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Microorganisms
Special Issues
The Interplay between Microbiota and Human Complex Traits
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The Interplay between Microbiota and Human Complex Traits

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

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 9263

Special Issue Editors

Dr. Giovanni Malerba

E-Mail Website
Guest Editor
GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
Interests: genomics and transcriptomics of Mendelian and complex traits; association and Linkage analyses; statistical genetics and bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Laura Veschetti

E-Mail Website
Guest Editor
1. GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
2. Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
Interests: microbial genomics; bacterial phylogenomics; multi-layer omics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The human microbiota is a complex community of microorganisms that reside in and on the human body. It plays a vital role in the maintenance of human health and is essential for various physiological processes. However, dysbiosis, defined as an imbalance in the microbiota, has been associated with a range of complex diseases, including metabolic, autoimmune, and neurodegenerative diseases.

High-throughput sequencing techniques, ranging from short-reads to long-reads sequencing, enabled researchers to unravel the complexity of microbiota composition and metabolic potential in different anatomical niches. Nonetheless, many methodological and analytical hurdles remain, including sample collection and storage, choice of the best molecular method, taxonomic identification, metabolic potential prediction and individual host–pathogen interactions. We encourage the exploration of the relationship between microbiota and complex human traits and/or diseases, therapeutic and preventive measures to contrast the progression of disease, as well as the investigation of novel methods to elucidate this relationship.

We welcome original research manuscripts, reviews, short communications, and case reports focusing on the association of microbiota (fungi, bacteria, viruses, metabolites, etc.) with the pathophysiology, biomarkers, and therapeutic strategies of complex human traits.

Dr. Giovanni Malerba
Dr. Laura Veschetti
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

  • microbiota
  • dysbiosis
  • human complex traits
  • 16S rRNA gene sequencing
  • shotgun metagenomics
  • long- and short-read sequencing
  • host–pathogen interaction
  • metabolic pathways
  • microbial identification

Published Papers (7 papers)

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Editorial

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2 pages, 185 KiB  
Editorial
The Interplay between Microbiota and Human Complex Traits
by Laura Veschetti, Mirko Treccani and Giovanni Malerba
Microorganisms 2023, 11(8), 2066; https://doi.org/10.3390/microorganisms11082066 - 11 Aug 2023
Viewed by 668
Abstract
Microorganisms have been one of the most influential drivers propelling some of the greatest environmental and evolutionary changes in the landscape and biology of the entire planet [...] Full article
(This article belongs to the Special Issue The Interplay between Microbiota and Human Complex Traits)

Research

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20 pages, 2481 KiB  
Article
Gut Microbiota and Biomarkers of Intestinal Barrier Damage in Cirrhosis
by Irina Efremova, Roman Maslennikov, Oleg Medvedev, Anna Kudryavtseva, Anastasia Avdeeva, George Krasnov, Filipp Romanikhin, Mikhail Diatroptov, Maria Fedorova, Elena Poluektova, Anna Levshina and Vladimir Ivashkin
Microorganisms 2024, 12(3), 463; https://doi.org/10.3390/microorganisms12030463 - 25 Feb 2024
Viewed by 786
Abstract
Gut dysbiosis and subclinical intestinal damage are common in cirrhosis. The aim of this study was to examine the association of intestinal damage biomarkers (diamine oxidase [DAO], claudin 3, and intestinal fatty acid binding protein [I-FABP; FABP2]) with the state of the gut [...] Read more.
Gut dysbiosis and subclinical intestinal damage are common in cirrhosis. The aim of this study was to examine the association of intestinal damage biomarkers (diamine oxidase [DAO], claudin 3, and intestinal fatty acid binding protein [I-FABP; FABP2]) with the state of the gut microbiota in cirrhosis. The blood levels of DAO were inversely correlated with blood levels of claudin 3, lipopolysaccharide (LPS), presepsin, TNF-α, and the severity of cirrhosis according to Child–Pugh scores. The blood level of I-FABP was directly correlated with the blood level of claudin 3 but not with that of DAO. Patients with small intestinal bacterial overgrowth (SIBO) had lower DAO levels than patients without SIBO. There was no significant difference in claudin 3 levels and I-FABP detection rates between patients with and without SIBO. The DAO level was directly correlated with the abundance of Akkermansiaceae, Akkermansia, Allisonella, Clostridiaceae, Dialister, Lactobacillus, Muribaculaceae, Negativibacillus, Ruminococcus, Thiomicrospiraceae, Verrucomicrobiae, and Verrucomicrobiota; and it was inversely correlated with the abundance of Anaerostipes, Erysipelatoclostridium, and Vibrio. The I-FABP level was directly correlated with Anaerostipes, Bacteroidia, Bacteroidota, Bilophila, Megamonas, and Selenomonadaceae; and it was inversely correlated with the abundance of Brucella, Pseudomonadaceae, Pseudomonas, and Vibrionaceae. The claudin 3 level was directly correlated with Anaerostipes abundance and was inversely correlated with the abundance of Brucella, Coriobacteriia, Eggerthellaceae, and Lactobacillus. Full article
(This article belongs to the Special Issue The Interplay between Microbiota and Human Complex Traits)
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15 pages, 690 KiB  
Article
Association between Gut Microbiota and Biological Aging: A Two-Sample Mendelian Randomization Study
by Chenglin Ye, Zhiqiang Li, Chun Ye, Li Yuan, Kailang Wu and Chengliang Zhu
Microorganisms 2024, 12(2), 370; https://doi.org/10.3390/microorganisms12020370 - 11 Feb 2024
Viewed by 1630
Abstract
Recent observational studies revealed an association between gut microbiota and aging, but whether gut microbiota are causally associated with the aging process remains unknown. We used a two-sample Mendelian randomization approach to investigate the causal association between gut microbiota and biological age acceleration [...] Read more.
Recent observational studies revealed an association between gut microbiota and aging, but whether gut microbiota are causally associated with the aging process remains unknown. We used a two-sample Mendelian randomization approach to investigate the causal association between gut microbiota and biological age acceleration using the largest available gut microbiota GWAS summary data from the MiBioGen consortium and GWAS data on biological age acceleration. We further conducted sensitivity analysis using MR-PRESSO, MR-Egger regression, Cochran Q test, and reverse MR analysis. Streptococcus (IVW, β = 0.16, p = 0.0001) was causally associated with Bioage acceleration. Eubacterium (rectale group) (IVW, β = 0.20, p = 0.0190), Sellimonas (IVW, β = 0.06, p = 0.019), and Lachnospira (IVW, β = −0.18, p = 0.01) were suggestive of causal associations with Bioage acceleration, with the latter being protective. Actinomyces (IVW, β = 0.26, p = 0.0083), Butyricimonas (IVW, β = 0.21, p = 0.0184), and Lachnospiraceae (FCS020 group) (IVW, β = 0.24, p = 0.0194) were suggestive of causal associations with Phenoage acceleration. This Mendelian randomization study found that Streptococcus was causally associated with Bioage acceleration. Further randomized controlled trials are needed to investigate its role in the aging process. Full article
(This article belongs to the Special Issue The Interplay between Microbiota and Human Complex Traits)
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12 pages, 2115 KiB  
Article
The Abnormal Accumulation of Lipopolysaccharide Secreted by Enriched Gram-Negative Bacteria Increases the Risk of Rotavirus Colonization in Young Adults
by Yifan Wu, Shuang Pei, Jie Wu, Xinru Tu, Lingling Ren, Yanli Ji, Yuyou Yao and Yehao Liu
Microorganisms 2023, 11(9), 2280; https://doi.org/10.3390/microorganisms11092280 - 11 Sep 2023
Viewed by 1021
Abstract
Human rotavirus (HRV) is an enteric virus that causes infantile diarrhea. However, the risk factors contributing to HRV colonization in young adults have not been thoroughly investigated. Here, we compared the differences in dietary habits and composition of gut microbiota between asymptomatic HRV-infected [...] Read more.
Human rotavirus (HRV) is an enteric virus that causes infantile diarrhea. However, the risk factors contributing to HRV colonization in young adults have not been thoroughly investigated. Here, we compared the differences in dietary habits and composition of gut microbiota between asymptomatic HRV-infected young adults and their healthy counterparts and investigated potential risk factors contributing to HRV colonization. Our results indicated that asymptomatic HRV-infected adults had an excessive intake of milk and dairy and high levels of veterinary antibiotics (VAs) and preferred veterinary antibiotic (PVAs) residues in urine samples. Their gut microbiota is characterized by abundant Gram-negative (G−) bacteria and high concentrations of lipopolysaccharide (LPS). Several opportunistic pathogens provide discriminatory power to asymptomatic, HRV-infected adults. Finally, we observed an association between HRV colonization and disrupted gut microbiota caused by the exposure to VAs and PVAs. Our study reveals the traits of disrupted gut microbiota in asymptomatic HRV-infected adults and provides a potential avenue for gut microbiota-based prevention strategies for HRV colonization. Full article
(This article belongs to the Special Issue The Interplay between Microbiota and Human Complex Traits)
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16 pages, 2643 KiB  
Article
Gut Dysbiosis and Hemodynamic Changes as Links of the Pathogenesis of Complications of Cirrhosis
by Irina Efremova, Roman Maslennikov, Elena Poluektova, Maria Zharkova, Anna Kudryavtseva, George Krasnov, Maria Fedorova, Elena Shirokova, Evgenii Kozlov, Anna Levshina and Vladimir Ivashkin
Microorganisms 2023, 11(9), 2202; https://doi.org/10.3390/microorganisms11092202 - 31 Aug 2023
Cited by 2 | Viewed by 965
Abstract
The aim was to evaluate the relationship between gut dysbiosis and hemodynamic changes (hyperdynamic circulation) in cirrhosis, and between hemodynamic changes and complications of this disease. This study included 47 patients with cirrhosis. Stool microbiome was assessed using 16S rRNA gene sequencing. Echocardiography [...] Read more.
The aim was to evaluate the relationship between gut dysbiosis and hemodynamic changes (hyperdynamic circulation) in cirrhosis, and between hemodynamic changes and complications of this disease. This study included 47 patients with cirrhosis. Stool microbiome was assessed using 16S rRNA gene sequencing. Echocardiography with a simultaneous assessment of blood pressure and heart rate was performed to assess systemic hemodynamics. Patients with hyperdynamic circulation had more severe cirrhosis, lower albumin, sodium and prothrombin levels, higher C-reactive protein, aspartate aminotransferase and total bilirubin levels, and higher incidences of portopulmonary hypertension, ascites, overt hepatic encephalopathy, hypoalbuminemia, hypoprothrombinemia, systemic inflammation, and severe hyperbilirubinemia than patients with normodynamic circulation. Patients with hyperdynamic circulation compared with those with normodynamic circulation had increased abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcaceae, Lactobacillaceae, Fusobacteria, Micrococcaceae, Intestinobacter, Clostridium sensu stricto, Proteus and Rumicoccus, and decreased abundance of Bacteroidetes, Bacteroidaceae, Holdemanella, and Butyrivibrio. The systemic vascular resistance and cardiac output values correlated with the abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcaceae, Lactobacillaceae, Micrococcaceae, and Fusobacteria. Heart rate and cardiac output value were negatively correlated with the abundance of Bacteroidetes. The mean pulmonary artery pressure value was positively correlated with the abundance of Proteobacteria and Micrococcaceae, and negatively with the abundance of Holdemanella. Full article
(This article belongs to the Special Issue The Interplay between Microbiota and Human Complex Traits)
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15 pages, 1866 KiB  
Article
Effects of Bacterial Lysates and Metabolites on Collagen Homeostasis in TNF-α-Challenged Human Dermal Fibroblasts
by Laura Huuskonen, Heli Anglenius, Ilmari Ahonen and Kirsti Tiihonen
Microorganisms 2023, 11(6), 1465; https://doi.org/10.3390/microorganisms11061465 - 31 May 2023
Cited by 1 | Viewed by 1883
Abstract
During skin aging, the production of extracellular matrix (ECM) proteins, such as type I collagen, decreases and the synthesis of ECM-degrading matrix metalloproteinases (MMPs) rises, leading to an imbalance in homeostasis and to wrinkle formation. In this study, we examined the effects of [...] Read more.
During skin aging, the production of extracellular matrix (ECM) proteins, such as type I collagen, decreases and the synthesis of ECM-degrading matrix metalloproteinases (MMPs) rises, leading to an imbalance in homeostasis and to wrinkle formation. In this study, we examined the effects of bacterial lysates and metabolites from three bifidobacteria and five lactobacilli on collagen homeostasis in human dermal fibroblasts during challenge with tumor necrosis factor alpha (TNF-α), modeling an inflammatory condition that damages the skin’s structure. Antiaging properties were measured, based on fibroblast cell viability and confluence, amount of type I pro-collagen, ratio of MMP-1 to type I pro-collagen, cytokines, and growth factors. The TNF-α challenge increased the MMP-1/type I pro-collagen ratio and levels of proinflammatory cytokines, as expected. With the probiotics, differences were clearly dependent on bacterial species, strain, and form. In general, the lysates elicited less pronounced responses in the biomarkers. Of all strains, the Bifidobacterium animalis ssp. lactis strains Bl-04 and B420 best maintained type I pro-collagen production and the MMP-1/collagen type I ratio under no-challenge and challenge conditions. Metabolites that were produced by bifidobacteria, but not their lysates, reduced several proinflammatory cytokines (IL-6, IL-8, and TNF-α) during the challenge, whereas those from lactobacilli did not. These results indicate that B. animalis ssp. lactis-produced metabolites, especially those of strains Bl-04 and B420, could support collagen homeostasis in the skin. Full article
(This article belongs to the Special Issue The Interplay between Microbiota and Human Complex Traits)
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Other

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16 pages, 2278 KiB  
Systematic Review
Safety and Efficacy of Fecal Microbiota Transplantation in Treatment of Inflammatory Bowel Disease in the Pediatric Population: A Systematic Review and Meta-Analysis
by Mark Hsu, Kyaw Min Tun, Kavita Batra, Lubaba Haque, Tahne Vongsavath and Annie S. Hong
Microorganisms 2023, 11(5), 1272; https://doi.org/10.3390/microorganisms11051272 - 12 May 2023
Cited by 4 | Viewed by 1684
Abstract
Background and Aims: Fecal microbiota transplantation (FMT) has been increasingly studied in the inflammatory bowel disease (IBD) population. However, most studies have focused on the adult population, and the safety and efficacy of FMT in a pediatric population is less well understood. This [...] Read more.
Background and Aims: Fecal microbiota transplantation (FMT) has been increasingly studied in the inflammatory bowel disease (IBD) population. However, most studies have focused on the adult population, and the safety and efficacy of FMT in a pediatric population is less well understood. This systematic review and meta-analysis investigates the safety and efficacy of FMT in a pediatric IBD population. Methods: A comprehensive literature search of publications published prior to 30 June 2022 was undertaken. Safety data, IBD-related outcomes, and microbiome analysis were obtained from these studies when accessible. Individual estimates of each study were pooled, and sensitivity analysis was conducted. Results: Eleven studies satisfied our eligibility criteria. The calculated pooled rate of adverse events was 29% (95% confidence interval [CI]: 15.0%, 44.0%; p < 0.001; I2 = 89.0%, Q = 94.53), and the calculated pooled rate of serious adverse events was 10% (95% confidence interval [CI]: 6.0%, 14.0%; p = 0.28; I2 = 18.0%, Q = 9.79). One month after FMT, clinical response was achieved in 20/34 (58.8%) pediatric IBD patients, clinical remission was achieved in 22/34 (64.7%), and both clinical response and remission were achieved in 15/34 (44.1%) pediatric IBD patients. Conclusions: FMT can be a safe and effective treatment in the pediatric IBD population and may demonstrate improved safety and efficacy in the pediatric population compared to the adult population. However, our results are limited by a lack of established protocol as well as long-term follow-up for FMT in a pediatric IBD population. Full article
(This article belongs to the Special Issue The Interplay between Microbiota and Human Complex Traits)
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