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Microorganisms
Special Issues
Current Understanding of the Human Microbiome in Health and Disease
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Current Understanding of the Human Microbiome in Health and Disease

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

Deadline for manuscript submissions: closed (1 April 2022) | Viewed by 14231

Special Issue Editors

Dr. George Tetz

E-Mail Website
Guest Editor
Human Microbiology Institute, 101 6th Street, New York, NY 10013, USA
Interests: neurodegeneration; Parkinson’s disease; microbiota; Alzheimer’s disease; bacteriophage; pamps; autoimmune; microbiota disease; phagobiota; phagobiome
Dr. Victor Tetz

E-Mail Website
Guest Editor
Human Microbiology Institute, 101 6th Street, New York, NY 10013, USA
Interests: microbiome; viruses; bacteriophages; extracellular DNA; previously unculturable bacteria; sporeforming bacteria

Special Issue Information

Dear Colleagues,

Our current understanding of the human microbiome is expanding rapidly, with emerging concepts of microbiota of the gut, mouth, lungs, skin, brain each separately and all together being implicated in health and disease.

We have only just skimmed the surface in understanding how the gut–brain axis, gut–lung axis, gut–immune axis, and gut–skin axis concepts coordinate reciprocal crosstalk between the microbiome and the human host. It has, however, become clear that each of the components of microbiota, i.e., bacteria (bacteriome), eucaryotic viruses (virome), bacteriophages (phagobiome), fungi (mycobiome), and archaea (archaeome), are major regulators of the host and are new frontiers for drug development and diagnostics for the next few decades.

This Special Issue of Microorganisms will be dedicated to the following themes: the microbiome in health and disease; the microbiome and neurodegenerative diseases; the microbiome and autoimmune disorders; the microbiome and cancer; mycobiome; archaeome; virome; phagobiome; challenges and tools of microbiome research (standardization, taxonomy, data analysis); metabolome; and translational application of microbiome for therapeutic and diagnostic interventions. Therefore, we encourage the submission of original research articles, reviews, and mini-reviews, perspective and commentary articles that aim to discuss important unresolved questions in the field and to also provide thought-provoking ideas that will serve to guide future discussion of microbiome research.

Dr. George Tetz
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

  • Microbiome 
  • Virome 
  • Phagobiome 
  • Metabolome 
  • Gut–brain axis 
  • Gut–immune axis 
  • Gut–skin axis 
  • Cancer microbiome 
  • Neurodegenerative diseases

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Published Papers (3 papers)

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Research

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12 pages, 2285 KiB  
Article
Culturable and Non-Culturable Blood Microbiota of Healthy Individuals
by Stefan Panaiotov, Yordan Hodzhev, Borislava Tsafarova, Vladimir Tolchkov and Reni Kalfin
Microorganisms 2021, 9(7), 1464; https://doi.org/10.3390/microorganisms9071464 - 8 Jul 2021
Cited by 20 | Viewed by 4056
Abstract
Next-generation sequencing (NGS) and metagenomics revolutionized our capacity for analysis and identification of the microbial communities in complex samples. The existence of a blood microbiome in healthy individuals has been confirmed by sequencing, but some researchers suspect that this is a cell-free circulating [...] Read more.
Next-generation sequencing (NGS) and metagenomics revolutionized our capacity for analysis and identification of the microbial communities in complex samples. The existence of a blood microbiome in healthy individuals has been confirmed by sequencing, but some researchers suspect that this is a cell-free circulating DNA in blood, while others have had isolated a limited number of bacterial and fungal species by culture. It is not clear what part of the blood microbiota could be resuscitated and cultured. Here, we quantitatively measured the culturable part of blood microbiota of healthy individuals by testing a medium supplemented with a high concentration of vitamin K (1 mg/mL) and culturing at 43 °C for 24 h. We applied targeted sequencing of 16S rDNA and internal transcribed spacer (ITS) markers on cultured and non-cultured blood samples from 28 healthy individuals. Dominant bacterial phyla among non-cultured samples were Proteobacteria 92.97%, Firmicutes 2.18%, Actinobacteria 1.74% and Planctomycetes 1.55%, while among cultured samples Proteobacteria were 47.83%, Firmicutes 25.85%, Actinobacteria 16.42%, Bacteroidetes 3.48%, Cyanobacteria 2.74%, and Fusobacteria 1.53%. Fungi phyla Basidiomycota, Ascomycota, and unidentified fungi were 65.08%, 17.72%, and 17.2% respectively among non-cultured samples, while among cultured samples they were 58.08%, 21.72%, and 20.2% respectively. In cultured and non-cultured samples we identified 241 OTUs belonging to 40 bacterial orders comprising 66 families and 105 genera. Fungal biodiversity accounted for 272 OTUs distributed in 61 orders, 105 families, and 133 genera. Bacterial orders that remained non-cultured, compared to blood microbiota isolated from fresh blood collection, were Sphingomonadales, Rhizobiales, and Rhodospirillales. Species of orders Bacillales, Lactobacillales, and Corynebacteriales showed the best cultivability. Fungi orders Tremellales, Polyporales, and Filobasidiales were mostly unculturable. Species of fungi orders Pleosporales, Saccharomycetales, and Helotiales were among the culturable ones. In this study, we quantified the capacity of a specific medium applied for culturing of blood microbiota in healthy individuals. Other culturing conditions and media should be tested for optimization and better characterization of blood microbiota in healthy and diseased individuals. Full article
(This article belongs to the Special Issue Current Understanding of the Human Microbiome in Health and Disease)
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22 pages, 6721 KiB  
Article
The Influence of Diet and Sex on the Gut Microbiota of Lean and Obese JCR:LA-cp Rats
by Craig Resch, Mihir Parikh, J. Alejandro Austria, Spencer D. Proctor, Thomas Netticadan, Heather Blewett and Grant N. Pierce
Microorganisms 2021, 9(5), 1037; https://doi.org/10.3390/microorganisms9051037 - 12 May 2021
Cited by 7 | Viewed by 2898
Abstract
There is an increased interest in the gut microbiota as it relates to health and obesity. The impact of diet and sex on the gut microbiota in conjunction with obesity also demands extensive systemic investigation. Thus, the influence of sex, diet, and flaxseed [...] Read more.
There is an increased interest in the gut microbiota as it relates to health and obesity. The impact of diet and sex on the gut microbiota in conjunction with obesity also demands extensive systemic investigation. Thus, the influence of sex, diet, and flaxseed supplementation on the gut microbiota was examined in the JCR:LA-cp rat model of genetic obesity. Male and female obese rats were randomized into four groups (n = 8) to receive, for 12 weeks, either (a) control diet (Con), (b) control diet supplemented with 10% ground flaxseed (CFlax), (c) a high-fat, high sucrose (HFHS) diet, or (d) HFHS supplemented with 10% ground flaxseed (HFlax). Male and female JCR:LA-cp lean rats served as genetic controls and received similar dietary interventions. Illumine MiSeq sequencing revealed a richer microbiota in rats fed control diets rather than HFHS diets. Obese female rats had lower alpha-diversity than lean female; however, both sexes of obese and lean JCR rats differed significantly in β-diversity, as their gut microbiota was composed of different abundances of bacterial types. The feeding of an HFHS diet affected the diversity by increasing the phylum Bacteroidetes and reducing bacterial species from phylum Firmicutes. Fecal short-chain fatty acids such as acetate, propionate, and butyrate-producing bacterial species were correspondingly impacted by the HFHS diet. Flax supplementation improved the gut microbiota by decreasing the abundance of Blautia and Eubacterium dolichum. Collectively, our data show that an HFHS diet results in gut microbiota dysbiosis in a sex-dependent manner. Flaxseed supplementation to the diet had a significant impact on gut microbiota diversity under both flax control and HFHS dietary conditions. Full article
(This article belongs to the Special Issue Current Understanding of the Human Microbiome in Health and Disease)
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Review

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25 pages, 666 KiB  
Review
Using Microbiome-Based Approaches to Deprogram Chronic Disorders and Extend the Healthspan following Adverse Childhood Experiences
by Rodney R. Dietert and Janice M. Dietert
Microorganisms 2022, 10(2), 229; https://doi.org/10.3390/microorganisms10020229 - 21 Jan 2022
Cited by 4 | Viewed by 5849
Abstract
Adverse childhood experiences (ACEs), which can include child trafficking, are known to program children for disrupted biological cycles, premature aging, microbiome dysbiosis, immune-inflammatory misregulation, and chronic disease multimorbidity. To date, the microbiome has not been a major focus of deprogramming efforts despite its [...] Read more.
Adverse childhood experiences (ACEs), which can include child trafficking, are known to program children for disrupted biological cycles, premature aging, microbiome dysbiosis, immune-inflammatory misregulation, and chronic disease multimorbidity. To date, the microbiome has not been a major focus of deprogramming efforts despite its emerging role in every aspect of ACE-related dysbiosis and dysfunction. This article examines: (1) the utility of incorporating microorganism-based, anti-aging approaches to combat ACE-programmed chronic diseases (also known as noncommunicable diseases and conditions, NCDs) and (2) microbiome regulation of core systems biology cycles that affect NCD comorbid risk. In this review, microbiota influence over three key cyclic rhythms (circadian cycles, the sleep cycle, and the lifespan/longevity cycle) as well as tissue inflammation and oxidative stress are discussed as an opportunity to deprogram ACE-driven chronic disorders. Microbiota, particularly those in the gut, have been shown to affect host–microbe interactions regulating the circadian clock, sleep quality, as well as immune function/senescence, and regulation of tissue inflammation. The microimmunosome is one of several systems biology targets of gut microbiota regulation. Furthermore, correcting misregulated inflammation and increased oxidative stress is key to protecting telomere length and lifespan/longevity and extending what has become known as the healthspan. This review article concludes that to reverse the tragedy of ACE-programmed NCDs and premature aging, managing the human holobiont microbiome should become a routine part of healthcare and preventative medicine across the life course. Full article
(This article belongs to the Special Issue Current Understanding of the Human Microbiome in Health and Disease)
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