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Bifidobacteria: From Molecular Research to Host Interaction

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

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 23035

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Special Issue Editors

Dr. Sabrina Duranti

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Guest Editor

Life Sciences and Environmental sustainability, Department of Chemistry, University of Parma, Parma, Italy
Interests: mammalian gut microbiota; infant gut microbiota; Probiotics (Bifidobacterium, Lactobacillus); metagenomics

Dr. Leonardo Mancabelli

E-Mail Website
Guest Editor

Life Sciences and Environmental Sustainability, Department of Chemistry, University of Parma, 43121 Parma, Italy
Interests: bifidobacteria; metagenomics

Special Issue Information

Dear Colleagues,

Bifidobacteria are Gram-positive, anaerobic, non-motile, and saccharolytic bacteria that belong to the Bifidobacteriaceae family of the phylum Actinobacteria. Considering the ecological origin of the known 85 bifidobacterial taxa, representing 75 species and 10 subspecies, bifidobacteria can be identified in seven different ecological niches, which are represented by human and animal intestine, insect, oral cavity, human blood, fermented milk, and sewage. In recent years, the scientific community has intensified their efforts in exploring the biology of this bacterial genus and in untangling the genetics sustaining the interactions with their host. In particular, their presence in the human gut has been correlated with health-promoting benefits, including the production of metabolites, such as vitamins and antioxidants, immune system development, and protection from certain gut diseases, including ulcerative colitis and acute diarrhea. However, little is known about the molecular mechanisms by which bifidobacteria interact with the host. For this reason, functional genomics investigations are needed in order to understand how the bifidobacterial population contributes to gut colonization.

The aim of this Special Issue is to contribute knowledge of the Bifidobacterium genus and the interaction of these bacteria with their host.

Dr. Sabrina Duranti
Dr. Leonardo Mancabelli
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. 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

bifidobacteria
microbiota
host-microbe interactions and gut commensals

Published Papers (6 papers)

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Research

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20 pages, 44652 KiB

Open AccessArticle

A Machine Learning Approach to Study Glycosidase Activities from Bifidobacterium

by Carlos Sabater, Lorena Ruiz and Abelardo Margolles

Microorganisms 2021, 9(5), 1034; https://doi.org/10.3390/microorganisms9051034 - 11 May 2021

Cited by 5 | Viewed by 2485

Abstract

This study aimed to recover metagenome-assembled genomes (MAGs) from human fecal samples to characterize the glycosidase profiles of Bifidobacterium species exposed to different prebiotic oligosaccharides (galacto-oligosaccharides, fructo-oligosaccharides and human milk oligosaccharides, HMOs) as well as high-fiber diets. A total of 1806 MAGs were recovered from 487 infant and adult metagenomes. Unsupervised and supervised classification of glycosidases codified in MAGs using machine-learning algorithms allowed establishing characteristic hydrolytic profiles for B. adolescentis, B. bifidum, B. breve, B. longum and B. pseudocatenulatum, yielding classification rates above 90%. Glycosidase families GH5 44, GH32, and GH110 were characteristic of B. bifidum. The presence or absence of GH1, GH2, GH5 and GH20 was characteristic of B. adolescentis, B. breve and B. pseudocatenulatum, while families GH1 and GH30 were relevant in MAGs from B. longum. These characteristic profiles allowed discriminating bifidobacteria regardless of prebiotic exposure. Correlation analysis of glycosidase activities suggests strong associations between glycosidase families comprising HMOs-degrading enzymes, which are often found in MAGs from the same species. Mathematical models here proposed may contribute to a better understanding of the carbohydrate metabolism of some common bifidobacteria species and could be extrapolated to other microorganisms of interest in future studies. Full article

(This article belongs to the Special Issue Bifidobacteria: From Molecular Research to Host Interaction)

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20 pages, 6595 KiB

Open AccessArticle

Colonization of Germ-Free Piglets with Mucinolytic and Non-Mucinolytic Bifidobacterium boum Strains Isolated from the Intestine of Wild Boar and Their Interference with Salmonella Typhimurium

by Alla Splichalova, Radko Pechar, Jiri Killer, Zdislava Splichalova, Vera Neuzil Bunesova, Eva Vlkova, Hana Subrtova Salmonova and Igor Splichal

Microorganisms 2020, 8(12), 2002; https://doi.org/10.3390/microorganisms8122002 - 15 Dec 2020

Cited by 7 | Viewed by 2043

Abstract

Non-typhoidal Salmonella serovars are worldwide spread foodborne pathogens that cause diarrhea in humans and animals. Colonization of gnotobiotic piglet intestine with porcine indigenous mucinolytic Bifidobacterium boum RP36 strain and non-mucinolytic strain RP37 and their interference with Salmonella Typhimurium infection were compared. Bacterial interferences and impact on the host were evaluated by clinical signs of salmonellosis, bacterial translocation, goblet cell count, mRNA expression of mucin 2, villin, claudin-1, claudin-2, and occludin in the ileum and colon, and plasmatic levels of inflammatory cytokines IL-8, TNF-α, and IL-10. Both bifidobacterial strains colonized the intestine comparably. Neither RP36 nor RP37 B. boum strains effectively suppressed signs of salmonellosis. Both B. boum strains suppressed the growth of S. Typhimurium in the ileum and colon. The mucinolytic RP36 strain increased the translocation of S. Typhimurium into the blood, liver, and spleen. Full article

(This article belongs to the Special Issue Bifidobacteria: From Molecular Research to Host Interaction)

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18 pages, 2700 KiB

Open AccessArticle

Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species

by Gabriele Andrea Lugli, Chiara Tarracchini, Giulia Alessandri, Christian Milani, Leonardo Mancabelli, Francesca Turroni, Vera Neuzil-Bunesova, Lorena Ruiz, Abelardo Margolles and Marco Ventura

Microorganisms 2020, 8(11), 1720; https://doi.org/10.3390/microorganisms8111720 - 03 Nov 2020

Cited by 16 | Viewed by 2338

Abstract

Members of the Bifidobacterium dentium species are usually identified in the oral cavity of humans and associated with the development of plaque and dental caries. Nevertheless, they have also been detected from fecal samples, highlighting a widespread distribution among mammals. To explore the genetic variability of this species, we isolated and sequenced the genomes of 18 different B. dentium strains collected from fecal samples of several primate species and an Ursus arctos. Thus, we investigated the genomic variability and metabolic abilities of the new B. dentium isolates together with 20 public genome sequences. Comparative genomic analyses provided insights into the vast metabolic repertoire of the species, highlighting 19 glycosyl hydrolases families shared between each analyzed strain. Phylogenetic analysis of the B. dentium taxon, involving 1140 conserved genes, revealed a very close phylogenetic relatedness among members of this species. Furthermore, low genomic variability between strains was also confirmed by an average nucleotide identity analysis showing values higher than 98.2%. Investigating the genetic features of each strain, few putative functional mobile elements were identified. Besides, a consistent occurrence of defense mechanisms such as CRISPR–Cas and restriction–modification systems may be responsible for the high genome synteny identified among members of this taxon. Full article

(This article belongs to the Special Issue Bifidobacteria: From Molecular Research to Host Interaction)

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16 pages, 1348 KiB

Open AccessArticle

Bifidobacterium β-Glucosidase Activity and Fermentation of Dietary Plant Glucosides Is Species and Strain Specific

by Nikol Modrackova, Eva Vlkova, Vaclav Tejnecky, Clarissa Schwab and Vera Neuzil-Bunesova

Microorganisms 2020, 8(6), 839; https://doi.org/10.3390/microorganisms8060839 - 03 Jun 2020

Cited by 22 | Viewed by 4247

Abstract

Dietary plant glucosides are phytochemicals whose bioactivity and bioavailability can be modified by glucoside hydrolase activity of intestinal microbiota through the release of acylglycones. Bifidobacteria are gut commensals whose genomic potential indicates host-adaption as they possess a diverse set of glycosyl hydrolases giving access to a variety of dietary glycans. We hypothesized bifidobacteria with β-glucosidase activity could use plant glucosides as fermentation substrate and tested 115 strains assigned to eight different species and from different hosts for their potential to express β-glucosidases and ability to grow in the presence of esculin, amygdalin, and arbutin. Concurrently, the antibacterial activity of arbutin and its acylglycone hydroquinone was investigated. Beta-glucosidase activity of bifidobacteria was species specific and most prevalent in species occurring in human adults and animal hosts. Utilization and fermentation profiles of plant glucosides differed between strains and might provide a competitive benefit enabling the intestinal use of dietary plant glucosides as energy sources. Bifidobacterial β-glucosidase activity can increase the bioactivity of plant glucosides through the release of acylglycone. Full article

(This article belongs to the Special Issue Bifidobacteria: From Molecular Research to Host Interaction)

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Review

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21 pages, 1675 KiB

Open AccessReview

The Role of Bifidobacteria in Predictive and Preventive Medicine: A Focus on Eczema and Hypercholesterolemia

by Luisa Marras, Michele Caputo, Sonia Bisicchia, Matteo Soato, Giacomo Bertolino, Susanna Vaccaro and Rosanna Inturri

Microorganisms 2021, 9(4), 836; https://doi.org/10.3390/microorganisms9040836 - 14 Apr 2021

Cited by 23 | Viewed by 6528

Abstract

Bifidobacteria colonize the human gastrointestinal tract early on in life, their interaction with the host starting soon after birth. The health benefits are strain specific and could be due to the produced polysaccharides. The consumption of probiotics may prevent obesity, irritable bowel syndrome, eczema or atopic dermatitis, and asthma. Non-replicative strains of Bifidobacterium longum (NCC3001 and NCC2705) promote the differentiation of normal human epidermal keratinocytes (NHEKs), inducing a high expression of differentiation markers (keratin —KRT1—, and transglutaminase —TGM1—) and pro-regeneration markers (cathepsins), including β-defensin-1, which plays an important role in modulating the cutaneous immune response. Strains belonging to the genera Bifidobacterium and Lactobacillus can increase tight-junction proteins in NHEKs and enhance barrier function. Bifidobacteria and lactobacilli may be used as prophylactic or therapeutic agents towards enteric pathogens, antibiotic-associated diarrhea, lactose intolerance, ulcerative colitis, irritable bowel syndrome, colorectal cancer, cholesterol reduction, and control of obesity and metabolic disorders. Bifidobacterium bifidum showed an in vitro capability of lowering cholesterol levels thanks to its absorption into the bacterial membrane. Several strains of the species Lactobacillus acidophilus, L. delbrueckii subsp. bulgaricus, L. casei, and L. gasseri led to a reduced amount of serum cholesterol due to their ability to assimilate cholesterol (in vitro). Lactococcus lactis KF147 and Lactobacillus plantarum Lp81 have also been shown to reduce cholesterol levels by 12%. Clarifying the specific health mechanisms of Bifidobacterium and Lactobacillus strains in preventing high-cost pathologies could be useful for delineating effective guidelines for the treatment of infants and adults. Full article

(This article belongs to the Special Issue Bifidobacteria: From Molecular Research to Host Interaction)

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18 pages, 986 KiB

Open AccessReview

Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut

by Sabrina Duranti, Giulia Longhi, Marco Ventura, Douwe van Sinderen and Francesca Turroni

Microorganisms 2021, 9(1), 8; https://doi.org/10.3390/microorganisms9010008 - 22 Dec 2020

Cited by 19 | Viewed by 4355

Abstract

The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. Amongst these latter microorganisms, bifidobacteria represent a key model to study host–microbe interaction within the mammalian gut. Remarkably, bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract. They constitute one of the dominant bacterial members of the intestinal microbiota and are among the first colonizers of the mammalian gut. Notably, the presence of bifidobacteria in the gut has been associated with several health-promoting activities. In this review, we aim to provide an overview of current knowledge on the genetic diversity and ecology of bifidobacteria. Furthermore, we will discuss how this important group of gut bacteria is able to colonize and survive in the mammalian gut, so as to facilitate host interactions. Full article

(This article belongs to the Special Issue Bifidobacteria: From Molecular Research to Host Interaction)

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