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Microorganisms
Special Issues
Gut Microbiome, Zoonotic Diseases, and Pathogen–Host Interactions
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Gut Microbiome, Zoonotic Diseases, and Pathogen–Host Interactions

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Veterinary Microbiology".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 4063

Special Issue Editors

Dr. He Zhang

E-Mail Website
Guest Editor
Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
Interests: porcine sapelovirus; porcine reproductive and respiratory syndrome virus
Special Issues, Collections and Topics in MDPI journals
Dr. Qiang Zhang

E-Mail Website
Guest Editor
College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
Interests: gene
Dr. Andreia J. Amaral

E-Mail Website
Guest Editor
Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
Interests: animal gene; animal science; bioinformatics; genetics

Special Issue Information

Dear Colleagues,

The following Special Issue of the journal Microorganisms, entitled "Gut Microbiome, Zoonotic Diseases, and Pathogen–Host Interactions", invites researchers to publish their latest findings and advancements in understanding the intricate interplay between the gut microbiome, zoonotic pathogens, and host immune responses. The following Special Issue aims to explore the pivotal role of the gut microbiome in zoonotic diseases and the development of host immune strategies against pathogenic microbial infections.

The gut microbiome plays a vital role in maintaining host health and immune function, while zoonotic diseases represent a global public health concern. Understanding the interactions between the gut microbiome and zoonotic pathogens is crucial for devising effective prevention and control measures. Novel detection methods for pathogenic microorganisms are key to preventing disease outbreaks, and elucidating the molecular mechanisms underlying pathogen–host interactions will further facilitate our ability to mitigate the detrimental effects of pathogens on host health.

The following Special Issue welcomes submissions addressing gut microbial ecology, the transmission dynamics of zoonotic diseases, host–microbiome interactions, and novel detection methods targeting zoonotic pathogens. Specifically, the Special Issue will cover the following core topics:

  1. The Gut Microbiome's Role in Host Health: Exploring its contributions through metabolite production, nutrient processing, gut barrier maintenance, and immune modulation.
  2. Zoonotic Pathogen Transmission and Pathogenesis: Analyzing routes, mechanisms, survival strategies, and immune adaptation in animals and humans.
  3. Host–Microbiome Interactions: Uncovering bidirectional communication using high-throughput sequencing, single-cell sequencing, and metabolomics. Exploring immune recognition and regulation.
  4. Novel Detection Methods: Introducing innovative technologies (gene chips, CRISPR-Cas, and Quantitative Real-Time PCR) for sensitive, specific, and rapid pathogen detection.
  5. Prevention and Control Strategies: Based on research, discussing gut microbiome modulation, vaccine development, and policy improvements to combat zoonotic diseases. Emphasizing interdisciplinary collaboration.

In summary, the above Special Issue aims to serve as a valuable platform for scholars in the fields of microbiology, infectious diseases, immunology, and related fields to exchange ideas, share achievements, and jointly advance our understanding and innovative developments in the study of the gut microbiome, zoonotic diseases, and pathogen–host interactions.

Researchers from diverse fields, including microbiology, infectious diseases, and veterinary medicine, are encouraged to contribute their original research articles, reviews, and communications.

Dr. He Zhang
Dr. Qiang Zhang
Dr. Andreia J. Amaral
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • gut microbiota
  • zoonotic diseases
  • antimicrobial resistance
  • Escherichia coli
  • resistance gene

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Research

11 pages, 3418 KiB  
Article
hnRNPH1 Inhibits Influenza Virus Replication by Binding Viral RNA
by Ruixue Xue, Danqi Bao, Tianxin Ma, Shiqi Niu, Zihua Wu, Xuehua Lv, Yunxiang Zhang, Guanlong Xu, Dawei Yan, Zhifei Zhang, Xue Pan, Minghao Yan, Qiaoyang Teng, Chunxiu Yuan, Zejun Li and Qinfang Liu
Microorganisms 2025, 13(1), 24; https://doi.org/10.3390/microorganisms13010024 - 26 Dec 2024
Viewed by 807
Abstract
During the life cycle of the influenza virus, viral RNPs (vRNPs) are transported to the nucleus for replication. Given that a large number of progeny viral RNA occupies the nucleus, whether there is any host protein located in the nucleus that recognizes the [...] Read more.
During the life cycle of the influenza virus, viral RNPs (vRNPs) are transported to the nucleus for replication. Given that a large number of progeny viral RNA occupies the nucleus, whether there is any host protein located in the nucleus that recognizes the viral RNA and inhibits the viral replication remains largely unknown. In this study, to explore the role of hnRNPH1 in influenza virus infection, we knocked down and over-expressed the hnRNPH1 proteins in 293T cells, then infected the cells with the influenza virus. The results showed that the host hnRNPH1 inhibits the replication of H1N1 and H9N2 influenza viruses by restraining the polymerase activity of viruses. hnRNPH1 contains two RNA recognition motifs (RRM1) and RRM2. Further studies indicated that hnRNPH1 specifically binds to the viral RNA of the PB1, PA, and NP genes. Mutation of the key residues tryptophan and tyrosine in RRM1 and RRM2 abolished the binding affinity to viral RNA and the suppression of polymerase activity of the influenza virus. All the results suggested that hnRNPH1 suppresses polymerase activity and replication of the influenza virus by binding viral RNA. Full article
(This article belongs to the Special Issue Gut Microbiome, Zoonotic Diseases, and Pathogen–Host Interactions)
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13 pages, 3453 KiB  
Article
Metagenome-Assembled Genomes of Pig Fecal Samples in Nine European Countries: Insights into Antibiotic Resistance Genes and Viruses
by Boxuan Yang, Jianbo Yang, Routing Chen, Jianmin Chai, Xiaoyuan Wei, Jiangchao Zhao, Yunxiang Zhao, Feilong Deng and Ying Li
Microorganisms 2024, 12(12), 2409; https://doi.org/10.3390/microorganisms12122409 - 24 Nov 2024
Cited by 1 | Viewed by 1157
Abstract
Gut microbiota plays a crucial role in the health and productivity of pigs. However, the spread of antibiotic resistance genes (ARGs) and viruses within the pig intestinal microbiota poses significant threats to animal and public health. This study utilized 181 pig samples from [...] Read more.
Gut microbiota plays a crucial role in the health and productivity of pigs. However, the spread of antibiotic resistance genes (ARGs) and viruses within the pig intestinal microbiota poses significant threats to animal and public health. This study utilized 181 pig samples from nine European countries and employed metagenomic assembly methods to investigate the dynamics and distribution of ARGs and viruses within the pig intestinal microbiota, aiming to observing their associations with potential bacterial hosts. We identified 4605 metagenome-assembled genomes (MAGs), corresponding to 19 bacterial phyla, 97 families, 309 genera, and a total of 449 species. Additionally, 44 MAGs were classified as archaea. Analysis of ARGs revealed 276 ARG types across 21 ARG classes, with Glycopeptide being the most abundant ARG class, followed by the class of Multidrug. Treponema D sp016293915 was identified as a primary potential bacterial host for Glycopeptide. Aligning nucleotide sequences with a viral database, we identified 1044 viruses. Among the viral genome families, Peduoviridae and Intestiviridae were the most prevalent, with CAG-914 sp000437895 being the most common potential host species for both. These findings highlight the importance of MAGs in enhancing our understanding of the gut microbiome, revealing microbial diversity, antibiotic resistance, and virus–bacteria interactions. The data analysis for the article was based on the public dataset PRJEB22062 in the European Nucleotide Archive. Full article
(This article belongs to the Special Issue Gut Microbiome, Zoonotic Diseases, and Pathogen–Host Interactions)
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15 pages, 2284 KiB  
Article
Silver and Copper Nanoparticles Hosted by Carboxymethyl Cellulose Reduce the Infective Effects of Enterotoxigenic Escherichia coli:F4 on Porcine Intestinal Enterocyte IPEC-J2
by Armelle Tchoumi Neree, Farzaneh Noori, Abdelkrim Azzouz, Marcio Costa, John Morris Fairbrother, Mircea Alexandru Mateescu and Younes Chorfi
Microorganisms 2024, 12(10), 2026; https://doi.org/10.3390/microorganisms12102026 - 7 Oct 2024
Viewed by 1246
Abstract
Zero-valent copper and silver metals (Ms) nanoparticles (NPs) supported on carboxymethylcellulose (CMC) were synthesized for treating Enterotoxigenic Escherichia coli fimbriae 4 (ETEC:F4), a major cause of diarrhea in post-weaned pigs. The antibacterial properties of Cu0/CMC and Ag0/CMC were assessed [...] Read more.
Zero-valent copper and silver metals (Ms) nanoparticles (NPs) supported on carboxymethylcellulose (CMC) were synthesized for treating Enterotoxigenic Escherichia coli fimbriae 4 (ETEC:F4), a major cause of diarrhea in post-weaned pigs. The antibacterial properties of Cu0/CMC and Ag0/CMC were assessed on infected porcine intestinal enterocyte IPEC-J2, an in vitro model mimicking the small intestine. The lower average particle size (218 nm) and polydispersity index [PDI]: 0.25) for Ag0/CMC, when compared with those of Cu0/CMC (367 nm and PDI 0.96), were explained by stronger Ag0/CMC interactions. The minimal inhibitory concentration (MIC) and half inhibitory concentration (IC50) of Ag0/CMC were lower in both bacteria and IPEC-J2 cells than those of Cu0/CMC, confirming that silver nanoparticles are more bactericidal than copper counterparts. IPEC-J2, less sensitive in MNP/CMC treatment, was used to further investigate the infective process by ETEC:F4. The IC50 of MNP/CMC increased significantly when infected IPEC-J2 cells and ETEC were co-treated, showing an inhibition of the cytotoxicity effect of ETEC:F4 infection and protection of treated IPEC-J2. Thus, it appears that metal insertion in CMC induces an inhibiting effect on ETEC:F4 growth and that MNP/CMC dispersion governs the enhancement of this effect. These results open promising prospects for metal-loaded biopolymers for preventing and treating swine diarrhea. Full article
(This article belongs to the Special Issue Gut Microbiome, Zoonotic Diseases, and Pathogen–Host Interactions)
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