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Deciphering the Human Microbiota: Methods and Impact on Human Health
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Deciphering the Human Microbiota: Methods and Impact on Human Health

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (28 February 2018) | Viewed by 52543

Special Issue Editors

Prof. Pierre-Edouard Fournier

E-Mail Website
Guest Editor
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
Interests: human microbiota; human-associated bacteria; taxonomy; genomics; intra-cellular bacteria; zoonoses
Special Issues, Collections and Topics in MDPI journals
Dr. Jean-Christophe Lagier

E-Mail Website
Guest Editor
URMITE, UM63, CNRS7278, IRD198, Inserm1095 IHU Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille cedex 5, France
Interests: Infectious diseases; clinical microbiology; culturomics; human gut microbiota

Special Issue Information

Dear Colleagues,

Metagenomics constituted a revolution for the study of complex microbiotas, notably in humans. This strategy enabled the highlighting of the relationships between human-associated microorganisms and health or diseases, notably, obesity, colorectal cancer, inflammatory bowel diseases and type 2 diabetes. However, metagenomics also unveiled a great number of previously unknown prokaryotes that were only identified on the basis of unique DNA signatures, preventing in-depth analysis of their roles and the development of adequate treatments. As a consequence, over the past few years, a renewed interest for bacterial culture, which had been neglected in the past 20 years, emerged. Initiatives, such as microbial culturomics that investigates microbial diversity by combining diversified culture conditions, MALDI-TOF MS testing and 16S rRNA sequencing, enabled doubling of the number of cultivated prokaryotic species associated to the human gut. To date, more than 1500 bacterial species have been cultivated from the human digestive tract, whereas this number was 690 prior to the first culturomics study. The great output of modern culture methods offers unprecedented access to the human microbiota repertoire and its role in human health. Complemented with other high throughput methods, such as genome sequencing or reverse vaccinology, it also permits the development of new diagnostic, therapeutic and prevention tools.

This Special Issue of IJMS will focus on the new tools and strategies to isolate and characterize new members of the human microbiota, and their potential consequences on human health.

Prof. Fournier Pierre-edouard
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 microbiota
  • culturomics
  • metagenomics
  • human health
  • new antibiotics
  • new diagnostic tools
  • reverse vaccinology
  • taxonomy

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Published Papers (4 papers)

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Research

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2237 KiB  
Article
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data
by Masanori Kakuta, Shuji Suzuki, Kazuki Izawa, Takashi Ishida and Yutaka Akiyama
Int. J. Mol. Sci. 2017, 18(10), 2124; https://doi.org/10.3390/ijms18102124 - 11 Oct 2017
Cited by 5 | Viewed by 4825
Abstract
Sequence similarity searches have been widely used in the analyses of metagenomic sequencing data. Finding homologous sequences in a reference database enables the estimation of taxonomic and functional characteristics of each query sequence. Because current metagenomic sequencing data consist of a large number [...] Read more.
Sequence similarity searches have been widely used in the analyses of metagenomic sequencing data. Finding homologous sequences in a reference database enables the estimation of taxonomic and functional characteristics of each query sequence. Because current metagenomic sequencing data consist of a large number of nucleotide sequences, the time required for sequence similarity searches account for a large proportion of the total time. This time-consuming step makes it difficult to perform large-scale analyses. To analyze large-scale metagenomic data, such as those found in the human oral microbiome, we developed GHOST-MP (Genome-wide HOmology Search Tool on Massively Parallel system), a parallel sequence similarity search tool for massively parallel computing systems. This tool uses a fast search algorithm based on suffix arrays of query and database sequences and a hierarchical parallel search to accelerate the large-scale sequence similarity search of metagenomic sequencing data. The parallel computing efficiency and the search speed of this tool were evaluated. GHOST-MP was shown to be scalable over 10,000 CPU (Central Processing Unit) cores, and achieved over 80-fold acceleration compared with mpiBLAST using the same computational resources. We applied this tool to human oral metagenomic data, and the results indicate that the oral cavity, the oral vestibule, and plaque have different characteristics based on the functional gene category. Full article
(This article belongs to the Special Issue Deciphering the Human Microbiota: Methods and Impact on Human Health)
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3527 KiB  
Article
Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing
by Stefano Leo, Nadia Gaïa, Etienne Ruppé, Stephane Emonet, Myriam Girard, Vladimir Lazarevic and Jacques Schrenzel
Int. J. Mol. Sci. 2017, 18(9), 2011; https://doi.org/10.3390/ijms18092011 - 20 Sep 2017
Cited by 39 | Viewed by 7470
Abstract
The applications of whole-metagenome shotgun sequencing (WMGS) in routine clinical analysis are still limited. A combination of a DNA extraction procedure, sequencing, and bioinformatics tools is essential for the removal of human DNA and for improving bacterial species identification in a timely manner. [...] Read more.
The applications of whole-metagenome shotgun sequencing (WMGS) in routine clinical analysis are still limited. A combination of a DNA extraction procedure, sequencing, and bioinformatics tools is essential for the removal of human DNA and for improving bacterial species identification in a timely manner. We tackled these issues with a broncho-alveolar lavage (BAL) sample from an immunocompromised patient who had developed severe chronic pneumonia. We extracted DNA from the BAL sample with protocols based either on sequential lysis of human and bacterial cells or on the mechanical disruption of all cells. Metagenomic libraries were sequenced on Illumina HiSeq platforms. Microbial community composition was determined by k-mer analysis or by mapping to taxonomic markers. Results were compared to those obtained by conventional clinical culture and molecular methods. Compared to mechanical cell disruption, a sequential lysis protocol resulted in a significantly increased proportion of bacterial DNA over human DNA and higher sequence coverage of Mycobacterium abscessus, Corynebacterium jeikeium and Rothia dentocariosa, the bacteria reported by clinical microbiology tests. In addition, we identified anaerobic bacteria not searched for by the clinical laboratory. Our results further support the implementation of WMGS in clinical routine diagnosis for bacterial identification. Full article
(This article belongs to the Special Issue Deciphering the Human Microbiota: Methods and Impact on Human Health)
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Review

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12 pages, 233 KiB  
Review
Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies
by Valeria D’Argenio
Int. J. Mol. Sci. 2018, 19(2), 383; https://doi.org/10.3390/ijms19020383 - 27 Jan 2018
Cited by 44 | Viewed by 8449
Abstract
The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite [...] Read more.
The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite the huge amount of data produced to date, less is known on how a microbial dysbiosis effectively contributes to a specific pathology. To fill in this gap, other approaches for microbiome study, more comprehensive than 16S rRNA gene sequencing, i.e., shotgun metagenomics and metatranscriptomics, are becoming more widely used. Methods standardization and the development of specific pipelines for data analysis are required to contribute to and increase our understanding of the human microbiome relationship with health and disease status. Full article
(This article belongs to the Special Issue Deciphering the Human Microbiota: Methods and Impact on Human Health)
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239 KiB  
Review
A Critical Review on Health Promoting Benefits of Edible Mushrooms through Gut Microbiota
by Muthukumaran Jayachandran, Jianbo Xiao and Baojun Xu
Int. J. Mol. Sci. 2017, 18(9), 1934; https://doi.org/10.3390/ijms18091934 - 8 Sep 2017
Cited by 194 | Viewed by 30220
Abstract
Mushrooms have long been used for medicinal and food purposes for over a thousand years, but a complete elucidation of the health-promoting properties of mushrooms through regulating gut microbiota has not yet been fully exploited. Mushrooms comprise a vast, and yet largely untapped, [...] Read more.
Mushrooms have long been used for medicinal and food purposes for over a thousand years, but a complete elucidation of the health-promoting properties of mushrooms through regulating gut microbiota has not yet been fully exploited. Mushrooms comprise a vast, and yet largely untapped, source of powerful new pharmaceutical substances. Mushrooms have been used in health care for treating simple and common diseases, like skin diseases and pandemic diseases like AIDS. This review is aimed at accumulating the health-promoting benefits of edible mushrooms through gut microbiota. Mushrooms are proven to possess anti-allergic, anti-cholesterol, anti-tumor, and anti-cancer properties. Mushrooms are rich in carbohydrates, like chitin, hemicellulose, β and α-glucans, mannans, xylans, and galactans, which make them the right choice for prebiotics. Mushrooms act as a prebiotics to stimulate the growth of gut microbiota, conferring health benefits to the host. In the present review, we have summarized the beneficial activities of various mushrooms on gut microbiota via the inhibition of exogenous pathogens and, thus, improving the host health. Full article
(This article belongs to the Special Issue Deciphering the Human Microbiota: Methods and Impact on Human Health)
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