Special Issue "Human Microbiome or Microbial Communities Related with Humans"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (31 July 2019).

Special Issue Editor

Prof. Silvia Turroni
E-Mail Website
Guest Editor
Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro, 6 – 40126 Bologna, Italy
Interests: microbiome; microbial ecology; microbiome-host interaction; co-evolution; dysbiosis; intervention strategies

Special Issue Information

Human beings are surrounded and inhabited by microbial communities, including bacteria, fungi, viruses, and protozoa, with distinct ensembles of microorganisms residing in specific body niches (such as mouth, nose, gastrointestinal tract, and vagina). In particular, the gut microbiome is recognized as the most densely populated microbial ecosystem on Earth, which has co-evolved with its host in a largely mutualistic relationship over millions of years, helping to shape our phenotypes across human evolutionary history. By producing a large and diverse repertoire of small bioactive molecules, through the metabolism of dietary or host-derived compounds, the intestinal microbiome has the potential to exert a strong influence on multiple aspects of our physiology, from energy balance and metabolic regulation to the development and functioning of the immune, endocrine, and nervous systems. The great deal of plasticity exhibited by microbial communities allows them to adapt quickly to endogenous and exogenous challenges (including changes in age, diet, lifestyle, or, more generally, environment), while persisting in eubiotic states, a condition instrumental to the maintenance of the host health. Though the key drivers of variation of the human microbiome are most probably still to be discovered, it is known that exposure to certain stressors may significantly disrupt or unbalance microbial communities towards a dysbiotic profile, with impairment of mutualism and triggering or consolidation of a disease state. To date, multiple disorders, at both the enteric and systemic level (including metabolic, autoimmune, cardiovascular, hepatic, respiratory, neurological, and oncologic diseases, often referred to as non-communicable or civilization diseases), have been associated with altered microbial layouts and, particularly, with an overall reduction of biodiversity, the loss of typically beneficial microbes, the bloom of pathobionts, or a broad ecosystem restructuring. Notwithstanding intriguing data, even on possible causal relationships, the actual role of human microbiomes in the pathological context and the underlying mechanisms remains mostly elusive. Similarly, the long-term effectiveness of microbiome-tailored intervention strategies in preventing or treating disorders and alleviating drug side effects must still be proven.

This Special Issue aims to provide a greater understanding of host–microbiome interactions and the role of human-related microbial communities in health and disease, through multiple approaches, also targeting in silico, in vitro, and in vivo functionality of microbes. We invite submissions of reviews, research articles, or short-communications reporting omics and mechanistic studies on microbiomes and their hosts.

Prof. Silvia Turroni
Guest Editor

Manuscript Submission Information

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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. Genes 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 1800 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
  • microbial ecology
  • microbiome–host interaction
  • co-evolution
  • dysbiosis
  • intervention strategies

Published Papers (4 papers)

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Research

Open AccessArticle
Human Endometrial Microbiota at Term of Normal Pregnancies
Genes 2019, 10(12), 971; https://doi.org/10.3390/genes10120971 - 26 Nov 2019
Abstract
The endometrium is a challenging site for metagenomic analysis due to difficulties in obtaining uncontaminated samples and the limited abundance of the bacterial population. Indeed, solid correlations between endometrial physio-pathologic conditions and bacteria compositions have not yet been firmly established. Nevertheless, the study [...] Read more.
The endometrium is a challenging site for metagenomic analysis due to difficulties in obtaining uncontaminated samples and the limited abundance of the bacterial population. Indeed, solid correlations between endometrial physio-pathologic conditions and bacteria compositions have not yet been firmly established. Nevertheless, the study of the endometrial microbiota is of great interest due to the close correlations between microbiota profiles, women’s health, and successful pregnancies. In this study, we decided to tackle the study of the endometrial microbiota through analysis of bacterial population in women subjected to elective caesarean delivery. As a pilot study, a cohort of 19 Caucasian women at full term of normal pregnancy and with a prospection of elective caesarean delivery was enrolled for endometrium sampling at the time of caesarean section. Sampling was carried out by endometrial biopsy soon after the delivery of the newborn and the discharge of the placenta and fetal membranes from the uterus. Bacterial composition was established by a deep metabarcoding next generation sequencing (NGS) procedure addressing the V5–V6 hypervariable region of the 16S rRNA gene. Amplicon sequences were analysed by bioinformatic procedures for denoising and taxonomic classification. The RDP database was used as 16S rRNA reference collection. Metabarcoding analysis showed the presence of a common bacterial composition, including six genera classifiable within the human microbiota (Cutibacterium, Escherichia, Staphylococcus, Acinetobacter, Streptococcus, Corynebacterium), that could be part of the core endometrial microbiota under the specific conditions examined. These results can provide useful information for future studies on the correlations between bacteria and successful pregnancies. Full article
(This article belongs to the Special Issue Human Microbiome or Microbial Communities Related with Humans)
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Open AccessArticle
Altered in Vitro Metabolomic Response of the Human Microbiota to Sweeteners
Genes 2019, 10(7), 535; https://doi.org/10.3390/genes10070535 - 15 Jul 2019
Cited by 1
Abstract
Non-nutritive sweeteners represent an ingredient class that directly affects human health, via the development of inflammatory processes that promote chronic diseases related to microbiota dysbiosis. Several in vitro tests were conducted in the static GIS1 simulator. The aim of the study was to [...] Read more.
Non-nutritive sweeteners represent an ingredient class that directly affects human health, via the development of inflammatory processes that promote chronic diseases related to microbiota dysbiosis. Several in vitro tests were conducted in the static GIS1 simulator. The aim of the study was to highlight the effect of sweeteners on the microbiota pattern of healthy individuals, associated with any alteration in the metabolomic response, through the production of organic acids and ammonium. The immediate effect of the in vitro treatment and the influence of the specific sweetener type on the occurrence of dysbiosis were evaluated by determining the biomarkers of the microbiota response. The presence of the steviol reduced the ammonium level (minimum of 410 mg/L), while the addition of cyclamate and saccharin caused a decrease in the number of microorganisms, in addition to lowering the total quantity of synthesized short-chain fatty acids (SCFAs). The bifidobacteria appeared to decrease below 102 genomes/mL in all the analyzed samples at the end of the in vitro simulation period. Barring the in vitro treatment of steviol, all the sweeteners tested exerted a negative influence on the fermentative profile, resulting in a decline in the fermentative processes, a rise in the colonic pH, and uniformity of the SCFA ratio. Full article
(This article belongs to the Special Issue Human Microbiome or Microbial Communities Related with Humans)
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Open AccessArticle
groEL Gene-Based Phylogenetic Analysis of Lactobacillus Species by High-Throughput Sequencing
Genes 2019, 10(7), 530; https://doi.org/10.3390/genes10070530 - 12 Jul 2019
Cited by 1
Abstract
Lactobacillus is a fairly diverse genus of bacteria with more than 260 species and subspecies. Many profiling methods have been developed to carry out phylogenetic analysis of this complex and diverse genus, but limitations remain since there is still a lack of comprehensive [...] Read more.
Lactobacillus is a fairly diverse genus of bacteria with more than 260 species and subspecies. Many profiling methods have been developed to carry out phylogenetic analysis of this complex and diverse genus, but limitations remain since there is still a lack of comprehensive and accurate analytical method to profile this genus at species level. To overcome these limitations, a Lactobacillus-specific primer set was developed targeting a hypervariable region in the groEL gene—a single-copy gene that has undergone rapid mutation and evolution. The results showed that this methodology could accurately perform taxonomic identification of Lactobacillus down to the species level. Its detection limit was as low as 104 colony-forming units (cfu)/mL for Lactobacillus species. The assessment of detection specificity using the Lactobacillus groEL profiling method found that Lactobacillus, Pediococcus, Weissella, and Leuconostoc genus could be distinguished, but non-Lactobacillus Genus Complex could not be detected. The groEL gene sequencing and Miseq high-throughput approach were adopted to estimate the richness and diversity of Lactobacillus species in different ecosystems. The method was tested using kurut (fermented yak milk) samples and fecal samples of human, rat, and mouse. The results indicated that Lactobacillus mucosae was the predominant gut Lactobacillus species among Chinese, and L. johnsonii accounted for the majority of lactobacilli in rat and mouse gut. Meanwhile, L. delbrueckii subsp. bulgaricus had the highest relative abundance of Lactobacillus in kurut. Thus, this groEL gene profiling method is expected to promote the application of Lactobacillus for industrial production and therapeutic purpose. Full article
(This article belongs to the Special Issue Human Microbiome or Microbial Communities Related with Humans)
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Open AccessArticle
Obesity, Xenobiotic Intake and Antimicrobial-Resistance Genes in the Human Gastrointestinal Tract: A Comparative Study of Eutrophic, Overweight and Obese Individuals
Genes 2019, 10(5), 349; https://doi.org/10.3390/genes10050349 - 07 May 2019
Cited by 1
Abstract
Although lifestyle and physiology in obese individuals are accepted to lead to changes in the intestinal microbiota, uncertainty remains about microbiota dysbiosis, and xenobiotics intake, as a source of selective pressure, independent of antimicrobial chemotherapy. The aim of this study was to compare [...] Read more.
Although lifestyle and physiology in obese individuals are accepted to lead to changes in the intestinal microbiota, uncertainty remains about microbiota dysbiosis, and xenobiotics intake, as a source of selective pressure, independent of antimicrobial chemotherapy. The aim of this study was to compare the occurrence of antimicrobial resistance genetic markers (ARG) in faecal specimens of eutrophic, overweight and obese individuals, and their correlation with xenobiotic intake and gut bacteria density. Methods: This was a cross-sectional case-controlled study including 72 adult participants with no record of intestinal or systemic diseases, or recent use of antimicrobials, grouped as eutrophic, overweight, or obese. Anthropometric profile, eating habits and oral xenobiotics intake were recorded. Faecal metagenomic DNA was used to screen for ARG by PCR, and to measure bacterial groups by fluorescence in situ hybridization (FISH). Student’s t and Wilcoxon tests were used to compare means and differences in ARG detection (95% confidence intervals). Correlation analyses (odds ratio) and relationships between bacteria density and ARG were determined. Results: Increase in abdominal circumference, waist circumference, hip, waist-hip ratio, BMI, carbohydrate, fibres, and total calorie intakes were different from eutrophic to obese participants. Habitual use of antihypertensive and anti-inflammatory drugs, antacids, and artificial sweeteners were associated mainly with obesity and overweight. Nutritional supplements were associated to the eutrophic group. ARG screening showed differences being more frequent among obese, and positive for 27 genetic markers related to β-lactams, tetracyclines, the macrolide lincosamide and streptogramin group, quinolones, sulfonamides, aminoglycosides, and efflux pump. Positive correlation between ARG and BMI, caloric intake, and intake of xenobiotics, was observed for obese individuals. Relationships among ARG detection and bacteria densities were also different. Conclusions: This study reinforces the hypothesis that obese individuals may harbour an altered gut microbiota, if compared to eutrophic. The overweight individuals display a transitional gut microbiota which seems to be between eutrophic and obese. Furthermore, the increased xenobiotic intake associated to obesity may play an important role in the antimicrobial resistance phenomenon. Full article
(This article belongs to the Special Issue Human Microbiome or Microbial Communities Related with Humans)
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