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Genetics and Genomics of Probiotic Organisms
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Genetics and Genomics of Probiotic Organisms

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (30 November 2020) | Viewed by 10450

Special Issue Editor

Dr. Paola Mattarelli

E-Mail Website
Guest Editor
Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
Interests: genetics; probiotics; metabolic activity; biomolecules

Special Issue Information

Dear Colleagues,

Probiotics are microorganisms typically associated with human and animal gastrointestinal tract strictly related to the wellbeing of the host. Bifidobacteria and lactobacilli are considered the main probiotics, but some strains of other genera such as Leuconostoc, Pediococcus and Lactococcus other than some yeasts are also considered and commercially utilized as probiotics. A rational design to screen the most relevant properties is fundamental for the selection of the most appropriate probiotic for specific targets such as immunostimulatory, anti-inflammatory, and antipathogenic activity.

More recently, comparative genomics of multiple genomes within and between related species and genera have been considered of great value to explore metabolic activities of probiotic microorganisms.

Genetic and genomic studies coupled with phenotypic data can be a powerful tool in understanding the commensal and probiotic relationship of bacteria with their human/animal host.

This Special Issue welcomes submissions related to genetic and genomic characterization of strains belonging to bacteria and yeasts to screen and identify interesting metabolic activities and or biomolecules for probe applications in animal and human hosts. Rational design of wet-lab experiments linked to genetic and genomic study to screen for the most relevant probiotic properties is also welcome.

Dr. Paola Mattarelli
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. Genes 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 2600 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

  • probiotics
  • genetics
  • microbial metabolism
  • Lactobacillus
  • Bifidobacterium
  • Lactococcus
  • metabolic activity

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Published Papers (2 papers)

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Research

12 pages, 2122 KiB  
Article
Host-Diet Effect on the Metabolism of Bifidobacterium
by Maria Satti, Monica Modesto, Akihito Endo, Takeshi Kawashima, Paola Mattarelli and Masanori Arita
Genes 2021, 12(4), 609; https://doi.org/10.3390/genes12040609 - 20 Apr 2021
Cited by 27 | Viewed by 4445
Abstract
Bifidobacterium has a diverse host range and shows several beneficial properties to the hosts. Many species should have co-evolved with their hosts, but the phylogeny of Bifidobacterium is dissimilar to that of host animals. The discrepancy could be linked to the niche-specific evolution [...] Read more.
Bifidobacterium has a diverse host range and shows several beneficial properties to the hosts. Many species should have co-evolved with their hosts, but the phylogeny of Bifidobacterium is dissimilar to that of host animals. The discrepancy could be linked to the niche-specific evolution due to hosts’ dietary carbohydrates. We investigated the relationship between bifidobacteria and their host diet using a comparative genomics approach. Since carbohydrates are the main class of nutrients for bifidobacterial growth, we examined the distribution of carbohydrate-active enzymes, in particular glycoside hydrolases (GHs) that metabolize unique oligosaccharides. When bifidobacterial species are classified by their distribution of GH genes, five groups arose according to their hosts’ feeding behavior. The distribution of GH genes was only weakly associated with the phylogeny of the host animals or with genomic features such as genome size. Thus, the hosts’ dietary pattern is the key determinant of the distribution and evolution of GH genes. Full article
(This article belongs to the Special Issue Genetics and Genomics of Probiotic Organisms)
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14 pages, 2071 KiB  
Article
Comparative Genomics of Lactobacillus crispatus from the Gut and Vagina Reveals Genetic Diversity and Lifestyle Adaptation
by Qiuxiang Zhang, Lili Zhang, Paul Ross, Jianxin Zhao, Hao Zhang and Wei Chen
Genes 2020, 11(4), 360; https://doi.org/10.3390/genes11040360 - 27 Mar 2020
Cited by 35 | Viewed by 5477
Abstract
Lactobacillus crispatus colonizes the human feces, human vagina, and the crops and ceca of chicken. To explore the genetic characteristics and evolutionary relationships of L. crispatus isolated from different niches, we selected 37 strains isolated from the human vagina (n = 17), human [...] Read more.
Lactobacillus crispatus colonizes the human feces, human vagina, and the crops and ceca of chicken. To explore the genetic characteristics and evolutionary relationships of L. crispatus isolated from different niches, we selected 37 strains isolated from the human vagina (n = 17), human feces (n = 11), and chicken feces (n = 9), and used comparative genomics to explore the genetic information of L. crispatus from the feces and vagina. No significant difference was found in the three sources of genomic features such as genome size, GC content, and number of protein coding sequences (CDS). However, in a phylogenetic tree constructed based on core genes, vagina-derived L. crispatus and feces-derived strains were each clustered separately. Therefore, the niche exerted an important impact on the evolution of L. crispatus. According to gene annotation, the L. crispatus derived from the vagina possessed a high abundance of genes related to acid tolerance, redox reactions, pullulanase, and carbohydrate-binding modules (CBMs). These genes helped L. crispatus to better adapt to the acidic environment of the vagina and obtain more nutrients, maintaining its dominance in the vagina in competition with other strains. In feces-derived bacteria, more genes encoding CRISPR/Cas system, glycoside hydrolases (GHs) family, and tetracycline/lincomycin resistance genes were found to adapt to the complex intestinal environment. This study highlights the evolutionary relationship of L. crispatus strains isolated from the vagina and feces, and the adaptation of L. crispatus to the host environment. Full article
(This article belongs to the Special Issue Genetics and Genomics of Probiotic Organisms)
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