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Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftmentPreprint

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Impact of Fiber-Containing Enteral Nutrition on Microbial Community Dynamics in Critically Ill Trauma Patients: A Pilot-Randomized TrialPreprint

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Administration of probiotics and synbiotics and systemic inflammation in Kenyan infants: an open label, randomised, phase II trialPreprint

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Identification of Novel Cryptic and Classical Clades in Clostridioides difficilePreprint

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Aerobic respiration Lactococcus lactis ameliorate Salmonella induced infection and intestinal dysfunctions by oxygen-scavenging and maintaining immune balance and regulating intestinal microbiota

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Screening of Chinese giant salamander meat hydrolysates with DPP-Ⅳ inhibitory activity and systematic elucidation of their hypoglycemic functions in mouse model

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Therapeutics involved in managing initial and recurrent Clostridium difficile infection: An updated literature review

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Risk factors for anastomotic leakage after surgery for colorectal cancer: protocol for a scoping review

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Whole‐Genome Sequencing and Functional Analysis of Klebsiella Strain mr‐1S Originating From Macrobrachium rosenbergii

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The Association Between Intestinal Dysbiosis and Recurrent Urinary Tract Infections: A Narrative Review

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To Combat Abnormal Cell Signaling Mediated Gastrointestinal Cancer by Therapeutic Modulation of Gut Microbiota Utilizing Prebiotics, Postbiotics, and Synbiotics

Sen, D., Datta, S., Biswas, S., Samadder, A., & Nandi, S. (2025) · Current Cancer Drug Targets · doi:10.2174/0115680096373099250709100217 · Cited by 1

Zinc methionine mitigates intestinal mucosal injury of broilers challenged with by modulating mucus secretion, tight junction and microbial composition

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Fecal microbiota composition and clinical characteristics of patients with carbapenem-resistant enterobacterales colonization vs. patients with spontaneous decolonization

Lima, O., Pérez‐Castro, S., Davina-Nunez, C., Represa, M., Rubiñán, P., Ávila-Núñez, M., Filgueira, A., Portela, C., SOPEÑA, B., & Pérez-Rodríguez, M. (2025) · Infection · doi:10.1007/s15010-025-02676-9 · Cited by 1

Succinate-driven virulence enhancement in hypervirulent Klebsiella pneumoniae via DcuSR two-component system

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Antibiotic impact on human microecology in low- and middle-income countries: a systematic age-stratified review of gut and respiratory microbiome and resistome

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Colonization status and risk factors for infection by carbapenem-resistant Gram-negative bacteria in intensive care units in Colombia

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Exploring the Role of Gut Microbiota in Chronic Spontaneous Urticaria: Mechanisms and Potential Therapeutic Implications

Xu, N., He, Y., Yang, G., & Huang, X. (2025) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10799-6 · Cited by 1

Microbiota decolonization of bacterial pathogens in pediatric surgery-related intestinal disorders: Insights on current strategies and future outlook

Vaou, N., Zavras, N. J., Fessatou, S., Voidarou, C. C., Vrioni, G., Tsakris, A., & Vaos, G. C. (2025) · World Journal of Clinical Pediatrics · doi:10.5409/wjcp.v14.i4.107722 · Cited by 1

Gut microbiota dysbiosis and predicted metabolic functional shifts associated with fowl typhoid in layer hens

Do, K.-H., Ryu, D.-H., Kim, M.-G., Ahn, H.-J., Go, Y.-K., Kim, H.-S., Park, Y. K., Shim, J. B., & Seo, K.-W. (2025) · Poultry Science · doi:10.1016/j.psj.2025.106369 · Cited by 1

Fusobacterium nucleatum Enhances Intestinal Adaptation of Vibrio cholerae via Interspecies Biofilm Formation

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Integrative genomic and functional characterization of a feline milk–derived Lactiplantibacillus plantarum MNN reveals host-specific adaptation and ecological safety

Gong, X., Wang, X., Chen, L., Huang, H., & Wen, M. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1742444 · Cited by 1

Molecular and mechanistic insights into the gut-liver axis in K. pneumoniae infections: current advances and future directions

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Early Discontinuation of Prophylactic Antibiotics Is Not Associated with Increased Surgical Site Infection Risk in Spine Surgery: A Nationwide Cohort Study

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Loss of Pum2 exacerbates colitis by disrupting macrophage–epithelial crosstalk and promoting epithelial necroptosis

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Infection strategies of Salmonella Typhimurium for gut-lumen colonization: Overcoming host defenses, exploiting host responses, and adapting to the enteric niche

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Synthetic bacterial communities confer protection against Vibrio parahaemolyticus infection via nutrient competition in Penaeus vannamei

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Flavonoids as Potential Therapeutic Agents Against Gastrointestinal Pathogen Growth and Their Mechanisms of Action: A Comprehensive Review

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Fermented millets as next-generation functional foods: insights into microbiota modulation and gastrointestinal health

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Feasibility and Safety of Washed Microbiota Transplantation as Salvage Therapy for Refractory Non‐ CDI Gut Pathogens in Critically Ill Patients

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Genetic and environmental factors of gluten-related disorders

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Gut Microbiota Characteristics in Ulcerative Colitis and other Gastrointestinal Diseases

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Uso de probióticos e seus efeitos no bem-estar de aves de produção de ovos

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SARS-CoV-2 and microbiome

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Prevalence and In Vivo Assessment of Virulence in Shiga Toxin-Producing Escherichia coli Clinical Isolates from Greater Cairo Area

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Effects of curcumin on antioxidant-related genes and caecal flora in rabbits

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Molecular Interplay of Oxidative Stress and Gut Microbiome in Aging

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Advanced data analytics and “omics” techniques to control enteric foodborne pathogens

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Differential antibiosis predisposes mice to Campylobacter jejuni infection: Deeper insights into the impact of the gut microbiota composition in colonization resistance

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Biodistribution and dosimetry of 89 Zirconium‐labeled microbiota transplants in the pig gut

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A dinâmica das infecções respiratórias The dinamics of respiratory infections

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Treatment Inefficacy for Salmonella During Schistosoma-Salmonella Co-Infections Background, Mechanisms and Future ExplorationPreprint

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Asymptomatic gut colonization by extended-spectrum beta-lactamase-producing Escherichia coli is not associated with an altered gut microbiome or metabolome in Dutch adultsPreprint

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La acuicultura en México, bases conceptuales y principios

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Different host plants alter structure, diversity, and function of gut bacterial communities in larval instars of Spodoptera frugiperdaPreprint

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Differences in Gut Microbiota Assembly Alter Its Ability to Metabolize Dietary Polysaccharides and Resist Clostridioides difficile ColonizationPreprint

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Microbial Metabolite Trimethylamine N-Oxide Promotes Campylobacter jejuni Infection by Escalating Intestinal Inflammation, Epithelial Damage, and Barrier DisruptionPreprint

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Bacterial microcompartment utilisation in the human commensal Escherichia coli Nissle 1917Preprint

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Colicin Receptor CirA Enhances Salmonella Typhimurium’s Resistance to Colicin Ib in the Absence of the Cognate Immunity ProteinPreprint

Gollan, B. C., Luo, L., Li, Y., Clark-Corrigall, J., Qadri, B., Alshuwaier, A., Hinton, J. C. D., & Khan, C. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.29.601355 · Cited by 1

The Arabidopsis amino acid transporter UmamiT20 confers Botrytis cinerea susceptibilityPreprint

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Metabolites produced by gut bacteria under anoxic conditions drive the suppression of Acinetobacter baumanniiPreprint

Winter, K. A., Osbelt, L., Lesker, T. R., Wende, M., Almási, É. D. H., Eisenhard, L., Knegendorf, L., Abt, B., Overmann, J., Hogardt, M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.29.676038 · Cited by 1

Drosophila-Lactobacillus plantarum as a model of facultative nutritional mutualism

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ESBL-producing Enterobacterales - Transmission, intestinal colonization and host response

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Bacterial meningitis in children : clinical aspects and preventive effects of vaccinations

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Intestinal Dysbiosis in Infectious Diseases

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The influence of host genetics, virome, and gut microbiota transfer methods in mouse model reproducibility

Zhang, C. (2021) · MOspace Institutional Repository (University of Missouri) · doi:10.32469/10355/85829

The Stickland fermentation precursor trans-4-hydroxyproline differentially impacts the metabolism of Clostridioides difficile and commensal ClostridiaPreprint

Reed, A. D., Fletcher, J. R., Huang, Y. Y., Thanissery, R., Rivera, A. J., Parsons, R., Stewart, A. K., Kountz, D. J., Shen, A., Balskus, E. P., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.12.468462

Decidual innate immune cell kinetics following lipopolysaccharide challengePreprint

St-Germain, L. E., Castellana, B., Baltayeva, J., & Beristain, A. G. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.27.478092

Faculty Opinions recommendation of NAIP-NLRC4-deficient mice are susceptible to shigellosis.

Hartland, E. L. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.738852813.793583212

Peer Review #2 of "Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing (v0.2)"

(2020) · PeerJ · doi:10.7287/peerj.8501v0.2/reviews/2

Peer Review #1 of "Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing (v0.3)"

(2020) · PeerJ · doi:10.7287/peerj.8501v0.3/reviews/1

Peer Review #3 of "Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing (v0.1)"

(2020) · PeerJ · doi:10.7287/peerj.8501v0.1/reviews/3

Faculty Opinions recommendation of NAIP-NLRC4-deficient mice are susceptible to shigellosis.

Brož, P. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.738852813.793579597

Peer Review #1 of "Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing (v0.1)"

(2020) · PeerJ · doi:10.7287/peerj.8501v0.1/reviews/1

Peer Review #2 of "Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing (v0.3)"

(2020) · PeerJ · doi:10.7287/peerj.8501v0.3/reviews/2

Peer Review #2 of "Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing (v0.1)"

(2020) · PeerJ · doi:10.7287/peerj.8501v0.1/reviews/2

Simplified fecal community transplant restores Clostridioides difficile colonization resistance to antibiotic perturbed murine communitiesPreprint

Lesniak, N. A., Tomkovich, S., Henry, A., Taylor, A., Colovas, J., Bishop, L., McBride, K., & Schloss, P. D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.11.491589

Disarming the pathogen

Pérez‐Morales, D., & Bustamante, V. H. (2022) · Nature Chemical Biology · doi:10.1038/s41589-022-01133-0

A risk prediction model associated with postoperative diarrhea in colorectal cancer patientsPreprint

Xu, J., Sun, J., Zhou, J., & Chen, H. (2022) · Research Square · doi:10.21203/rs.3.rs-2305819/v1

Quo Vadis NADPH Oxidases: Perspectives on Clinical Translation

Knaus, U. G., Shah, A. M., & Thannickal, V. J. (2023) · Springer eBooks · doi:10.1007/978-3-031-23752-2_34

Role of the microbiome in essential metabolism in the human gut and its implications for Clostridioides difficile infection

Chopra, T., Hylemon, P. B., & Tillotson, G. (2023) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofad447

Fitness landscape of substrate-adaptive mutations in evolved APC transporters

Karapanagioti, F., Atlason, Ú. Á., Slotboom, D. J., Poolman, B., & Obermaier, S. (2023) · doi:10.1101/2023.10.12.562049

Chronic infection: as an ecological model for emergence of the chronic obstructive pulmonary disease

Alekseev, D. V., Lyamin, A. V., & Kaiumov, K. A. (2023) · Novel Research in Microbiology Journal · doi:10.21608/nrmj.2023.319451

The Importance of a Broad Consortium of Bacteria for a Healthy Gastrointestinal tract: A Narrative Review of the Live Biotherapeutic Product REBYOTA

Tillotson, G., Vedantam, G., Shin, J. H., & Warren, C. A. (2023) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofad529

Antimicrobial Resistance: A One Health Perspective in India

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The Role of Enteric Infection and the Microbiome in Human Health and Disease

Riddle, M. S. (2023) · Springer eBooks · doi:10.1007/978-3-031-46712-7_3

Profiling the Faecal Microbiome and its Modulators Across the Lifespan in the NetherlandsPreprint

Boverhoff, D., Kool, J., Pijnacker, R., Ducarmon, Q. R., Zeller, G., Shetty, S. A., Sie, S., Mulder, A. C., van der Klis, F. R. M., Franz, E., et al. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4757043

Additional file 1 of Metagenomic analysis of gut microbiome and resistome of Whooper and Black Swans: a one health perspective

Fu, Y., Zhang, K., Shan, F., Li, J., Wang, Y., Li, X., Xu, H., Qin, Z., & Zhang, L. (2023) · Figshare · doi:10.6084/m9.figshare.24431936

Colonisation of the gut microbiome by Escherichia coli during international travel

Davies, M. A. (2024) · Research Publications (Maastricht University) · doi:10.26481/dis.20240417md

Assessment of antibiotic resistance patterns in enteric fever patients

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Dynamics of Commensals Virulence: Preventive Phenotypical Mutability

Chepur, S. V., Nn, P., Sayganov, S. A., Chubar, O. V., Сергеевна, Б. Л., & Litvinenko, I. (2023) · Успехи современной биологии · doi:10.31857/s0042132423030043

Multi-omics in Study of Skin Microbiome

Joshi, K., Panchasara, M., Goswami, H., Bishoyi, A. K., & Sanghvi, G. V. (2024) · Springer eBooks · doi:10.1007/978-981-97-1844-3_10

Innate immune response of host cells infected with Salmonella

Fan, H., Lu, J., Wu, H., Ruan, H., & Song, W. (2024) · BIO Web of Conferences · doi:10.1051/bioconf/202411101022

Intestinal barrier immunity: key players in the gut microbial “meet and greet or get-rid” event

Bhattacharjee, A. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-90144-4.00001-x

Efficacy and Safety of Pro- and Synbiotics in Reducing Systemic Inflammation Through Improved Gut Health in Kenyan Infants (PROSYNK): An Open Label, Randomised, Phase 2 TrialPreprint

Otiti, M. I., June, M. J., K’Oloo, A., Chomba, M., Dodd, J., Kiu, R., Hall, L. J., Wang, D., Otieno, K., Kariuki, S., et al. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.5001482

Gut microbiota changes and enteric therapies in critically ill patients: a narrative review

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Next-generation microbiome therapeutics: why it is important to consider the space left in the wake of antibiotic treatment

King, O. G., Horrocks, V., Yip, A., & McDonald, J. A. K. (2024) · Future Microbiology · doi:10.1080/17460913.2024.2421113

Perturbations in the gut microbiome of C57BL/6 mice by the sobriety aid Antabuse® (disulfiram)

Evans, S. E., Valentine, M. E., Gallimore, F., Meka, Y., Koehler, S. I., Yu, H. D., Valentovic, M. A., & Long, T. E. (2024) · Journal of Applied Microbiology · doi:10.1093/jambio/lxae305

Distinct antibiotic treatment regimens differentially affect colonization resistance against multi-drug resistant Pseudomonas aeruginosa in mice

Heimesaat, M. M., Mousavi, S., Shayya, N. W., Bittroff‐Leben, A., Puschendorf, I., Reifenberger, G., & Bereswill, S. (2025) · European Journal of Microbiology and Immunology · doi:10.1556/1886.2025.00015

The Microbiome Connection

Ahamad, R., Ali, A., Manna, P., Quadri, N., Khan, Z., Pal, R., Muztaba, M., Ghazanfar, S., Islam, A., Iqbal, A., et al. (2025) · Wiley eBooks · doi:10.1002/9781394313785.ch10

Shigellose

Sansonetti, P. J., & Germani, Y. (2025) · EMC-Maladies infectieuses/Encyclopédie médico-chirurgicale. Maladies infectieuses · doi:10.1016/s1166-8598(25)64847-2

Recent Advances in Host Immune Mechanisms Against Listeria monocytogenes Infection

Shang, L., Xiang, W., Lun, M., Qu, S., Yin, Y., Ya, X., Zhou, Y.-Q., Zhu, P., & Song, Y. (2025) · Journal of Inflammation Research · doi:10.2147/jir.s535302

Identification of a Differential Microbiological Signature of Extended‐Spectrum ß‐Lactamases Producing Escherichia Carriers in Spanish Community Children

Cardinali‐Benigni, M., Khannous‐Lleiffe, O., Saus, E., Carmena, D., McConnell, M. J., Gabaldón, T., & López‐Siles, M. (2025) · MicrobiologyOpen · doi:10.1002/mbo3.70077

Gut Microbiota-Driven Modulation of Intestinal Barrier Function, Antioxidant Capacity, and Immune Response in Green-Footed Chicken by Dietary Fermented Chinese Herbal Compounds

Wang, W., Liang, Y., Cheng, T., Du, J., Zhang, Y., Li, J., Luo, X., & Wang, Y. (2025) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10857-z

Inference of causal interaction networks of gut microbiota using transfer entropy

Park, C., Kim, J., & Lee, J. (2025) · BMC Genomics · doi:10.1186/s12864-025-12384-1

The influence of short-chain fatty acids on the survival and virulence of Arcobacter butzleri

Fonseca, I. M., Mateus, C., Vieira, A., Domingues, F., Manageiro, V., Oleastro, M., & Ferreira, S. M. P. (2025) · Journal of Applied Microbiology · doi:10.1093/jambio/lxaf303

Additional file 1 of Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home

Ducarmon, Q. R., Terveer, E. M., Nooij, S., Bloem, M. N., Vendrik, K. E. W., Caljouw, M. A. A., Sanders, I. M. J. G., van Dorp, S. M., Wong, M. C., Zwittink, R. D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14385340

Additional file 1 of To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131

Tantoso, E., Eisenhaber, B., Kirsch, M., Shitov, V., Zhao, Z., & Eisenhaber, F. (2022) · Figshare · doi:10.6084/m9.figshare.20087966

Additional file 1 of The oral bacterial microbiota facilitates the stratification for ulcerative colitis patients with oral ulcers

Xu, J., Zhang, Y., Fang, X.-H., Liu, Y., Huang, Y.-B., Ke, Z.-L., Wang, Y., Zhang, Y. Y., Zhang, Y., Zhou, J., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26637837

Additional file 3 of Metagenomic analysis of gut microbiome and resistome of Whooper and Black Swans: a one health perspective

Fu, Y., Zhang, K., Shan, F., Li, J., Wang, Y., Li, X., Xu, H., Qin, Z., & Zhang, L. (2024) · Figshare · doi:10.6084/m9.figshare.26630929

Additional file 1 of Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota

Aljahdali, N. H., Sanad, Y. M., Han, J., & Foley, S. L. (2020) · Figshare · doi:10.6084/m9.figshare.13250814

Colonization resistance: the role of gut microbiota in preventing Salmonella invasion and infection

Deng, L., & Wang, S. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2424914 · Cited by 76

Mechanisms controlling pathogen colonization of the gut

Stecher, B., & Hardt, W. (2010) · Current Opinion in Microbiology · doi:10.1016/j.mib.2010.10.003 · Cited by 431

Gut microbial ecosystem and colonization resistance

Su-yun, C. (2012) · Zhongguo weishengtaixue zazhi · Cited by 1

Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection

Khan, I., Bai, Y., Zha, L., Ullah, N., Ullah, H., Shah, S. R. H., Sun, H., & Zhang, C. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.716299 · Cited by 291

The gut microbiota and host immunity synergistically orchestrate colonization resistance

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