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Microorganisms
Special Issues
Factors Affecting the Composition and Functions of Human Microbiome
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Factors Affecting the Composition and Functions of Human Microbiome

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

Deadline for manuscript submissions: closed (30 December 2020) | Viewed by 17429

Special Issue Editor

Dr. Jae-ho Shin

E-Mail Website
Guest Editor
School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
Interests: human microbiome; animal microbiome; plant microbiome; metagenomics; probiotics; plant growth promoting bacteria

Special Issue Information

Dear Colleagues,

The human body harbors around 100 trillion microbial cells, including bacteria, archaea, fungi, and viruses, which outnumber our human cells ten to one. Over the past few decades, research studies have reported that various factors could shape the microbial composition of different body sites. However, there are still huge gaps in understanding the association of microbiota composition with host, external, environmental factors and their interactions. Many variables from these factors have not been assessed for their influence on the human microbiome. Understanding the influence of the above factors and their interactions on the composition and functioning of human microbiome has many implications in designing and developing microbiome-targeted therapy.

Hence, the aim of this Special Issue is to collect more information on the influence of short- and long-term effects of host, external, environmental factors and their interactions on the composition and functioning of the human microbiome. I would like to invite you to submit original research articles and short communications to this Special Issue based on short- and long-term human microbiome studies. Studies on the mechanism of the above factors on the modulation of microbiome of gut, skin, oral, vaginal, and other body sites are welcome.

Dr. Jae-ho Shin
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

  • environmental factors
  • external factors
  • host factors
  • human microbiome
  • human mycobiome
  • human virome
  • human health

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Published Papers (4 papers)

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Research

11 pages, 2681 KiB  
Article
Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study
by Gi-Ung Kang, Da-Ryung Jung, Yoon Hee Lee, Se Young Jeon, Hyung Soo Han, Gun Oh Chong and Jae-Ho Shin
Microorganisms 2021, 9(2), 294; https://doi.org/10.3390/microorganisms9020294 - 31 Jan 2021
Cited by 32 | Viewed by 3806
Abstract
Convincing studies demonstrated that vaginal flora is one of the most impactful key components for the well-being of the genital tract in women. Nevertheless, the potential capability of vaginal-derived bacterial communities as biomarkers to monitor cervical carcinogenesis (CC) has yet to be studied [...] Read more.
Convincing studies demonstrated that vaginal flora is one of the most impactful key components for the well-being of the genital tract in women. Nevertheless, the potential capability of vaginal-derived bacterial communities as biomarkers to monitor cervical carcinogenesis (CC) has yet to be studied actively compared to those of bacterial vaginosis (BV). We hypothesized that vaginal microbiota might be associated with the progression of CC. In this study, we enrolled 23 participants, including healthy controls (HC group; n = 7), patients with cervical intraepithelial neoplasia (CIN) 2 and 3 (CIN group, n = 8), and patients with invasive cervical cancer (CAN group; n = 8). Amplicon sequencing was performed using the Ion Torrent PGM to characterize the vaginal microbiota. Patients with CIN and CAN presented vaginal microbiota dysbiosis compared with HC. The alpha diversity analysis revealed that CC has a trend to be increased in terms of diversity indexes. Moreover, CC was associated with the abundance of specific microbes, of which Lactobacillus and Gardnerella were the most significantly different between HC and CIN, whereas Streptococcus was differentially abundant in CAN compared with CIN. We then evaluated their diagnostic abilities. Testing in terms of diagnostic ability using the three genera revealed considerably high performance with an area under the receiver-operating characteristic curve of 0.982, 0.953, and 0.922. The current study suggests that the presence of Gardnerella and Streptococcus may be involved in the advancment of CC. Full article
(This article belongs to the Special Issue Factors Affecting the Composition and Functions of Human Microbiome)
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19 pages, 3040 KiB  
Article
Effect of Sample Collection (Manual Expression vs. Pumping) and Skimming on the Microbial Profile of Human Milk Using Culture Techniques and Metataxonomic Analysis
by Maricela Rodríguez-Cruz, Claudio Alba, Marina Aparicio, María Ángeles Checa, Leonides Fernández and Juan Miguel Rodríguez
Microorganisms 2020, 8(9), 1278; https://doi.org/10.3390/microorganisms8091278 - 21 Aug 2020
Cited by 14 | Viewed by 2845
Abstract
Human milk microbiota is a unique bacterial community playing a relevant role in infant health, but its composition depends on different factors (woman health, lactation stage, and geographical lactation). However, information is lacking regarding some other factors that may affect the bacterial community [...] Read more.
Human milk microbiota is a unique bacterial community playing a relevant role in infant health, but its composition depends on different factors (woman health, lactation stage, and geographical lactation). However, information is lacking regarding some other factors that may affect the bacterial community of human milk. In this study we aimed to study the impact of the sample collection method and the skimming procedure using culture-dependent and culture-independent techniques to study the human milk microbial profile. One set of milk samples was provided by women (n = 10) in two consecutive days; half of the samples were collected the first day by manual expression and the other half on the second day by pumping. The rest of the participants (n = 17) provided milk samples that were fractionated by centrifugation; the bacterial profiles of whole milk and skimmed milk were compared by culture techniques in 10 milk samples, while those of whole milk, fat and skimmed milk were subjected to metataxonomic analysis in seven samples. Globally, the results obtained revealed high interindividual variability but that neither the use of single-use sterile devices to collect the sample nor the skimming procedure have a significant impact of the microbial profile of human samples. Full article
(This article belongs to the Special Issue Factors Affecting the Composition and Functions of Human Microbiome)
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16 pages, 1490 KiB  
Article
Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change
by YeonGyun Jung, Setu Bazie Tagele, HyunWoo Son, Jerald Conrad Ibal, Dorsaf Kerfahi, Hyunju Yun, Bora Lee, Clara Yongjoo Park, Eun Soo Kim, Sang-Jun Kim and Jae-Ho Shin
Microorganisms 2020, 8(9), 1265; https://doi.org/10.3390/microorganisms8091265 - 20 Aug 2020
Cited by 12 | Viewed by 4142
Abstract
Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, [...] Read more.
Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and β -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa. Full article
(This article belongs to the Special Issue Factors Affecting the Composition and Functions of Human Microbiome)
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14 pages, 2012 KiB  
Article
The Association between Gut Microbiota and Uremia of Chronic Kidney Disease
by Ji Eun Kim, Hyo-Eun Kim, Ji In Park, Hyunjeong Cho, Min-Jung Kwak, Byung-Yong Kim, Seung Hee Yang, Jung Pyo Lee, Dong Ki Kim, Kwon Wook Joo, Yon Su Kim, Bong-Soo Kim and Hajeong Lee
Microorganisms 2020, 8(6), 907; https://doi.org/10.3390/microorganisms8060907 - 16 Jun 2020
Cited by 43 | Viewed by 5409
Abstract
Chronic kidney disease (CKD)-associated uremia aggravates—and is aggravated by—gut dysbiosis. However, the correlation between CKD severity and gut microbiota and/or their uremic metabolites is unclear. We enrolled 103 CKD patients with stage 1 to 5 and 46 healthy controls. We analyzed patients’ gut [...] Read more.
Chronic kidney disease (CKD)-associated uremia aggravates—and is aggravated by—gut dysbiosis. However, the correlation between CKD severity and gut microbiota and/or their uremic metabolites is unclear. We enrolled 103 CKD patients with stage 1 to 5 and 46 healthy controls. We analyzed patients’ gut microbiota by MiSeq system and measured the serum concentrations of four uremic metabolites (p-cresyl sulfate, indoxyl sulfate, p-cresyl glucuronide, and trimethylamine N-oxide) by liquid chromatography–tandem mass spectrometry. Serum concentrations of the uremic metabolites increased with kidney function deterioration. Gut microbial diversity did not differ among the examined patient and control groups. In moderate or higher stage CKD groups, Oscillibacter showed positive interactions with other microbiota, and the proportions of Oscillibacter were positively correlated with those of the uremic metabolites. The gut microbiota, particularly Oscillibacter, was predicted to contribute to pyruvate metabolism which increased with CKD progression. Relative abundance of Oscillibacter was significantly associated with both serum uremic metabolite levels and kidney function. Predicted functional analysis suggested that kidney-function-associated changes in the contribution of Oscillibacter to pyruvate metabolism in CKD may greatly affect the gut environment according to kidney function, resulting in dysbiosis concomitant with uremic toxin production. The gut microbiota could be associated with uremia progression in CKD. These results may provide basis for further metagenomics analysis of kidney diseases. Full article
(This article belongs to the Special Issue Factors Affecting the Composition and Functions of Human Microbiome)
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