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Microorganisms
Special Issues
Precision Microbiomics: Environment to Human Health
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Precision Microbiomics: Environment to Human Health

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

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 8122

Special Issue Editors

Dr. Christopher Bagwell

E-Mail Website
Guest Editor
Pacific Northwest National Laboratory, Earth Systems Science, Richland, WA, USA
Interests: microbial ecology and physiology; biogeochemistry; systems biology; environmental processes
Dr. Jason Mcdermott

E-Mail Website
Guest Editor
Pacific Northwest National Laboratory, Richland, WA, USA
Interests: systems biology; network inference; data integration; biological networks; machine learning

Special Issue Information

Dear Colleagues,

High-resolution multi-omics tools have shed new light on the existence of tremendous microbial and biomolecular diversity in natural and engineered environments. While it is customary to utilize omics-based analytical techniques to capture descriptive snapshots of microbial community potential and expression patterns, expanded high-fidelity omics data sets and robust data analysis and visualization tools are needed to unlock a fundamental understanding of the complex and varied interactions that manifest as emergent properties, such as higher-level organization, coordination, stability, and resilience. Major advances have been made to decipher the inner workings of simplified microbial assemblies, but major challenges remain to extend this utility to complex and dynamic microbiological systems. The aim of this Special Issue is to highlight recent advancements in our collective understanding of environmental microbiomes and the potential to translate this knowledge into eventual applications in human health and medical diagnostics, agro-industrial–environmental process engineering, and environmental sustainability and recovery.

Dr. Christopher Bagwell
Dr. Jason Mcdermott
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

  • fundamental and applied microbiomics
  • Multi-omics
  • data analytics and visualization

Published Papers (3 papers)

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Research

20 pages, 2843 KiB  
Article
The Domestic Environment and the Lung Mycobiome
by Esther Rubio-Portillo, David Orts, Eleuterio Llorca, Cleofé Fernández, Josefa Antón, Consuelo Ferrer, Beatriz Gálvez, Violeta Esteban, Elena Revelles, Carlos Pérez-Martín, Enrique Gómez-Imbernón, Jorge Adsuar, Pedro Piqueras, Beatriz Amat, José Franco and María Francisca Colom
Microorganisms 2020, 8(11), 1717; https://doi.org/10.3390/microorganisms8111717 - 2 Nov 2020
Cited by 10 | Viewed by 2610
Abstract
This study analyzes the relationship between the mycobiome of the Lower Respiratory Tract (LRT) and the fungi in the domestic environment. Samples studied consisted of Broncho-Alveolar Lavage (BAL) from 45 patients who underwent bronchoscopy for different diagnostic purposes, and dust and air from [...] Read more.
This study analyzes the relationship between the mycobiome of the Lower Respiratory Tract (LRT) and the fungi in the domestic environment. Samples studied consisted of Broncho-Alveolar Lavage (BAL) from 45 patients who underwent bronchoscopy for different diagnostic purposes, and dust and air from the houses (ENV) of 20 of them (44.4%). Additionally, five bronchoscopes (BS) were also analyzed and negative controls were included for every procedure. All samples were processed for DNA extraction and cultures, which were performed in Sabouraud Dextrose and Potato Dextrose Agar. The fungal Internal Transcribed Spacer (ITS2) was sequenced by the Solexa/Illumina system and sequences were analyzed by QIIME 1.8.0 and compared with the UNITE Database for identification. The similarity between the two fungal communities (BAL and ENV) for a specific patient was assessed via the percentage of coincidence in the detection of specific operational taxonomic units (OTUs), and about 75% of co-occurrence was detected between the mycobiome of the LRT and the houses. Cultures confirmed the presence of the core mycobiome species. However, the low rate of isolation from BAL suggests that most of its mycobiome corresponds to non-culturable cells. This likely depends on the patient’s immune system activity and inflammatory status. Full article
(This article belongs to the Special Issue Precision Microbiomics: Environment to Human Health)
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23 pages, 3194 KiB  
Article
Spatial Changes in Microbial Communities along Different Functional Zones of a Free-Water Surface Wetland
by Mikhail V. Semenov, George S. Krasnov, Ksenia Y. Rybka, Sergey L. Kharitonov, Yulia A. Zavgorodnyaya, Anna V. Yudina and Nataliya M. Shchegolkova
Microorganisms 2020, 8(10), 1604; https://doi.org/10.3390/microorganisms8101604 - 18 Oct 2020
Cited by 8 | Viewed by 2623
Abstract
Constructed wetlands (CWs) are complicated ecosystems that include vegetation, sediments, and the associated microbiome mediating numerous processes in wastewater treatment. CWs have various functional zones where contrasting biochemical processes occur. Since these zones are characterized by different particle-size composition, physicochemical conditions, and vegetation, [...] Read more.
Constructed wetlands (CWs) are complicated ecosystems that include vegetation, sediments, and the associated microbiome mediating numerous processes in wastewater treatment. CWs have various functional zones where contrasting biochemical processes occur. Since these zones are characterized by different particle-size composition, physicochemical conditions, and vegetation, one can expect the presence of distinct microbiomes across different CW zones. Here, we investigated spatial changes in microbiomes along different functional zones of a free-water surface wetland located in Moscow, Russia. The microbiome structure was analyzed using Illumina MiSeq amplicon sequencing. We also determined particle diameter and surface area of sediments, as well as chemical composition of organic pollutants in different CW zones. Specific organic particle aggregates similar to activated sludge flocs were identified in the sediments. The highest accumulation of hydrocarbons was found in the zones with predominant sedimentation of fine fractions. Phytofilters had the highest rate of organic pollutants decomposition and predominance of Smithella, Ignavibacterium, and Methanothrix. The sedimentation tank had lower microbial diversity, and higher relative abundances of Parcubacteria, Proteiniclasticum, and Macellibacteroides, as well as higher predicted abundances of genes related to methanogenesis and methanotrophy. Thus, spatial changes in microbiomes of constructed wetlands can be associated with different types of wastewater treatment processes. Full article
(This article belongs to the Special Issue Precision Microbiomics: Environment to Human Health)
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11 pages, 1181 KiB  
Article
Fused Omics Data Models Reveal Gut Microbiome Signatures Specific of Inactive Stage of Juvenile Idiopathic Arthritis in Pediatric Patients
by Pamela Vernocchi, Federico Marini, Giorgio Capuani, Alberta Tomassini, Giorgia Conta, Federica Del Chierico, Clara Malattia, Fabrizio De Benedetti, Alberto Martini, Bruno Dallapiccola, E. H. Pieter van Dijkhuizen, Alfredo Miccheli and Lorenza Putignani
Microorganisms 2020, 8(10), 1540; https://doi.org/10.3390/microorganisms8101540 - 6 Oct 2020
Cited by 5 | Viewed by 2345
Abstract
Juvenile idiopathic arthritis (JIA) is the most common rheumatic disease in children. Herein, we evaluated the relationship between the gut microbiome (GM) and disease phenotype by an integrated omics fused approach. In a multicenter, observational cohort study, stools from Italian JIA patients were [...] Read more.
Juvenile idiopathic arthritis (JIA) is the most common rheumatic disease in children. Herein, we evaluated the relationship between the gut microbiome (GM) and disease phenotype by an integrated omics fused approach. In a multicenter, observational cohort study, stools from Italian JIA patients were collected at baseline, active, and inactive disease stages, and their GM compared to healthy controls (CTRLs). The microbiota metabolome was analyzed to detect volatile- and non-volatile organic compounds (VOCs); the data were fused with operational taxonomic units (OTUs) from 16S RNA targeted-metagenomics and classified by chemometric models. Non-VOCs did not characterize JIA patients nor JIA activity stages compared to CTRLs. The core of VOCs, (Ethanol, Methyl-isobutyl-ketone, 2,6-Dimethyl-4-heptanone and Phenol) characterized patients at baseline and inactive disease stages, while the OTUs represented by Ruminococcaceae, Lachnospiraceae and Clostridiacea discriminated between JIA inactive stage and CTRLs. No differences were highlighted amongst JIA activity stages. Finally, the fused data discriminated inactive and baseline stages versus CTRLs, based on the contribution of the invariant core of VOCs while Ruminococcaceae concurred for the inactive stage versus CTRLs comparison. In conclusion, the GM signatures enabled to distinguish the inactive disease stage from CTRLs. Full article
(This article belongs to the Special Issue Precision Microbiomics: Environment to Human Health)
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