaction perspective

Zhao, Y., Ren, Z., Xu, Q., Zhu, T., Hu, H., Fu, Y., Jiang, J., & Zhai, Q. (2026) · Current Research in Food Science · doi:10.1016/j.crfs.2026.101361 · Cited by 13

Malaria parasite infection compromises colonization resistance to an enteric pathogen by reducing gastric acidity

Walker, G. T., Yang, G., Tsai, J. Y., Rodriguez, J. L., English, B. C., Faber, F., Souvannaseng, L., Butler, B. P., & Tsolis, R. M. (2021) · Science Advances · doi:10.1126/sciadv.abd6232 · Cited by 12

Metabolomic signatures of intestinal colonization resistance against Campylobacter jejuni in mice

Shayya, N. W., Bandick, R., Busmann, L. V., Mousavi, S., Bereswill, S., & Heimesaat, M. M. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1331114 · Cited by 12

Opioids and Immunosuppression: Clinical Evidence, Mechanisms of Action, and Potential Therapies

Bettinger, J. J., & Friedman, B. C. (2024) · Palliative Medicine Reports · doi:10.1089/pmr.2023.0049 · Cited by 15

Exploring the impact of Anaplasma phagocytophilum on colonization resistance of Ixodes scapularis microbiota using network node manipulation

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Rosmarinic acid alleviated intestinal barrier damage caused by Escherichia coli by regulating the gut microbiota and inhibiting the NF-κB signalling pathway in mice

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Microbes in Health and Disease: Human Gut Microbiota

Hu, C., & Shen, H. (2024) · Applied Sciences · doi:10.3390/app142311354 · Cited by 17

Quorum sensing of Bifidobacteria: Research and progress

Li, H., He, B., Ma, N., Liu, C., Cai, K., Zhang, X., & Ma, X. (2025) · Microbiological Research · doi:10.1016/j.micres.2025.128102 · Cited by 13

Defined Pig Microbiota with a Potential Protective Effect against Infection with Salmonella Typhimurium

Horváthová, K., Modráčková, N., Šplı́chal, I., Šplı́chalová, A., Amin, A., Ingribelli, E., Killer, J., Doskočil, I., Pechar, R., Kodešová, T., et al. (2023) · Microorganisms · doi:10.3390/microorganisms11041007 · Cited by 15

Casual effects of gut microbiota on risk of infections: a two-sample Mendelian randomization study

Lyu, B.-B., Ma, J., Bai, Y., & Feng, Z. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1284723 · Cited by 12

Immunostimulating Commensal Bacteria and Their Potential Use as Therapeutics

McCuaig, B., & Goto, Y. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242115644 · Cited by 15

Development of a novel human intestinal model to elucidate the effect of anaerobic commensals on Escherichia coli infection

McGrath, C. J., Laveckis, E., Bell, A., Crost, E. H., Juge, N., & Schüller, S. (2022) · Disease Models & Mechanisms · doi:10.1242/dmm.049365 · Cited by 12

Decoding the Interactive Effects of Litchi Pectin and EGCG on Immune Microenvironment Remodeling: A Microbiota–Metabolic–Immune Perspective

Wang, D., Yu, J., Li, L., Zhu, Y., Wang, Y., Zhao, L., Wang, K., Liu, X., & Hu, Z. (2025) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.5c03033 · Cited by 11

A carvacrol-based product reduces Campylobacter jejuni load and alters microbiota composition in the caeca of chickens

Allaoua, M., Bonnafé, E., Etienne, P. L., Noirot, V., Gabarrou, J.-F., Castinel, A., Pascal, G., Darbot, V., Treilhou, M., & Combes, S. (2022) · Journal of Applied Microbiology · doi:10.1111/jam.15521 · Cited by 11

Contribution of Symptomatic, Herbal Treatment Options to Antibiotic Stewardship and Microbiotic Health

Nausch, B., Bittner, C. B., Höller, M., Abramov-Sommariva, D., Hiergeist, A., & Gessner, A. (2022) · Antibiotics · doi:10.3390/antibiotics11101331 · Cited by 14

Gut Microbiota Resilience Mechanisms Against Pathogen Infection and its Role in Inflammatory Bowel Disease

Cipelli, M., da Silva, E. M., & Câmara, N. O. S. (2023) · Current Clinical Microbiology Reports · doi:10.1007/s40588-023-00207-4 · Cited by 11

Regulation of Gene Expression through Gut Microbiota-Dependent DNA Methylation in Colonic Epithelial Cells

Takahashi, K., Sugi, Y., Nakano, K., Kobayakawa, T., Nakanishi, Y., Tsuda, M., Hosono, A., & Kaminogawa, S. (2020) · ImmunoHorizons · doi:10.4049/immunohorizons.1900086 · Cited by 11

Gut microbiota interplay with autophagy-EMT dynamics in colorectal cancer

Vescovo, T., Bontempi, G., Bayat, M., Piredda, L., Fidaleo, M., Strippoli, R., & Antonioli, M. (2025) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2025.1608248 · Cited by 11

Influence of probiotic and prebiotic supplementation on intestinal microbiota and resistance to Edwardsiella ictaluri infection in channel catfish (Ictalurus punctatus) following florfenicol administration

Older, C. E., Griffin, M. J., Richardson, B. M., Waldbieser, G. C., Reifers, J. G., Goodman, P. M., Ware, C. C., Gatlin, D. M., Wise, D. J., & Yamamoto, F. Y. (2023) · Journal of Fish Diseases · doi:10.1111/jfd.13910 · Cited by 10

Immune modulation and cecal microbiome changes in broilers fed with fenugreek seeds and Bacillus-based probiotics

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Neuromicrobiology Comes of Age: The Multifaceted Interactions between the Microbiome and the Nervous System

Devason, A. S., Thaiss, C. A., & de la Fuente‐Núñez, C. (2024) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.4c00307 · Cited by 11

Causal Link between Gut Microbiota and Infertility: A Two-sample Bidirectional Mendelian Randomization Study

Zhang, J.-X., Li, Q., Wang, X., Zhang, C.-C., Chen, S.-T., Liu, X., Dong, X.-Y., Hu, Z., & Huang, D. (2024) · Current Medical Science · doi:10.1007/s11596-024-2931-x · Cited by 10

From mother to piglet: the lasting influence of the maternal microbiome

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Review and Commentary on the Importance of Bile Acids in the Life Cycle ofClostridioides difficilein Children and Adults

Faden, H. S. (2020) · Journal of the Pediatric Infectious Diseases Society · doi:10.1093/jpids/piaa150 · Cited by 12

Ex Vivo Evaluation of Egg Yolk IgY Degradation in Chicken Gastrointestinal Tract

Wang, H., Zeng, X., & Lin, J. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.746831 · Cited by 10

A Promising Insight: The Potential Influence and Therapeutic Value of the Gut Microbiota in GI GVHD

Li, J., Zhang, X., Chen, Y., Zheng, Q., Zhao, M., & Jiang, H. (2022) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2022/2124627 · Cited by 10

Evaluation of Bile Salts on the Survival and Modulation of Virulence of Aliarcobacter butzleri

Mateus, C., Maia, C. J., Domingues, F., Bücker, R., Oleastro, M., & Ferreira, S. M. P. (2023) · Antibiotics · doi:10.3390/antibiotics12091387 · Cited by 10

The Microbiome and Pediatric Transplantation

Elgarten, C. W., Margolis, E. B., & Kelly, M. S. (2023) · Journal of the Pediatric Infectious Diseases Society · doi:10.1093/jpids/piad062 · Cited by 9

Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case–control study in infectious diseases department

Boyd, A. C., Dani, M. E., Ajrouche, R., Démontant, V., Cheval, J., Lacombe, K., Cosson, G., Rodriguez, C., Pawlotsky, J., Woerther, P., et al. (2024) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2024.03.016 · Cited by 9

Global trends in research related to the links between microbiota and antibiotics: a visualization study

Zyoud, S. H., Shakhshir, M. H., Abushanab, A. S., Koni, A. A., Taha, A. A., Abushamma, F., Sabateen, A., & Al‐Jabi, S. W. (2023) · Scientific Reports · doi:10.1038/s41598-023-34187-8 · Cited by 10

Gut Microbiota and Antibiotic Treatments for the Main Non-Oncologic Hepato-Biliary-Pancreatic Disorders

Vincenzo, F. D., Nicoletti, A., Negri, M., Vitale, F., Verme, L. Z. D., Gasbarrini, A., Ponziani, F. R., & Cerrito, L. (2023) · Antibiotics · doi:10.3390/antibiotics12061068 · Cited by 9

Influence of infant microbiome on health and development

Younge, N. E. (2023) · Korean Journal of Pediatrics · doi:10.3345/cep.2023.00598 · Cited by 11

A comprehensive review on the pharmacological role of gut microbiome in neurodegenerative disorders: potential therapeutic targets

Aziz, N., Wal, P., Patel, A., & Prajapati, H. (2024) · Naunyn-Schmiedeberg s Archives of Pharmacology · doi:10.1007/s00210-024-03109-4 · Cited by 12

Gut Health Optimization in Canines and Felines: Exploring the Role of Probiotics and Nutraceuticals

Atuahene, D., Shaikh, A. M., Balouei, F., & Antwi, A. (2024) · Pets · doi:10.3390/pets1020011 · Cited by 9

Modeling the effects of prebiotic interventions on luminal and mucosa-associated gut microbiota without and with Clostridium difficile challenge in vitro

Wiese, M., van der Wurff, M., Ouwens, A. M. T., van Leijden, B., Verheij, E. R., Heerikhuisen, M., & van der Vossen, J. M. B. M. (2024) · Frontiers in Nutrition · doi:10.3389/fnut.2024.1403007 · Cited by 11

Host–Pathogen Interactions during Shiga Toxin-Producing Escherichia coli Adherence and Colonization in the Bovine Gut: A Comprehensive Review

Edison, L. K., Kudva, I. T., & Kariyawasam, S. (2024) · Microorganisms · doi:10.3390/microorganisms12102009 · Cited by 9

Rosmarinic Acid Attenuates Salmonella enteritidis-Induced Inflammation via Regulating TLR9/NF-κB Signaling Pathway and Intestinal Microbiota

Yi, D., Wang, M., Liu, X., Qin, L., Liu, Y., Zhao, L., Peng, Y., Liang, Z., & He, J. (2024) · Antioxidants · doi:10.3390/antiox13101265 · Cited by 10

Lactobacillus acidophilus alleviate Salmonella enterica Serovar Typhimurium-induced murine inflammatory/oxidative responses via the p62-Keap1-Nrf2 signaling pathway and cecal microbiota

Li, H., Ma, X., Shang, Z., Liu, X., & Qiao, J. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1483705 · Cited by 12

Impact of gut microbiota on colorectal anastomotic healing (Review)

Chen, Y., Wu, N., Yan, X., Kang, L., Ou, G., Zhou, Z., Xu, C., Feng, J., & Shi, T. (2025) · Molecular and Clinical Oncology · doi:10.3892/mco.2025.2847 · Cited by 9

Biotic resistance predictably shifts microbial invasion regimes

Ye, X., Shalev, O., & Ratzke, C. (2025) · Nature Communications · doi:10.1038/s41467-025-59285-1 · Cited by 10

The exploitation of nutrient metals by bacteria for survival and infection in the gut

Bushman, S. D., & Skaar, E. P. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013580 · Cited by 11

Alteration of Gut Microbiota by Ketogenic Diet as an Alternative Therapeutic Target for Drug-Resistant Epilepsy

Tang, M., Wang, W., Wang, J., & Wang, Y. (2025) · Microorganisms · doi:10.3390/microorganisms13112539 · Cited by 10

Principes, cadre d'analyse et leviers d'action à l’échelle de l’élevage pour une gestion intégrée de la santé chez les animaux monogastriques

Fortun‐Lamothe, L., Collin, A., Combes, S., Ferchaud, S., Germain, K., Guilloteau, L. L. A., Gunia, M., Floc'H, N. L., Manoli, C., Montagné, L., et al. (2023) · INRAE Productions Animales · doi:10.20870/productions-animales.2022.35.4.7225 · Cited by 9

Personalized infection prevention and control: a concept whose time has arrived

Savoldi, A., Mutters, N. T., & Tacconelli, E. (2023) · Antimicrobial Stewardship & Healthcare Epidemiology · doi:10.1017/ash.2023.429 · Cited by 9

Campylobacter in Africa – A specific viewpoint

Paintsil, E. K., Masanta, W. O., Dreyer, A., Ushanov, L., Smith, S. I., Frickmann, H., & Zautner, A. E. (2023) · European Journal of Microbiology and Immunology · doi:10.1556/1886.2023.00043 · Cited by 9

Drosophila symbionts in infection: when a friend becomes an enemy

Yu, Y., & Iatsenko, I. (2025) · Infection and Immunity · doi:10.1128/iai.00511-24 · Cited by 10

Monoassociation of Preterm Germ-Free Piglets with Bifidobacterium animalis Subsp. lactis BB-12 and Its Impact on Infection with Salmonella Typhimurium

Šplı́chalová, A., Donovan, S. M., Tlaskalová‐Hogenová, H., Straňák, Z., Splichalova, Z., & Šplı́chal, I. (2021) · Biomedicines · doi:10.3390/biomedicines9020183 · Cited by 10

Modulating Oral Delivery and Gastrointestinal Kinetics of Recombinant Proteins via Engineered Fungi

Heavey, M. K., & Anselmo, A. C. (2021) · The AAPS Journal · doi:10.1208/s12248-021-00606-9 · Cited by 10

Fecal Microbiota Transplantation for People Living with Human Immunodeficiency Virus: A Scoping Review

Caira‐Chuquineyra, B., Fernandez‐Guzman, D., Soriano‐Moreno, D. R., Fernandez-Morales, J., Flores-Lovon, K., Medina-Ramírez, S. A., Gonzales-Uribe, A., Pelayo-Luis, I. P., Zamora, J. A. G., & Huaringa-Marcelo, J. (2022) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2022.0016 · Cited by 9

A high-sucrose diet causes microbiota composition shift and promotes the susceptibility of mice to Salmonella Typhimurium infection

Liu, J., Liu, H., Teng, Y., Qin, N., Ren, X., & Xia, X. (2023) · Food & Function · doi:10.1039/d2fo03467k · Cited by 9

Gut Microbiome: An Intersection between Human Genome, Diet, and Epigenetics

Muhammad, A. Y., Amonov, M., Baig, A. A., & Alvi, F. J. (2024) · Advanced Gut & Microbiome Research · doi:10.1155/2024/6707728 · Cited by 13

Analyzing the correlation between quinolone-resistant Escherichia coli resistance rates and climate factors: A comprehensive analysis across 31 Chinese provinces

Zhao, Y., Sun, Z., Xiao, M.-X., Li, J.-K., Liu, H.-Y., Cai, H., Cao, W., Yu, F., Zhang, B., & Yan, M. (2023) · Environmental Research · doi:10.1016/j.envres.2023.117995 · Cited by 8

Gut microbiome and plasma lipidome analysis reveals a specific impact of Clostridioides difficile infection on intestinal bacterial communities and sterol metabolism

Arcay, R. M., Barceló‐Nicolau, M., Suárez-Bode, L., Martín, L., Reigada, R., Höring, M., Liebisch, G., Garrido, C., Cabot, G., Vílchez, H., et al. (2024) · mBio · doi:10.1128/mbio.01347-24 · Cited by 8

The interplay between host immunity and Clostridioides difficile infection

Li, D., & Saavedra, P. H. V. (2025) · mBio · doi:10.1128/mbio.03562-24 · Cited by 9

Mechanisms of anastomotic leakage in colorectal cancer surgery: unraveling the roles of inflammation, immunity, and microbiota – a narrative review

Ma, K., Gu, T., Wu, Z., & Li, Z. (2025) · International Journal of Surgery · doi:10.1097/js9.0000000000003151 · Cited by 12

Effect of hot-melt extruded Morus alba leaves on intestinal microflora and epithelial cells

Kim, H., Go, E. J., & Baek, J.-S. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e23954 · Cited by 8

Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM 12 mice reveals pathogen-specific host and microbiota responses

Herzog, M. K.-M., Peters, A., Shayya, N. W., Cazzaniga, M., Kakabra, K., Arora, T., Barthel, M., Gül, E., Maurer, L., Kiefer, P., et al. (2025) · Gut Microbes · doi:10.1080/19490976.2024.2447832 · Cited by 9

Viewing Bacterial Colonization through the Lens of Systems Biology

Barron, M. R., & Young, V. B. (2022) · mSystems · doi:10.1128/msystems.01383-21 · Cited by 9

A multi-omics approach reveals the changes in the gut microbiome and metabolism of large yellow croaker (Larimichthys crocea) by dietary supplementation with Bacillus

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Bacterial microcompartment utilization in the human commensal Escherichia coli Nissle 1917

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