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Microorganisms
Special Issues
Advances in Human Microbiomes
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Advances in Human Microbiomes

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

Deadline for manuscript submissions: 15 January 2025 | Viewed by 8717

Special Issue Editor

Dr. Suzette Sørensen

E-Mail Website
Guest Editor
Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark
Interests: human microbiome; microbiota; dysbiosis; gut microbiota; host-microbiome interactions

Special Issue Information

Dear Colleagues,

The human microbiome has important functions and roles in their hosts and is tightly connected to human health and disease. Numerous studies have demonstrated imbalances in microbiota composition between patients and healthy controls, and further in vitro and animal studies have highlighted the functional impact of the microbiome on disease development or symptom maintenance. This has attracted great interest in targeting the human microbiome for therapeutical purposes. Current strategies include diet interventions, intake of pre- and probiotics or fecal microbiota transplantation, where the latter has proven highly effective for the treatment of recurrent C. difficile infections. Other effective curative or symptom-reducing options have proven more challenging, despite extensive mapping and thorough characterization of the human microbiome. This indicates that researchers still need to obtain a greater understanding of how the microbiome communicates and interacts with host cells or organs, and further identify which factors are important for shifts in microbiota composition. 

MDPI’s Microorganisms announces the launch of the Special Issue entitled “Advances in Human Microbiomes”. We invite submissions of manuscripts and research articles (original and review articles) addressing the direct interactions between human microbiomes and their hosts, and on the factors involved in microbiome community structure. The goal of this Special Issue is to enhance our current understanding and advancements in the field of microbiome–host communication research and based on this discuss future therapeutic possibilities.

This Special Issue will focus on the communication between a healthy or dysbiotic human microbiome and host cells or organs, and on microbiome community structure. We welcome all studies that help pave the way for new and improved microbiota-targeting therapeutics.

Dr. Suzette Sørensen
Guest Editor

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

  • human microbiome
  • microbiota
  • dysbiosis
  • therapeutics
  • microbiome–host communication

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Published Papers (7 papers)

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Research

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16 pages, 3650 KiB  
Article
A Comparison of Three Automated Nucleic Acid Extraction Systems for Human Stool Samples
by Wit Thun Kwa, Choon Kiat Sim, Adrian Low and Jonathan Wei Jie Lee
Microorganisms 2024, 12(12), 2417; https://doi.org/10.3390/microorganisms12122417 - 25 Nov 2024
Viewed by 237
Abstract
Automated nucleic acid extractors are useful instruments for the high-throughput processing of bio-samples and are expected to improve research throughput in addition to decreased inter-sample variability inherent to manual processing. We evaluated three commercial nucleic acid extractors Bioer GenePure Pro (Bioer Technology, Hangzhou, [...] Read more.
Automated nucleic acid extractors are useful instruments for the high-throughput processing of bio-samples and are expected to improve research throughput in addition to decreased inter-sample variability inherent to manual processing. We evaluated three commercial nucleic acid extractors Bioer GenePure Pro (Bioer Technology, Hangzhou, China), Maxwell RSC 16 (Promega Corporation, Madison, WI, USA), and KingFisher Apex (ThermoFisher Scientific, Waltham, MA, USA) based on their DNA yield, DNA purity, and 16S rRNA gene amplicon results using both human fecal samples and a mock community (ZymoBIOMICS Microbial Community Standard (Zymo Research Corp., Irvine, CA, USA)). Bead-beating provided incremental yield to effectively lyse and extract DNA from stool samples compared to lysis buffer alone. Differential abundance analysis and comparison of prevalent bacterial species revealed a greater representation of Gram-positive bacteria in samples subjected to mechanical lysis, regardless of sample type. All three commercial extractors had differences in terms of yield, inter-sample variability, and subsequent sequencing readouts, which we subsequently share in the paper and believe are significant considerations for all researchers undertaking human fecal microbiota research. Full article
(This article belongs to the Special Issue Advances in Human Microbiomes)
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16 pages, 3063 KiB  
Article
Aging-Induced Changes in Cutibacterium acnes and Their Effects on Skin Elasticity and Wrinkle Formation
by YeonGyun Jung, Ikwhan Kim, Da-Ryung Jung, Ji Hoon Ha, Eun Kyung Lee, Jin Mo Kim, Jin Young Kim, Jun-Hwan Jang, Jun-Tae Bae, Jae-Ho Shin and Yoon Soo Cho
Microorganisms 2024, 12(11), 2179; https://doi.org/10.3390/microorganisms12112179 - 29 Oct 2024
Viewed by 735
Abstract
Skin aging involves biomechanical changes like decreased elasticity, increased wrinkle formation, and altered barrier function. The skin microbiome significantly impacts this process. Here, we investigated the effects of decreased Cutibacterium acnes abundance and increase in other skin microorganisms on skin biomechanical properties in [...] Read more.
Skin aging involves biomechanical changes like decreased elasticity, increased wrinkle formation, and altered barrier function. The skin microbiome significantly impacts this process. Here, we investigated the effects of decreased Cutibacterium acnes abundance and increase in other skin microorganisms on skin biomechanical properties in 60 healthy Koreans from Seoul, divided into younger (20–29 years) and older (60–75 years) groups. Metagenomic sequencing and skin assessments showed that the older group exhibited decreased C. acnes dominance and increased microbial diversity, correlating with reduced skin elasticity and increased wrinkles. In the younger age group, the enriched pathways included zeatin biosynthesis, distinct biotin metabolism pathways, and cofactor and vitamin metabolism in the younger age group, whereas pathways related to lipid metabolism, energy metabolism, and responses to environmental stressors, including UV damage and pollution, were enriched in the older group, according to functional analysis results. Network analysis indicated higher microbial connectivity in the younger group, suggesting a more stable community, whereas the older group’s community displayed higher modularity, indicating more independent and specialized clusters. This study enhances our understanding of the impact of skin microbiome changes on skin aging, particularly the anti-aging effects of C. acnes. Future research should focus on the physiological mechanisms of skin microbiota on skin aging and explore therapeutic potentials to enhance skin health. Full article
(This article belongs to the Special Issue Advances in Human Microbiomes)
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11 pages, 1550 KiB  
Article
Temporal Investigation of the Maternal Origins of Fetal Gut Microbiota
by Corrie Miller, Kayti Luu, Brandi Mikami, Jonathan Riel, Yujia Qin, Vedbar Khadka and Men-Jean Lee
Microorganisms 2024, 12(9), 1865; https://doi.org/10.3390/microorganisms12091865 - 9 Sep 2024
Cited by 1 | Viewed by 845
Abstract
In utero colonization or deposition of beneficial microorganisms and their by-products likely occurs through various mechanisms, such as hematogenous spread or ascension from the reproductive tract. With high-throughput sequencing techniques, the identification of microbial components in first-pass neonatal meconium has been achieved. While [...] Read more.
In utero colonization or deposition of beneficial microorganisms and their by-products likely occurs through various mechanisms, such as hematogenous spread or ascension from the reproductive tract. With high-throughput sequencing techniques, the identification of microbial components in first-pass neonatal meconium has been achieved. While these components are low-biomass and often not abundant enough to culture, the presence of microbial DNA signatures may promote fetal immune tolerance or epigenetic regulation prior to birth. The aim of this study was to investigate the maternal source of the neonatal first-pass meconium microbiome. Maternal vaginal and anal samples collected from twenty-one maternal–infant dyad pairs were compared via principal component analysis to first-pass neonatal meconium microbial compositions. Results demonstrated the greatest degree of similarity between the maternal gut microbiome in the second and third trimesters and vaginal microbiome samples across pregnancy, suggesting that the maternal gut microbiota may translocate to the fetal gut during pregnancy. This study sheds light on the origin and timing of the potential transfer of maternal microbial species to offspring in utero. Full article
(This article belongs to the Special Issue Advances in Human Microbiomes)
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16 pages, 3362 KiB  
Article
Identification and Characterization of Human Breast Milk and Infant Fecal Cultivable Lactobacilli Isolated in Bulgaria: A Pilot Study
by Asya Asenova, Hristiyana Hristova, Stanimira Ivanova, Viliana Miteva, Ivelina Zhivkova, Katerina Stefanova, Penka Moncheva, Trayana Nedeva, Zoltan Urshev, Victoria Marinova-Yordanova, Tzveta Georgieva, Margarita Tzenova, Maria Russinova, Tzvetomira Borisova, Deyan Donchev, Petya Hristova and Iliyana Rasheva
Microorganisms 2024, 12(9), 1839; https://doi.org/10.3390/microorganisms12091839 - 5 Sep 2024
Viewed by 1014
Abstract
During the last few decades, the main focus of numerous studies has been on the human breast milk microbiota and its influence on the infant intestinal microbiota and overall health. The presence of lactic acid bacteria in breast milk affects both the quantitative [...] Read more.
During the last few decades, the main focus of numerous studies has been on the human breast milk microbiota and its influence on the infant intestinal microbiota and overall health. The presence of lactic acid bacteria in breast milk affects both the quantitative and qualitative composition of the infant gut microbiota. The aim of this study was to assess the most frequently detected cultivable rod-shaped lactobacilli, specific for breast milk of healthy Bulgarian women and fecal samples of their infants over the first month of life, in 14 mother–infant tandem pairs. Additionally, we evaluated the strain diversity among the most common isolated species. A total of 68 Gram-positive and catalase-negative strains were subjected to identification using the MALDI-TOF technique. Predominant cultivable populations belonging to the rod-shaped lactic acid bacteria have been identified as Lacticaseibacillus rhamnosus, Limosilactobacillus fermentum, Lacticaseibacillus paracasei, and Limosilactobacillus reuteri. Also, we confirmed the presence of Lactiplantibacillus plantarum and Lactobacillus gasseri. Up to 26 isolates were selected as representatives and analyzed by 16S rRNA sequencing for strain identity confirmation and a phylogenetic tree based on 16S rRNA gene sequence was constructed. Comparative analysis by four RAPD primers revealed genetic differences between newly isolated predominant L. rhamnosus strains. This pilot study provides data for the current first report concerning the investigation of the characteristic cultivable lactobacilli isolated from human breast milk and infant feces in Bulgaria. Full article
(This article belongs to the Special Issue Advances in Human Microbiomes)
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13 pages, 5953 KiB  
Article
Racial Disparities in Plasma Cytokine and Microbiome Profiles
by Kevin D. Fan, Elizabeth Ogunrinde, Zhuang Wan, Chao Li and Wei Jiang
Microorganisms 2024, 12(7), 1453; https://doi.org/10.3390/microorganisms12071453 - 17 Jul 2024
Viewed by 834
Abstract
Background: Many health issues prevalent in African American (AA) populations are associated with chronic inflammation and related health conditions, including autoimmune diseases, infectious diseases, neurologic disorders, metabolic syndromes, and others. The current study aims to understand plasma microbiome translocation as a potential trigger [...] Read more.
Background: Many health issues prevalent in African American (AA) populations are associated with chronic inflammation and related health conditions, including autoimmune diseases, infectious diseases, neurologic disorders, metabolic syndromes, and others. The current study aims to understand plasma microbiome translocation as a potential trigger for chronic inflammation. Methods: In this study, 16 Caucasian American (CA) and 22 African American (AA) healthy individuals were recruited. Microbial DNA was isolated from the plasma samples and sequenced via microbial 16S rRNA V3-4 sequencing. The plasma levels of 33 cytokines and chemokines were evaluated. The proinflammatory microbiomes were verified using human THP-1 cells in vitro. Results: The plasma levels of IL-6, IL-15, MIP-1α, MIP-1β, and MIP-3α were higher in the AA people, whereas IL-1α and IL-27 were elevated in the CA people. The plasma microbiomes exhibited eight bacterial genera/phyla differentially enriched in the CA and AA people. Given the critical role of IL-6 in chronic inflammation and associated diseases, we identified five bacteria genera significantly associated with IL-6. The abundance of Actinomyces was positively correlated with the plasma IL-6 level (r = 0.41, p = 0.01), while the abundance of Kurthia (r = −0.34, p = 0.04), Noviherbaspirillum (r = −0.34, p = 0.04), Candidatus Protochlamydia (r = −0.36, p = 0.03), and Reyranella (r = −0.39, p = 0.02) was negatively correlated with this. Finally, the THP-1 cells treated with heat-killed bacteria produced higher levels of IL-6 in vitro in response to the Actinomyces species compared to the species in the genus either uncorrelated or negatively correlated with IL-6. Conclusions: This is the first study to report potential blood microbiome translocation as a driver for persistently elevated IL-6 levels in the periphery in healthy AA versus CA people. Understanding the plasma microbiome linked to the IL-6 levels in people with different racial backgrounds is essential to unraveling the therapeutic approaches to improve precision medicine. Full article
(This article belongs to the Special Issue Advances in Human Microbiomes)
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18 pages, 4661 KiB  
Article
Identification of the Microbiome Associated with Prognosis in Patients with Chronic Liver Disease
by Kenta Yamamoto, Takashi Honda, Yosuke Inukai, Shinya Yokoyama, Takanori Ito, Norihiro Imai, Yoji Ishizu, Masanao Nakamura and Hiroki Kawashima
Microorganisms 2024, 12(3), 610; https://doi.org/10.3390/microorganisms12030610 - 19 Mar 2024
Viewed by 1436
Abstract
We investigated the prognostic role of the gut microbiome and clinical factors in chronic liver disease (hepatitis, cirrhosis, and hepatocellular carcinoma [HCC]). Utilizing data from 227 patients whose stool samples were collected over the prior 3 years and a Cox proportional hazards model, [...] Read more.
We investigated the prognostic role of the gut microbiome and clinical factors in chronic liver disease (hepatitis, cirrhosis, and hepatocellular carcinoma [HCC]). Utilizing data from 227 patients whose stool samples were collected over the prior 3 years and a Cox proportional hazards model, we integrated clinical attributes and microbiome composition based on 16S ribosomal RNA sequencing. HCC was the primary cause of mortality, with the Barcelona Clinic Liver Cancer staging system-derived B/C significantly increasing the mortality risk (hazard ratio [HR] = 8.060; 95% confidence interval [CI]: 3.6509–17.793; p < 0.001). Cholesterol levels < 140 mg/dL were associated with higher mortality rates (HR = 4.411; 95% CI: 2.0151–9.6555; p < 0.001). Incertae sedis from Ruminococcaceae showed a protective effect, reducing mortality risk (HR = 0.289; 95% CI: 0.1282 to 0.6538; p = 0.002), whereas increased Veillonella presence was associated with a higher risk (HR = 2.733; 95% CI: 1.1922–6.2664; p = 0.017). The potential of specific bacterial taxa as independent prognostic factors suggests that integrating microbiome data could improve the prognosis and treatment of chronic liver disease. These microbiome-derived markers have prognostic significance independently and in conjunction with clinical factors, suggesting their utility in improving a patient’s prognosis. Full article
(This article belongs to the Special Issue Advances in Human Microbiomes)
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Review

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33 pages, 1500 KiB  
Review
Impact of Novel Foods on the Human Gut Microbiome: Current Status
by Ailín Martínez, Lidiana Velázquez, Rommy Díaz, Rodrigo Huaiquipán, Isabela Pérez, Alex Muñoz, Marcos Valdés, Néstor Sepúlveda, Erwin Paz and John Quiñones
Microorganisms 2024, 12(9), 1750; https://doi.org/10.3390/microorganisms12091750 - 23 Aug 2024
Viewed by 3008
Abstract
The microbiome is a complex ecosystem of microorganisms that inhabit a specific environment. It plays a significant role in human health, from food digestion to immune system strengthening. The “Novel Foods” refer to foods or ingredients that have not been consumed by humans [...] Read more.
The microbiome is a complex ecosystem of microorganisms that inhabit a specific environment. It plays a significant role in human health, from food digestion to immune system strengthening. The “Novel Foods” refer to foods or ingredients that have not been consumed by humans in the European Union before 1997. Currently, there is growing interest in understanding how “Novel Foods” affect the microbiome and human health. The aim of this review was to assess the effects of “Novel Foods” on the human gut microbiome. Research was conducted using scientific databases, focusing on the literature published since 2000, with an emphasis on the past decade. In general, the benefits derived from this type of diet are due to the interaction between polyphenols, oligosaccharides, prebiotics, probiotics, fibre content, and the gut microbiome, which selectively promotes specific microbial species and increases microbial diversity. More research is being conducted on the consumption of novel foods to demonstrate how they affect the microbiome and, thus, human health. Consumption of novel foods with health-promoting properties should be further explored to maintain the diversity and functionality of the gut microbiome as a potential tool to prevent the onset and progression of chronic diseases. Full article
(This article belongs to the Special Issue Advances in Human Microbiomes)
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