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Microorganisms
Special Issues
Probiotics: From Quality Assessment to Microbial Ecology
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Probiotics: From Quality Assessment to Microbial Ecology

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

Deadline for manuscript submissions: closed (30 November 2019) | Viewed by 48465

Special Issue Editors

Dr. Simone Guglielmetti

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Guest Editor
Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
Interests: probiotics; food microbiology; impact of food components on the intestinal microbial ecosystem; host-associated microbial ecology
Dr. Valentina Taverniti

E-Mail Website
Guest Editor
Department of Food, Universita degli Studi di Milano, Milan, Italy
Interests: probiotics; food microbiology; interaction with host’s immune system; microbe-associated molecular patterns (MAMPs); probiotic quality assessment; probiotics in vitro and in vivo study

Special Issue Information

Dear Colleagues,

The use of selected microbial cultures to prevent or treat pathologic conditions has gained a wide popularity, leading to the development of a constantly increasing number of foods and supplements (probiotics, sensu strictu) and medical applications (more properly defined as live biotherapeutics).

This Special Issue of Microorganisms focuses on the ecological and microbiological aspects related to probiotic products and their impact on host-associated microbiotas. We invite you to send contributions on the most recent scientific research on probiotics, including:

- microbiological aspects of probiotics and live biotherapeutic formulations (e.g., assessment of microbial viability and taxonomic quality of probiotic commercial products);

- probiotic persistence in and colonization of host’s ecological niches (e.g., probiotic recovery studies);

- modulation of host-associated microbiotas and microbiomes by probiotics;

- impact of probiotics on the microbial metabolism of food components in the host’s gastro-intestinal tract (including the oral cavity);

- isolation and characterization of next-generation probiotics to be employed as live biotherapeutics.

This Special Issue is not restricted to reports describing the oral intake of probiotics and the related effects on the gastrointestinal tract, but also comprises studies on the topical administration of probiotics, for instance skin and vaginal applications. In addition, studies on inactivated microorganisms (paraprobiotics) or their secreted products (postbiotics) are also welcome.

Prof. Simone Guglielmetti
Dr. Valentina Taverniti
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

  • probiotics
  • live biotherapeutics
  • microbiota
  • microbiome

Published Papers (12 papers)

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11 pages, 1491 KiB  
Article
Impact of a Multistrain Probiotic Formulation with High Bifidobacterial Content on the Fecal Bacterial Community and Short-Chain Fatty Acid Levels of Healthy Adults
by Giorgio Gargari, Valentina Taverniti, Ranjan Koirala, Claudio Gardana and Simone Guglielmetti
Microorganisms 2020, 8(4), 492; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8040492 - 30 Mar 2020
Cited by 7 | Viewed by 3112
Abstract
The consumption of probiotic products is continually increasing, supported by growing scientific evidence of their efficacy. Considering that probiotics may primarily affect health (either positively or negatively) through gut microbiota modulation, the first aspect that should be evaluated is their impact on the [...] Read more.
The consumption of probiotic products is continually increasing, supported by growing scientific evidence of their efficacy. Considering that probiotics may primarily affect health (either positively or negatively) through gut microbiota modulation, the first aspect that should be evaluated is their impact on the intestinal microbial ecosystem. In this study, we longitudinally analyzed the bacterial taxonomic composition and organic acid levels in four fecal samples collected over the course of four weeks from 19 healthy adults who ingested one capsule a day for two weeks of a formulation containing at least 70 billion colony-forming units, consisting of 25% lactobacilli and 75% Bifidobacterium animalis subsp. lactis. We found that 16S rRNA gene profiling showed that probiotic intake only induced an increase in a single operational taxonomic unit ascribed to B. animalis, plausibly corresponding to the ingested bifidobacterial strain. Furthermore, liquid chromatography/mass spectrometry revealed a significant increase in the lactate and acetate/butyrate ratio and a trend toward a decrease in succinate following probiotic administration. The presented results indicate that the investigated probiotic formulation did not alter the intestinal bacterial ecosystem of healthy adults and suggest its potential ability to promote colonization resistance in the gut through a transient increase in fecal bifidobacteria, lactic acid, and the acetate/butyrate ratio. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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7 pages, 1052 KiB  
Communication
Dose-Response Recovery of Probiotic Strains in Simulated Gastro-Intestinal Passage
by Sofia Forssten and Arthur C. Ouwehand
Microorganisms 2020, 8(1), 112; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8010112 - 13 Jan 2020
Cited by 12 | Viewed by 3424
Abstract
The probiotic definition stipulates “adequate amounts”. Here, we investigated the metabolic output and recovery rate of probiotic strains using a simulated upper gastro-intestinal passage and colonic fermentation. Two different doses, 7 × 109 colony forming units (CFU) and 7 × 1010 [...] Read more.
The probiotic definition stipulates “adequate amounts”. Here, we investigated the metabolic output and recovery rate of probiotic strains using a simulated upper gastro-intestinal passage and colonic fermentation. Two different doses, 7 × 109 colony forming units (CFU) and 7 × 1010 CFU, of a probiotic mixture (Bifidobacterium lactis Bl-04, Lactobacillus acidophilus La-14, Lactobacillus paracasei Lpc-37, and Lactobacillus plantarum Lp-115) or placebo were tested. The four strains were quantified by qPCR and the metabolites analyzed by gas chromatography. There was a dose-response in the detection of all four strains. There was a slightly larger increase between the two doses for L. paracasei Lpc-37 as compared with the other strains; this may suggest a greater robustness of this strain. Compared with the placebo, the high dose simulations generated more propionic acid and a higher total of short chain fatty acids (SCFA). Higher doses of a species are required to reach measurable increases above the baseline level of this species. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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20 pages, 4344 KiB  
Article
Probiotic Supplementation in a Clostridium difficile-Infected Gastrointestinal Model Is Associated with Restoring Metabolic Function of Microbiota
by Mohd Baasir Gaisawat, Chad W. MacPherson, Julien Tremblay, Amanda Piano, Michèle M. Iskandar, Thomas A. Tompkins and Stan Kubow
Microorganisms 2020, 8(1), 60; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8010060 - 29 Dec 2019
Cited by 18 | Viewed by 4966
Abstract
Clostridium (C.) difficile-infection (CDI), a nosocomial gastrointestinal disorder, is of growing concern due to its rapid rise in recent years. Antibiotic therapy of CDI is associated with disrupted metabolic function and altered gut microbiota. The use of probiotics as an [...] Read more.
Clostridium (C.) difficile-infection (CDI), a nosocomial gastrointestinal disorder, is of growing concern due to its rapid rise in recent years. Antibiotic therapy of CDI is associated with disrupted metabolic function and altered gut microbiota. The use of probiotics as an adjunct is being studied extensively due to their potential to modulate metabolic functions and the gut microbiota. In the present study, we assessed the ability of several single strain probiotics and a probiotic mixture to change the metabolic functions of normal and C. difficile-infected fecal samples. The production of short-chain fatty acids (SCFAs), hydrogen sulfide (H2S), and ammonia was measured, and changes in microbial composition were assessed by 16S rRNA gene amplicon sequencing. The C. difficile-infection in fecal samples resulted in a significant decrease (p < 0.05) in SCFA and H2S production, with a lower microbial alpha diversity. All probiotic treatments were associated with significantly increased (p < 0.05) levels of SCFAs and restored H2S levels. Probiotics showed no effect on microbial composition of either normal or C. difficile-infected fecal samples. These findings indicate that probiotics may be useful to improve the metabolic dysregulation associated with C. difficile infection. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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26 pages, 5293 KiB  
Article
Lactobacillus acidophilus JCM 1132 Strain and Its Mutant with Different Bacteriocin-Producing Behaviour Have Various In Situ Effects on the Gut Microbiota of Healthy Mice
by Gang Wang, Yunxia Yu, Enriqueta Garcia-Gutierrez, Xing Jin, Yufeng He, Linlin Wang, Peijun Tian, Zhenmin Liu, Jianxin Zhao, Hao Zhang and Wei Chen
Microorganisms 2020, 8(1), 49; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8010049 - 25 Dec 2019
Cited by 27 | Viewed by 5607
Abstract
The production of bacteriocin is considered to be a probiotic trait of lactic acid bacteria (LAB). However, not all strains of LAB harbour bacteriocin genes, even within the same species. Moreover, the effects of bacteriocins on the host gut microbiota and on host [...] Read more.
The production of bacteriocin is considered to be a probiotic trait of lactic acid bacteria (LAB). However, not all strains of LAB harbour bacteriocin genes, even within the same species. Moreover, the effects of bacteriocins on the host gut microbiota and on host physiological indicators are rarely studied. This study evaluated the effects of the bacteriocin-producing Lactobacillus acidophilus strain JCM1132 and its non-producing spontaneous mutant, L. acidophilus CCFM720, on the physiological statuses and gut microbiota of healthy mice. Mice that received the bacteriocin-producing strain JCM1132 exhibited reduced water and food intake. Furthermore, the administration of these strains induced significant changes in the compositional abundance of faecal microbiota at the phylum and genus levels, and some of these changes were more pronounced after one week of withdrawal. The effects of CCFM720 treatment on the gut microbiota seemed to favour the prevention of metabolic diseases to some extent. However, individuals that received JCM1132 treatment exhibited weaker inflammatory responses than those that received CCFM720 treatment. Our results indicate that treatment with bacteriocin-producing or non-producing strains can have different effects on the host. Accordingly, this trait should be considered in the applications of LAB. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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7 pages, 489 KiB  
Communication
Enumeration of Escherichia coli in Probiotic Products
by Camille Zimmer and Caetano Dorea
Microorganisms 2019, 7(10), 437; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7100437 - 11 Oct 2019
Cited by 12 | Viewed by 3844
Abstract
Probiotic products typically take the form of oral supplements or food-based products containing microorganisms, typically bacteria. The number of bacteria present in a dose of probiotic can be several orders of magnitude lower than the label claims, and in some cases, undetectable. The [...] Read more.
Probiotic products typically take the form of oral supplements or food-based products containing microorganisms, typically bacteria. The number of bacteria present in a dose of probiotic can be several orders of magnitude lower than the label claims, and in some cases, undetectable. The objective of this study was to assess probiotic products containing Escherichia coli to verify manufacturer claims, which have not yet been independently assessed, regarding the number of viable E. coli per suggested dose. It was found that the products tested contained E. coli in numbers several orders of magnitude less than claimed, and when subjected to simulated stomach conditions, the number of viable E. coli was significantly reduced. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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14 pages, 1781 KiB  
Article
Viability and Composition Validation of Commercial Probiotic Products by Selective Culturing Combined with Next-Generation Sequencing
by Mati Ullah, Ali Raza, Li Ye and Zhu Yu
Microorganisms 2019, 7(7), 188; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7070188 - 29 Jun 2019
Cited by 19 | Viewed by 4501
Abstract
The consumption of dietary supplements to treat health complications or to improve overall health conditions has become a globally increasing trend that leads to the development of a large number of health-related novel products and expands the associated manufacturing industries around the world. [...] Read more.
The consumption of dietary supplements to treat health complications or to improve overall health conditions has become a globally increasing trend that leads to the development of a large number of health-related novel products and expands the associated manufacturing industries around the world. In the current study, we applied selective culturing combined with next-generation sequencing to examine the microbial viability in terms of its culturability on culture medium, composition, and possible contamination in the selected 17 commercial probiotic products sold in the mainland China market. Additionally, the relative abundance of each individual bacterial content was also evaluated by using the generated sequencing reads. The tested probiotic product samples were subjected to Illumina HiSeq-2000 sequencing platform and thoroughly analyzed by the in-house developed bioinformatics pipeline. The comprehensive culturing and sequencing analysis revealed both viability and composition inaccuracy among the several tested probiotic products, however, no contaminant was identified during the analysis. Among the total, five probiotic products (29.41%) were found with an inaccurate or lower colony-forming unit (CFU) counts on culture media while four probiotic products (23.52%) have inaccurately labeled classification. This study provides an ideal qualitative and quantitative assessment approach, which can be used as a diagnostic tool for the accurate assessment of commercial probiotic supplements. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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9 pages, 846 KiB  
Article
Short-Term Probiotic Administration Increases Fecal-Anti Candida Activity in Healthy Subjects
by Massimiliano De Angelis, Carolina Scagnolari, Alessandra Oliva, Eugenio Nelson Cavallari, Luigi Celani, Letizia Santinelli, Giuseppe Pietro Innocenti, Cristian Borrazzo, Giancarlo Ceccarelli, Vincenzo Vullo and Gabriella d’Ettorre
Microorganisms 2019, 7(6), 162; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7060162 - 03 Jun 2019
Cited by 7 | Viewed by 3424
Abstract
Background: Candida albicans’ ability to evade host immune responses represents a serious threat for vulnerable patients. Objectives: To investigate if (1) feces from healthy subjects exert anti-Candida activity; (2) fecal anti-Candida activity is modified by probiotic administration and (3) different [...] Read more.
Background: Candida albicans’ ability to evade host immune responses represents a serious threat for vulnerable patients. Objectives: To investigate if (1) feces from healthy subjects exert anti-Candida activity; (2) fecal anti-Candida activity is modified by probiotic administration and (3) different probiotic differently modulate anti-Candida activity. Patients and methods: Feces from healthy donors were analyzed before and after seven days of dietary supplementation with two different probiotic formulations (VSL#3®; Vivomixx®). Candida albicans was cultured with decreasing concentrations of diluted feces, obtained before and after the treatment period. The relationship between anti-Candida activity of feces, interferon-α, anti-interferon-α antibodies and the expression of MxA, ISG15 and IFNAR1 was also evaluated. Results: Feces obtained prior to probiotic intake and feces collected after supplementation with VSL#3® did not affect Candida albicans growth. On the contrary, a 3log10 inhibition of Candida development was observed after Vivomixx® intake. Interferon-α played a role in the inhibition of Candida growth. Conclusion: Fecal anti-Candida activity was not observed prior to probiotic supplementation. Seven days of administration of Vivomixx® increased fecal anti-Candida activity, the same effect was not observed after intake of VSL#3®. The probiotic-induced anti-Candida activity seems to be related to an increased local production and release of interferon-α. Clinical trials are needed to determine if a short pretreatment with specific probiotic formulations may increase anti-Candida defenses in patients at risk. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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10 pages, 1661 KiB  
Article
Inhibition of Nitric Oxide Production, Oxidative Stress Prevention, and Probiotic Activity of Lactic Acid Bacteria Isolated from the Human Vagina and Fermented Food
by Chang-Ho Kang, Seul Hwa Han, Jin-Seong Kim, YongGyeong Kim, Yulah Jeong, Hye Min Park and Nam-Soo Paek
Microorganisms 2019, 7(4), 109; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7040109 - 23 Apr 2019
Cited by 12 | Viewed by 5184
Abstract
In this study, lactic acid bacteria (LAB) with antioxidative and probiotic activities were isolated from the vaginas of Korean women and from fermented food. Among 34 isolated LAB strains, four strains (MG4221, MG4231, MG4261, and MG4270) exhibited inhibitory activity against nitric oxide production. [...] Read more.
In this study, lactic acid bacteria (LAB) with antioxidative and probiotic activities were isolated from the vaginas of Korean women and from fermented food. Among 34 isolated LAB strains, four strains (MG4221, MG4231, MG4261, and MG4270) exhibited inhibitory activity against nitric oxide production. The MG4221 and MG4270 strains were identified as Lactobacillus plantarum, and MG4231 and MG4261 were identified as Lactobacillus fermentum. These strains were able to tolerate pepsin and pancreatin, which is required for probiotic potential. The antioxidant effects of culture filtrates obtained from selected strains included 2,2-diphenyl-1-picryl-hydrazyl (DPPH) radical scavenging capacity. Most of the culture filtrates had effective DPPH scavenging activity.In conclusion, the selected strains have significant activities and are potentially applicable to the development of functional foods. These strains might also contribute to the prevention and control of several diseases associated with oxidative stress, when used as functional probiotics. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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17 pages, 2766 KiB  
Article
The Foodborne Strain Lactobacillus fermentum MBC2 Triggers pept-1-Dependent Pro-Longevity Effects in Caenorhabditis elegans
by Emily Schifano, Paola Zinno, Barbara Guantario, Marianna Roselli, Sante Marcoccia, Chiara Devirgiliis and Daniela Uccelletti
Microorganisms 2019, 7(2), 45; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7020045 - 07 Feb 2019
Cited by 36 | Viewed by 5444
Abstract
Lactic acid bacteria (LAB) are involved in several food fermentations and many of them provide strain-specific health benefits. Herein, the probiotic potential of the foodborne strain Lactobacillus fermentum MBC2 was investigated through in vitro and in vivo approaches. Caenorhabditis elegans was used as [...] Read more.
Lactic acid bacteria (LAB) are involved in several food fermentations and many of them provide strain-specific health benefits. Herein, the probiotic potential of the foodborne strain Lactobacillus fermentum MBC2 was investigated through in vitro and in vivo approaches. Caenorhabditis elegans was used as an in vivo model to analyze pro-longevity and anti-aging effects. L. fermentum MBC2 showed a high gut colonization capability compared to E. coli OP50 (OP50) or L. rhamnosus GG (LGG). Moreover, analysis of pumping rate, lipofuscin accumulation, and body bending showed anti-aging effects in L. fermentum MBC2-fed worms. Studies on PEPT-1 mutants demonstrated that pept-1 gene was involved in the anti-aging processes mediated by this bacterial strain through DAF-16, whereas the oxidative stress protection was PEPT-1 independent. Moreover, analysis of acid tolerance, bile tolerance, and antibiotic susceptibility were evaluated. L. fermentum MBC2 exerted beneficial effects on nematode lifespan, influencing energy metabolism and oxidative stress resistance, resulted in being tolerant to acidic pH and able to adhere to Caco-2 cells. Overall, these findings provide new insight for application of this strain in the food industry as a newly isolated functional starter. Furthermore, these results will also shed light on C. elegans molecular players involved in host-microbe interactions. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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17 pages, 2103 KiB  
Article
Employment of L. paracasei K5 as a Novel Potentially Probiotic Freeze-Dried Starter for Feta-Type Cheese Production
by Antonia Terpou, Ioanna Mantzourani, Alex Galanis, Maria Kanellaki, Eugenia Bezirtzoglou, Argyro Bekatorou, Athanasios A. Koutinas and Stavros Plessas
Microorganisms 2019, 7(1), 3; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7010003 - 26 Dec 2018
Cited by 20 | Viewed by 4166
Abstract
In the present study, a novel potentially probiotic Lactobacillus paracasei strain, previously isolated from dairy products, was evaluated as a starter culture of Feta-type cheese production. Targeting industrial applications, the starter culture was applied as a ready-to-use freeze-dried culture that was either free [...] Read more.
In the present study, a novel potentially probiotic Lactobacillus paracasei strain, previously isolated from dairy products, was evaluated as a starter culture of Feta-type cheese production. Targeting industrial applications, the starter culture was applied as a ready-to-use freeze-dried culture that was either free or immobilized. The immobilized biocatalyst composed of Lactobacillus paracasei K5 cells absorbed within delignified wheat bran prebiotic carrier. All produced cheeses were compared with cheese manufactured by renin enzyme. Several parameters that affect acceptability, quality and shelf-life of Feta-type cheese were investigated, including microbial populations, physicochemical characteristics and cheese volatiles through 90 days of ripening and storage. Survival of L. paracasei K5 remained in high levels (≥6.0 log cfu/g) after the 90th day of cheese production, as recorded by combining microbiological enumeration and strain-specific multiplex PCR analysis. The use of the freeze-dried novel starter culture (free or immobilized) enhanced the aromatic profile of Feta-type cheeses. Finally, the use of the potentially synbiotic immobilized biocatalyst further improved aromatic characteristics of produced cheese and decrease of possible spoilage or pathogenic microorganisms. These findings indicate the potential industrial use of freeze-dried L. paracasei K5 as starter culture for the production of good-quality functional Feta-type cheese. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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2 pages, 165 KiB  
Comment
Comment on “Enumeration of Escherichia coli in Probiotic Products. Microorganisms 2019, 7, 437”
by Trudy M. Wassenaar, Rudolf von Bünau and Kurt Zimmermann
Microorganisms 2020, 8(2), 245; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020245 - 12 Feb 2020
Viewed by 2118
Abstract
Recently, Zimmer and Dorea published a communication on the enumeration of Escherichia coli in probiotic products containing this species [...] Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
1 pages, 158 KiB  
Reply
Reply to Comment on “Enumeration of Escherichia coli in Probiotic Products. Microorganisms 2019, 7, 437”
by Camille Zimmer and Caetano C. Dorea
Microorganisms 2020, 8(2), 242; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020242 - 12 Feb 2020
Viewed by 1656
Abstract
We thank Wassenaar and colleagues for their Comment on our recent paper [...] Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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