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Metabarcoding and Metagenomics in Health and Environment

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

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 6479

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Guest Editor
Faculty of Science and Technology, University of the Faroe Islands, Faroe Islands, Tórshavn, Denmark
Interests: Molecular life sciences; evolution; connexins; mass spectrometry; proteomics; environmental genomics

Special Issue Information

Dear Colleagues,

It has now been 50 years since the principle of targeted and repeated molecular copying of DNA in a test tube was first demonstrated (Kleppe et al. (1971) J Mol Biol 56(2):341-361), and the method was subsequently made practical in use by the thermostable DNA polymerases and named PCR by the Nobel laureate Kary Mullis. Around 15 years ago, the next-generation sequencing (NGS) machines entered the market. This was another technical revolution making the whole life-science environment see possibilities that were previously out of reach for most laboratories. Combining the massive parallel sequencing with the development of tagging different samples with different codes (Binladen et al. (2007) PLoS ONE 2(2):e197) it became possible to pool many samples in one sequencing run, and unforeseen powers came to the fingertips of life-science researchers. These methods are now in use for investigations in countless fields: identifying the complete microbiomes in humans (and many other species) and linking the microbiomes to different health and unhealth parameters; finding invasive species; pointing out that there are high numbers of unknown bacteria in many types of environments and devising methods to sequence their genomes without needing the microorganisms to be isolated and cultured; investigating which food items wild animals eat; showing that diverse species of flies are visiting different flowers; investigating the biodiversity in soil, sediments, or even in rocks far below the surface of the Earth; providing alternative methods for monitoring fish populations and migrations; and many other things. Terms like metagenomics, metabarcoding, eDNA, etc. are used for these approaches. In this Special Issue of the International Journal Molecular Sciences, we want to celebrate the advances these approaches have made in our knowledge in many areas, as well as the hopes and promises that they give for the future. We welcome contributions covering a wide range of fields, from basal research to applied research, from species-specific investigations (including humans) to environmental research and monitoring, from the microbiome’s influence on health of the host to stock assessment and a more sustainable exploitation of the Earth’s resources.

Prof. Dr. Svein-Ole Mikalsen
Guest Editor

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Keywords

  • eDNA
  • metagenomics
  • metabarcoding
  • microbiomes
  • environment
  • health
  • environmental surveillance

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Published Papers (2 papers)

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Research

12 pages, 2829 KiB  
Article
Lung and Gut Microbiota Changes Associated with Pseudomonas aeruginosa Infection in Mouse Models of Cystic Fibrosis
by Giovanni Bacci, Alice Rossi, Federica Armanini, Lisa Cangioli, Ida De Fino, Nicola Segata, Alessio Mengoni, Alessandra Bragonzi and Annamaria Bevivino
Int. J. Mol. Sci. 2021, 22(22), 12169; https://doi.org/10.3390/ijms222212169 - 10 Nov 2021
Cited by 8 | Viewed by 3114
Abstract
Cystic fibrosis (CF) disease leads to altered lung and gut microbiomes compared to healthy subjects. The magnitude of this dysbiosis is influenced by organ-specific microenvironmental conditions at different stages of the disease. However, how this gut-lung dysbiosis is influenced by Pseudomonas aeruginosa chronic [...] Read more.
Cystic fibrosis (CF) disease leads to altered lung and gut microbiomes compared to healthy subjects. The magnitude of this dysbiosis is influenced by organ-specific microenvironmental conditions at different stages of the disease. However, how this gut-lung dysbiosis is influenced by Pseudomonas aeruginosa chronic infection is unclear. To test the relationship between CFTR dysfunction and gut-lung microbiome under chronic infection, we established a model of P. aeruginosa infection in wild-type (WT) and gut-corrected CF mice. Using 16S ribosomal RNA gene, we compared lung, stool, and gut microbiota of C57Bl/6 Cftr tm1UNCTgN(FABPCFTR) or WT mice at the naïve state or infected with P. aeruginosa. P. aeruginosa infection influences murine health significantly changing body weight both in CF and WT mice. Both stool and gut microbiota revealed significantly higher values of alpha diversity in WT mice than in CF mice, while lung microbiota showed similar values. Infection with P. aeruginosa did not changed the diversity of the stool and gut microbiota, while a drop of diversity of the lung microbiota was observed compared to non-infected mice. However, the taxonomic composition of gut microbiota was shown to be influenced by P. aeruginosa infection in CF mice but not in WT mice. This finding indicates that P. aeruginosa chronic infection has a major impact on microbiota diversity and composition in the lung. In the gut, CFTR genotype and P. aeruginosa infection affected the overall diversity and taxonomic microbiota composition, respectively. Overall, our results suggest a cross-talk between lung and gut microbiota in relation to P. aeruginosa chronic infection and CFTR mutation. Full article
(This article belongs to the Special Issue Metabarcoding and Metagenomics in Health and Environment)
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11 pages, 1275 KiB  
Article
COVID-19 Lockdowns May Reduce Resistance Genes Diversity in the Human Microbiome and the Need for Antibiotics
by João S. Rebelo, Célia P. F. Domingues, Francisco Dionisio, Manuel C. Gomes, Ana Botelho and Teresa Nogueira
Int. J. Mol. Sci. 2021, 22(13), 6891; https://doi.org/10.3390/ijms22136891 - 26 Jun 2021
Cited by 5 | Viewed by 2701
Abstract
Recently, much attention has been paid to the COVID-19 pandemic. Yet bacterial resistance to antibiotics remains a serious and unresolved public health problem that kills hundreds of thousands of people annually, being an insidious and silent pandemic. To contain the spreading of the [...] Read more.
Recently, much attention has been paid to the COVID-19 pandemic. Yet bacterial resistance to antibiotics remains a serious and unresolved public health problem that kills hundreds of thousands of people annually, being an insidious and silent pandemic. To contain the spreading of the SARS-CoV-2 virus, populations confined and tightened hygiene measures. We performed this study with computer simulations and by using mobility data of mobile phones from Google in the region of Lisbon, Portugal, comprising 3.7 million people during two different lockdown periods, scenarios of 40 and 60% mobility reduction. In the simulations, we assumed that the network of physical contact between people is that of a small world and computed the antibiotic resistance in human microbiomes after 180 days in the simulation. Our simulations show that reducing human contacts drives a reduction in the diversity of antibiotic resistance genes in human microbiomes. Kruskal–Wallis and Dunn’s pairwise tests show very strong evidence (p < 0.000, adjusted using the Bonferroni correction) of a difference between the four confinement regimes. The proportion of variability in the ranked dependent variable accounted for by the confinement variable was η2 = 0.148, indicating a large effect of confinement on the diversity of antibiotic resistance. We have shown that confinement and hygienic measures, in addition to reducing the spread of pathogenic bacteria in a human network, also reduce resistance and the need to use antibiotics. Full article
(This article belongs to the Special Issue Metabarcoding and Metagenomics in Health and Environment)
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