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Multiomic Approaches in the Microbiome and Microbial Ecology of Health and Disease

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (30 April 2022)

Special Issue Editors

Dr. Gary A. Toranzos

E-Mail Website
Guest Editor
Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan, PR 00932, USA
Interests: environmental microbiology; microbial ecology; indicators of fecal contamination; ancient microbiomes and viromes; virology
Special Issues, Collections and Topics in MDPI journals
Dr. Tasha M. Santiago-Rodríguez

E-Mail
Guest Editor
Diversigen Inc., 2450 Holcombe Blvd, Suite BCMA, Houston, TX 77021, USA
Interests: modern and ancient human microbiomes; viromes and resistomes in association with health and disease; development of standards in microbiome research; indicators of water quality; environmental microbiology; and bacteriophage biology and ecology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Advances in microbiome research have provided insights into microbial taxonomic membership and microbial ecology in health and various disease phenotypes. The field has also benefited from the application of other ‘omics including meta-(transcriptomics), meta-(proteomics) and metabolomics for the characterization of transcriptional and translational activities within microbial communities. Most microbiome studies, thus far, have applied a single-omics approach, and few have shown the utility of combining various ‘omics datasets to understand microbial membership and function. Challenges exist for multiomics data generation, integration, normalization, database selection, data storage and dissemination.

The present Special Issue welcomes studies of the microbiome as well as the microbial ecology of health and disease using multiomics approaches. Sample types may include, but are not limited to those originating from human, animal or environment (e.g., built, soil, water and wastewater). Articles describing one or several of the mentioned challenges in the field of multiomics are also welcomed.

Dr. Gary A. Toranzos
Dr. Tasha M. Santiago-Rodríguez
Guest Editors

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

Health and disease

Meta-transcriptomics

Meta-proteomics

Metabolomics

Microbiome

Multiomics

Viromics

Published Papers (7 papers)

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Editorial

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5 pages, 1047 KiB  
Editorial
MULTI-OMICS as Invaluable Tools for the Elucidation of Host–Microbe–Microbiota Interactions
by Gary A. Toranzos and Tasha M. Santiago-Rodriguez
Int. J. Mol. Sci. 2022, 23(21), 13303; https://doi.org/10.3390/ijms232113303 - 01 Nov 2022
Cited by 1 | Viewed by 962
Abstract
“Omics” is becoming an increasingly recognizable term, even to the general public, as it is used more and more often in everyday scientific research [...] Full article
(This article belongs to the Special Issue Multiomic Approaches in the Microbiome and Microbial Ecology of Health and Disease)
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3 pages, 154 KiB  
Editorial
Multiomics and Health: A Holistic Approach to Better Understand the Role of the Microbiome
by Gary A. Toranzos and Tasha M. Santiago-Rodriguez
Int. J. Mol. Sci. 2021, 22(19), 10786; https://doi.org/10.3390/ijms221910786 - 05 Oct 2021
Cited by 1 | Viewed by 1330
Abstract
The present Special Issue focuses on the latest approaches to health and public health microbiology using multiomics [...] Full article
(This article belongs to the Special Issue Multiomic Approaches in the Microbiome and Microbial Ecology of Health and Disease)

Research

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27 pages, 7591 KiB  
Article
Cross-Omics Analysis of Fenugreek Supplementation Reveals Beneficial Effects Are Caused by Gut Microbiome Changes Not Mammalian Host Physiology
by Katarina A. Jones, Allison J. Richard, J. Michael Salbaum, Susan Newman, Richard Carmouche, Sara Webb, Annadora J. Bruce-Keller, Jacqueline M. Stephens and Shawn R. Campagna
Int. J. Mol. Sci. 2022, 23(7), 3654; https://doi.org/10.3390/ijms23073654 - 26 Mar 2022
Cited by 2 | Viewed by 2476
Abstract
Herbal remedies are increasing in popularity as treatments for metabolic conditions such as obesity and Type 2 Diabetes. One potential therapeutic option is fenugreek seeds (Trigonella foenum-graecum), which have been used for treating high cholesterol and Type 2 diabetes. A proposed [...] Read more.
Herbal remedies are increasing in popularity as treatments for metabolic conditions such as obesity and Type 2 Diabetes. One potential therapeutic option is fenugreek seeds (Trigonella foenum-graecum), which have been used for treating high cholesterol and Type 2 diabetes. A proposed mechanism for these benefits is through alterations in the microbiome, which impact mammalian host metabolic function. This study used untargeted metabolomics to investigate the fenugreek-induced alterations in the intestinal, liver, and serum profiles of mice fed either a 60% high-fat or low-fat control diet each with or without fenugreek supplementation (2% w/w) for 14 weeks. Metagenomic analyses of intestinal contents found significant alterations in the relative composition of the gut microbiome resulting from fenugreek supplementation. Specifically, Verrucomicrobia, a phylum containing beneficial bacteria which are correlated with health benefits, increased in relative abundance with fenugreek. Metabolomics partial least squares discriminant analysis revealed substantial fenugreek-induced changes in the large intestines. However, it was observed that while the magnitude of changes was less, significant modifications were present in the liver tissues resulting from fenugreek supplementation. Further analyses revealed metabolic processes affected by fenugreek and showed broad ranging impacts in multiple pathways, including carnitine biosynthesis, cholesterol and bile acid metabolism, and arginine biosynthesis. These pathways may play important roles in the beneficial effects of fenugreek. Full article
(This article belongs to the Special Issue Multiomic Approaches in the Microbiome and Microbial Ecology of Health and Disease)
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19 pages, 3692 KiB  
Article
Botrytis cinerea Loss and Restoration of Virulence during In Vitro Culture Follows Flux in Global DNA Methylation
by James Breen, Luis Alejandro Jose Mur, Anushen Sivakumaran, Aderemi Akinyemi, Michael James Wilkinson and Carlos Marcelino Rodriguez Lopez
Int. J. Mol. Sci. 2022, 23(6), 3034; https://doi.org/10.3390/ijms23063034 - 11 Mar 2022
Cited by 8 | Viewed by 2003
Abstract
Pathogenic fungi can lose virulence after protracted periods of culture, but little is known of the underlying mechanisms. Here, we present the first analysis of DNA methylation flux at a single-base resolution for the plant pathogen B. cinerea and identify differentially methylated genes/genomic [...] Read more.
Pathogenic fungi can lose virulence after protracted periods of culture, but little is known of the underlying mechanisms. Here, we present the first analysis of DNA methylation flux at a single-base resolution for the plant pathogen B. cinerea and identify differentially methylated genes/genomic regions associated with virulence erosion during in vitro culture. Cultures were maintained for eight months, with subcultures and virulence testing every month. Methylation-sensitive amplified polymorphisms were performed at monthly intervals to characterise global changes to the pathogen’s genome during culture and also on DNA from mycelium inoculated onto Arabidopsis thaliana after eight months in culture. Characterisation of culture-induced epialleles was assessed by whole-genome re-sequencing and whole-genome bisulfite sequencing. Virulence declined with time in culture and recovered after inoculation on A. thaliana. Variation detected by methylation-sensitive amplified polymorphisms followed virulence changes during culture. Whole-genome (bisulfite) sequencing showed marked changes in global and local methylation during culture but no significant genetic changes. We imply that virulence is a non-essential plastic character that is at least partly modified by the changing levels of DNA methylation during culture. We hypothesise that changing DNA methylation during culture may be responsible for the high virulence/low virulence transition in B. cinerea and speculate that this may offer fresh opportunities to control pathogen virulence. Full article
(This article belongs to the Special Issue Multiomic Approaches in the Microbiome and Microbial Ecology of Health and Disease)
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15 pages, 2287 KiB  
Article
Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome
by Cynthia B. Silveira, Ana G. Cobián-Güemes, Carla Uranga, Jonathon L. Baker, Anna Edlund, Forest Rohwer and Douglas Conrad
Int. J. Mol. Sci. 2021, 22(21), 12050; https://doi.org/10.3390/ijms222112050 - 07 Nov 2021
Cited by 13 | Viewed by 3737
Abstract
Ecological networking and in vitro studies predict that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes. The metabolic byproducts from these bacteria facilitate the colonization and growth of CF pathogens like Pseudomonas aeruginosa. Here, a multi-omics study informed the [...] Read more.
Ecological networking and in vitro studies predict that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes. The metabolic byproducts from these bacteria facilitate the colonization and growth of CF pathogens like Pseudomonas aeruginosa. Here, a multi-omics study informed the control of putative anaerobic keystone species during a transition in antibiotic therapy of a CF patient. A quantitative metagenomics approach combining sequence data with epifluorescence microscopy showed that during periods of rapid lung function loss, the patient’s lung microbiome was dominated by the anaerobic, mucus-degrading bacteria belonging to Streptococcus, Veillonella, and Prevotella genera. Untargeted metabolomics and community cultures identified high rates of fermentation in these sputa, with the accumulation of lactic acid, citric acid, and acetic acid. P. aeruginosa utilized these fermentation products for growth, as indicated by quantitative transcriptomics data. Transcription levels of P. aeruginosa genes for the utilization of fermentation products were proportional to the abundance of anaerobic bacteria. Clindamycin therapy targeting Gram-positive anaerobes rapidly suppressed anaerobic bacteria and the accumulation of fermentation products. Clindamycin also lowered the abundance and transcription of P. aeruginosa, even though this patient’s strain was resistant to this antibiotic. The treatment stabilized the patient’s lung function and improved respiratory health for two months, lengthening by a factor of four the between-hospitalization time for this patient. Killing anaerobes indirectly limited the growth of P. aeruginosa by disrupting the cross-feeding of fermentation products. This case study supports the hypothesis that facultative anaerobes operated as keystone species in this CF microbiome. Personalized multi-omics may become a viable approach for routine clinical diagnostics in the future, providing critical information to inform treatment decisions. Full article
(This article belongs to the Special Issue Multiomic Approaches in the Microbiome and Microbial Ecology of Health and Disease)
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Review

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17 pages, 721 KiB  
Review
Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics
by Srinithi Purushothaman, Marco Meola and Adrian Egli
Int. J. Mol. Sci. 2022, 23(17), 9834; https://doi.org/10.3390/ijms23179834 - 30 Aug 2022
Cited by 19 | Viewed by 5877
Abstract
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from [...] Read more.
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis. Full article
(This article belongs to the Special Issue Multiomic Approaches in the Microbiome and Microbial Ecology of Health and Disease)
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14 pages, 913 KiB  
Review
Microbiome Changes in Connective Tissue Diseases and Vasculitis: Focus on Metabolism and Inflammation
by Lidia La Barbera, Federica Macaluso, Serena Fasano, Giulia Grasso, Francesco Ciccia and Giuliana Guggino
Int. J. Mol. Sci. 2022, 23(12), 6532; https://doi.org/10.3390/ijms23126532 - 10 Jun 2022
Cited by 7 | Viewed by 2103
Abstract
The microbial community acts as an active player in maintaining homeostasis and immune functions through a continuous and changeable cross-talk with the host immune system. Emerging evidence suggests that altered microbial composition, known as dysbiosis, might perturb the delicate balance between the microbiota [...] Read more.
The microbial community acts as an active player in maintaining homeostasis and immune functions through a continuous and changeable cross-talk with the host immune system. Emerging evidence suggests that altered microbial composition, known as dysbiosis, might perturb the delicate balance between the microbiota and the immune system, triggering inflammation and potentially contributing to the pathogenesis and development of chronic inflammatory diseases. This review will summarize the current evidence about the microbiome-immunity cross-talk, especially focusing on the microbiota alterations described in patients with rheumatic diseases and on the recent findings concerning the interaction between microbiota, metabolic function, and the immune system. Full article
(This article belongs to the Special Issue Multiomic Approaches in the Microbiome and Microbial Ecology of Health and Disease)
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