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Microorganisms
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Microbiome in Infectious Diseases
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Microbiome in Infectious Diseases

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

Deadline for manuscript submissions: closed (29 February 2024) | Viewed by 14712

Special Issue Editors

Dr. Elda Righi

E-Mail Website
Guest Editor
Infectious Diseases Section, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
Interests: antibiotic resistance; antimicrobial stewardship; microbiome; infections in immunocompromised patients
Dr. Assunta Sartor

E-Mail Website
Guest Editor
Microbiology Unit, Udine University Hospital, 33100 Udine, Italy
Interests: antimicrobial resistance; Gram-negative bacteria; automated systems for resistance detection

Special Issue Information

Dear Colleagues,

Studies on microbiome signatures, bacterial abundance and beta diversity in infections are increasing exponentially. The COVID-19 pandemic has increased the interest in the study of gut and respiratory microbiome, especially in viral diseases. An increase in opportunistic pathogens and a decrease of beneficial symbionts was observed for severe forms of COVID-19, while the abundance of specific bacteria was shown in COVID-19 compared to influenza.

While the research on microbiome is well established in inflammatory disease, infectious diseases still offer opportunities for further investigation that may be useful to identify markers of disease progression or the consequences of the use of antibiotics in gut dysbiosis, increasing the risk of clinically relevant infections.

This Special Issue of Microorganisms specifically focuses on the study of dysbiosis in different types of infectious diseases, on the use of antibiotics and on the potential consequences for antibiotic resistance and antimicrobial stewardship. The Issue invites researchers to contribute research articles, reviews, and opinions addressing the latest knowledge on microbiomes and different types of infections or gut dysbiosis and antibiotic use, including reviews, microbiology studies, clinical studies, whole-genome and 16S sequencing, etc., in basic research, in vivo research and its clinical applications. This Special Issue is divided into two blocks: i) microbiome changes in infections (including COVID-19); and ii) potential consequences of gut dysbiosis in infectious diseases, antibiotic use, and antibiotic resistance. Manuscripts covering these areas of knowledge, and others related to microbiome signatures and infections, are of interest for this Special Issue.

Reviews, original research papers, and communications will be welcomed.

Dr. Elda Righi
Dr. Assunta Sartor
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.

Published Papers (7 papers)

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Research

Jump to: Review

20 pages, 1886 KiB  
Article
Vaginal Microbial Network Analysis Reveals Novel Taxa Relationships among Adolescent and Young Women with Incident Sexually Transmitted Infection Compared with Those Remaining Persistently Negative over a 30-Month Period
by Supriya D. Mehta, Walter Agingu, Garazi Zulaika, Elizabeth Nyothach, Runa Bhaumik, Stefan J. Green, Anna Maria van Eijk, Fredrick O. Otieno, Penelope A. Phillips-Howard and John Schneider
Microorganisms 2023, 11(8), 2035; https://doi.org/10.3390/microorganisms11082035 - 8 Aug 2023
Cited by 1 | Viewed by 1372
Abstract
A non-optimal vaginal microbiome (VMB) is typically diverse with a paucity of Lactobacillus crispatus and is often associated with bacterial vaginosis (BV) and sexually transmitted infections (STIs). Although compositional characterization of the VMB is well-characterized, especially for BV, knowledge remains limited on how [...] Read more.
A non-optimal vaginal microbiome (VMB) is typically diverse with a paucity of Lactobacillus crispatus and is often associated with bacterial vaginosis (BV) and sexually transmitted infections (STIs). Although compositional characterization of the VMB is well-characterized, especially for BV, knowledge remains limited on how different groups of bacteria relate to incident STIs, especially among adolescents. In this study, we compared the VMB (measured via 16S ribosomal RNA gene amplicon sequencing) of Kenyan secondary school girls with incident STIs (composite of chlamydia, gonorrhea, and trichomoniasis) to those who remained persistently negative for STIs and BV over 30 months of follow-up. We applied microbial network analysis to identify key taxa (i.e., those with the greatest connectedness in terms of linkages to other taxa), as measured by betweenness and eigenvector centralities, and sub-groups of clustered taxa. VMB networks of those who remained persistently negative reflected greater connectedness compared to the VMB from participants with STI. Taxa with the highest centralities were not correlated with relative abundance and differed between those with and without STI. Subject-level analyses indicated that sociodemographic (e.g., age and socioeconomic status) and behavioral (e.g., sexual activity) factors contribute to microbial network structure and may be of relevance when designing interventions to improve VMB health. Full article
(This article belongs to the Special Issue Microbiome in Infectious Diseases)
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12 pages, 1088 KiB  
Article
Insights into the Genital Microbiota of Women Who Experienced Fetal Death in Utero
by Mira Holliday, Kumar Uddipto, Gerardo Castillo, Luz Estela Vera, Julie A. Quinlivan and George L. Mendz
Microorganisms 2023, 11(8), 1877; https://doi.org/10.3390/microorganisms11081877 - 25 Jul 2023
Cited by 2 | Viewed by 1051
Abstract
The aim of this work was to achieve a better understanding of the bacterial pathogens associated with stillbirths that would serve to inform clinical interventions directed at reducing this adverse pregnancy outcome. A prospective observational study was conducted with the participation of 22 [...] Read more.
The aim of this work was to achieve a better understanding of the bacterial pathogens associated with stillbirths that would serve to inform clinical interventions directed at reducing this adverse pregnancy outcome. A prospective observational study was conducted with the participation of 22 women from northern Peru, of whom 11 experienced fetal death in utero and 11 delivered preterm births. Swabs were taken from the vagina, placenta, amniotic fluid and axilla of the infant at birth by Caesarean section. The bacterial populations in the vagina and the amniotic space of each participant were determined by employing the amplicon sequencing of the V4 region of the 16S rRNA genes. The sequence data were analysed using bioinformatics tools. The work showed differences in the composition of the genital microbiomes of women who experienced preterm birth or fetal death in utero. There were no differences in the alpha diversity between the genital microbiotas of both groups of women, but there were more different taxa in the vagina and amniotic space of the preterm participants. Lactobacillus spp. was less abundant in the stillbirth cases. E. coli/Shigella, Staphylococcus, Gardnerella, Listeria and Bacteroides taxa were associated with the stillbirths. In each woman, there was a minimal concordance between the bacterial populations in the vagina and amniotic space. Full article
(This article belongs to the Special Issue Microbiome in Infectious Diseases)
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14 pages, 1663 KiB  
Article
Impact of Nystatin Oral Rinse on Salivary and Supragingival Microbial Community among Adults with Oral Candidiasis
by Lanxin Zhang, Samantha Manning, Tong Tong Wu, Yan Zeng, Aaron Lee, Yan Wu, Bruce J. Paster, George Chen, Kevin Fiscella and Jin Xiao
Microorganisms 2023, 11(6), 1497; https://doi.org/10.3390/microorganisms11061497 - 5 Jun 2023
Viewed by 1837
Abstract
This study aimed to evaluate the impact of Nystatin oral rinse on salivary and supragingival microbiota in adults with oral candidiasis and identify predictive factors related to individuals’ responses to Nystatin. The trial involved twenty participants who used 600,000 International Units/application of Nystatin [...] Read more.
This study aimed to evaluate the impact of Nystatin oral rinse on salivary and supragingival microbiota in adults with oral candidiasis and identify predictive factors related to individuals’ responses to Nystatin. The trial involved twenty participants who used 600,000 International Units/application of Nystatin oral rinse for seven days, four times a day, and were followed up at one week and three months after the rinse. The salivary and plaque microbiome of the participants were assessed via 16S rDNA amplicon sequencing. Overall, salivary and plaque microbiomes remained stable. However, among the participants (53 percent) who responded to Nystatin rinse (defined as free of oral Candida albicans post treatment), Veillonella emerged as a core genus alongside Streptococcus and Actinomyces in supragingival plaque at the 3-month follow-up. Furthermore, statistical models were fit to identify predictive factors of Nystatin rinse success (elimination of C. albicans) or failure (remaining C. albicans). The results revealed that an increased level of salivary Interferon (IFN)-γ-inducible protein (IP-10), also known as C-X-C motif chemokine ligand 10 (CXCL10), was an indicator of a failure of responding to Nystatin rinse. Future clinical trials are warranted to comprehensively assess the impact of antifungal treatment on the oral flora. Full article
(This article belongs to the Special Issue Microbiome in Infectious Diseases)
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28 pages, 3823 KiB  
Article
The Gut Microbiome of an Indigenous Agropastoralist Population in a Remote Area of Colombia with High Rates of Gastrointestinal Infections and Dysbiosis
by Simone Kann, Kirsten Eberhardt, Rebecca Hinz, Norbert Georg Schwarz, Juan Carlos Dib, Andres Aristizabal, Gustavo Andrés Concha Mendoza, Ralf Matthias Hagen, Hagen Frickmann, Israel Barrantes and Bernd Kreikemeyer
Microorganisms 2023, 11(3), 625; https://doi.org/10.3390/microorganisms11030625 - 28 Feb 2023
Cited by 1 | Viewed by 1850
Abstract
An Indigenous agropastoralist population called the Wiwa from the Sierra Nevada de Santa Marta, in North-East Colombia, shows high rates of gastrointestinal infections. Chronic gut inflammatory processes and dysbiosis could be a reason, suggesting an influence or predisposing potential of the gut microbiome [...] Read more.
An Indigenous agropastoralist population called the Wiwa from the Sierra Nevada de Santa Marta, in North-East Colombia, shows high rates of gastrointestinal infections. Chronic gut inflammatory processes and dysbiosis could be a reason, suggesting an influence or predisposing potential of the gut microbiome composition. The latter was analyzed by 16S rRNA gene amplicon next generation sequencing from stool samples. Results of the Wiwa population microbiomes were associated with available epidemiological and morphometric data and compared to control samples from a local urban population. Indeed, locational-, age-, and gender-specific differences in the Firmicutes/Bacteriodetes ratio, core microbiome, and overall genera-level microbiome composition were shown. Alpha- and ß-diversity separated the urban site from the Indigenous locations. Urban microbiomes were dominated by Bacteriodetes, whereas Indigenous samples revealed a four times higher abundance of Proteobacteria. Even differences among the two Indigenous villages were noted. PICRUSt analysis identified several enriched location-specific bacterial pathways. Moreover, on a general comparative scale and with a high predictive accuracy, we found Sutterella associated with the abundance of enterohemorrhagic Escherichia coli (EHEC), Faecalibacteria associated with enteropathogenic Escherichia coli (EPEC) and helminth species Hymenolepsis nana and Enterobius vermicularis. Parabacteroides, Prevotella, and Butyrivibrio are enriched in cases of salmonellosis, EPEC, and helminth infections. Presence of Dialister was associated with gastrointestinal symptoms, whereas Clostridia were exclusively found in children under the age of 5 years. Odoribacter and Parabacteroides were exclusively identified in the microbiomes of the urban population of Valledupar. In summary, dysbiotic alterations in the gut microbiome in the Indigenous population with frequent episodes of self-reported gastrointestinal infections were confirmed with epidemiological and pathogen-specific associations. Our data provide strong hints of microbiome alterations associated with the clinical conditions of the Indigenous population. Full article
(This article belongs to the Special Issue Microbiome in Infectious Diseases)
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Review

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24 pages, 5448 KiB  
Review
Gut Microbiome Disruption Following SARS-CoV-2: A Review
by Elda Righi, Ilaria Dalla Vecchia, Nina Auerbach, Matteo Morra, Anna Górska, Concetta Sciammarella, Lorenza Lambertenghi, Elisa Gentilotti, Massimo Mirandola, Evelina Tacconelli and Assunta Sartor
Microorganisms 2024, 12(1), 131; https://doi.org/10.3390/microorganisms12010131 - 9 Jan 2024
Cited by 1 | Viewed by 1438
Abstract
COVID-19 has been associated with having a negative impact on patients’ gut microbiome during both active disease and in the post-acute phase. In acute COVID-19, rapid alteration of the gut microbiome composition was observed, showing on one side a reduction in beneficial symbionts [...] Read more.
COVID-19 has been associated with having a negative impact on patients’ gut microbiome during both active disease and in the post-acute phase. In acute COVID-19, rapid alteration of the gut microbiome composition was observed, showing on one side a reduction in beneficial symbionts (e.g., Roseburia, Lachnospiraceae) and on the other side an increase in opportunistic pathogens such as Enterococcus and Proteobacteria. Alpha diversity tends to decrease, especially initially with symptom onset and hospital admission. Although clinical recovery appears to align with improved gut homeostasis, this process could take several weeks, even in mild infections. Moreover, patients with COVID-19 post-acute syndrome showed changes in gut microbiome composition, with specific signatures associated with decreased respiratory function up to 12 months following acute disease. Potential treatments, especially probiotic-based therapy, are under investigation. Open questions remain on the possibility to use gut microbiome data to predict disease progression and on potential confounders that may impair result interpretation (e.g., concomitant therapies in the acute phase; reinfection, vaccines, and occurrence of novel conditions or diseases in the post-acute syndrome). Understanding the relationships between gut microbiome dynamics and disease progression may contribute to better understanding post-COVID syndrome pathogenesis or inform personalized treatment that can affect specific targets or microbiome markers. Full article
(This article belongs to the Special Issue Microbiome in Infectious Diseases)
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19 pages, 838 KiB  
Review
The Role of Gut Dysbiosis in the Loss of Intestinal Immune Cell Functions and Viral Pathogenesis
by Farzaneh Fakharian, Siva Thirugnanam, David A. Welsh, Woong-Ki Kim, Jay Rappaport, Kyle Bittinger and Namita Rout
Microorganisms 2023, 11(7), 1849; https://doi.org/10.3390/microorganisms11071849 - 21 Jul 2023
Cited by 9 | Viewed by 4615
Abstract
The gut microbiome plays a critical role in maintaining overall health and immune function. However, dysbiosis, an imbalance in microbiome composition, can have profound effects on various aspects of human health, including susceptibility to viral infections. Despite numerous studies investigating the influence of [...] Read more.
The gut microbiome plays a critical role in maintaining overall health and immune function. However, dysbiosis, an imbalance in microbiome composition, can have profound effects on various aspects of human health, including susceptibility to viral infections. Despite numerous studies investigating the influence of viral infections on gut microbiome, the impact of gut dysbiosis on viral infection and pathogenesis remains relatively understudied. The clinical variability observed in SARS-CoV-2 and seasonal influenza infections, and the presence of natural HIV suppressors, suggests that host-intrinsic factors, including the gut microbiome, may contribute to viral pathogenesis. The gut microbiome has been shown to influence the host immune system by regulating intestinal homeostasis through interactions with immune cells. This review aims to enhance our understanding of how viral infections perturb the gut microbiome and mucosal immune cells, affecting host susceptibility and response to viral infections. Specifically, we focus on exploring the interactions between gamma delta (γδ) T cells and gut microbes in the context of inflammatory viral pathogenesis and examine studies highlighting the role of the gut microbiome in viral disease outcomes. Furthermore, we discuss emerging evidence and potential future directions for microbiome modulation therapy in the context of viral pathogenesis. Full article
(This article belongs to the Special Issue Microbiome in Infectious Diseases)
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20 pages, 2673 KiB  
Review
Intelligent Biological Networks: Improving Anti-Microbial Resistance Resilience through Nutritional Interventions to Understand Protozoal Gut Infections
by Avinash V. Karpe, David J. Beale and Cuong D. Tran
Microorganisms 2023, 11(7), 1800; https://doi.org/10.3390/microorganisms11071800 - 13 Jul 2023
Viewed by 1579
Abstract
Enteric protozoan pathogenic infections significantly contribute to the global burden of gastrointestinal illnesses. Their occurrence is considerable within remote and indigenous communities and regions due to reduced access to clean water and adequate sanitation. The robustness of these pathogens leads to a requirement [...] Read more.
Enteric protozoan pathogenic infections significantly contribute to the global burden of gastrointestinal illnesses. Their occurrence is considerable within remote and indigenous communities and regions due to reduced access to clean water and adequate sanitation. The robustness of these pathogens leads to a requirement of harsh treatment methods, such as medicinal drugs or antibiotics. However, in addition to protozoal infection itself, these treatments impact the gut microbiome and create dysbiosis. This often leads to opportunistic pathogen invasion, anti-microbial resistance, or functional gastrointestinal disorders, such as irritable bowel syndrome. Moreover, these impacts do not remain confined to the gut and are reflected across the gut–brain, gut–liver, and gut–lung axes, among others. Therefore, apart from medicinal treatment, nutritional supplementation is also a key aspect of providing recovery from this dysbiosis. Future proteins, prebiotics, probiotics, synbiotics, and food formulations offer a good solution to remedy this dysbiosis. Furthermore, nutritional supplementation also helps to build resilience against opportunistic pathogens and potential future infections and disorders that may arise due to the dysbiosis. Systems biology techniques have shown to be highly effective tools to understand the biochemistry of these processes. Systems biology techniques characterize the fundamental host–pathogen interaction biochemical pathways at various infection and recovery stages. This same mechanism also allows the impact of the abovementioned treatment methods of gut microbiome remediation to be tracked. This manuscript discusses system biology approaches, analytical techniques, and interaction and association networks, to understand (1) infection mechanisms and current global status; (2) cross-organ impacts of dysbiosis, particularly within the gut–liver and gut–lung axes; and (3) nutritional interventions. This study highlights the impact of anti-microbial resistance and multi-drug resistance from the perspective of protozoal infections. It also highlights the role of nutritional interventions to add resilience against the chronic problems caused by these phenomena. Full article
(This article belongs to the Special Issue Microbiome in Infectious Diseases)
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