Special Issue "Safety Aspects of Lactic Acid Bacteria"

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

Deadline for manuscript submissions: closed (20 December 2019).

Special Issue Editor

Dr. Franca Rossi
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Guest Editor
Istituto Zooprofilattico dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy; Dipartimento di Biotecnologie, Universita degli Studi di Verona, Verona, Italy
Interests: food safety; food microbiology, microbial genetics and physiology, gene cloning, antibiotic resistance, foodborne pathogens, bacteriocins, food microbial ecology, fermentation and ripening, gene expression
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Special Issue Information

Dear colleagues,

Lactic acid bacteria (LAB) are low G+C Gram-positive, non-spore forming microorganisms that produce lactic acid as the main end product of carbohydrate metabolism and include among others the genera Lactobacillus, Streptococcus, Enterococcus, Lactococcus and Leuconostoc. They are naturally associated to fermented food products, in which they carry out metabolic processes that improve their nutritional and sensory properties and ensure their safety and preservability. Moreover, LAB are a normal component of the oral, intestinal, and genito-urinary tract microflora and do activities that have been proven to be beneficial for human health, as demonstrated by numerous in vivo and in vitro studies. These include the treatment and prevention of infections, of antibiotic-associated diarrhea, and of many other medical conditions. Indeed, LAB comprise important probiotics commonly used to allow the instauration of a beneficial intestinal microbiota and for stimulation and modulation of the host's immune system.

However, LAB, though generally regarded as innocuous microorganisms, can occasionally pose health hazards that include the formation of toxic substances, such as biogenic amines in food, the production of host tissue-degrading enzymes, e.g., gelatinases, haemolysins, cytolysins, and infections, occurring mainly in individuals with underlying conditions, such as endocarditis, bacteremia, neonatal meningitis, and pleuro-pulmonary and urinary tract infections.

Another aspect regarding LAB safe use is the possibility that these bacteria participate to the spread of antibiotic resistance (AR) genes associated with mobile genetic elements or unstable chromosomal regions. Determinants for resistance to different antibiotic classes have been detected in nearly all LAB genera and the necessity to thoroughly check strains intentionally added to the diet or naturally present in food products for a comprehensive panel of AR genes is needed to avoid exposure to LAB strains carrying those genes and preventing their dissemination with the related risk for public health.

Given the high doses at which these bacteria are usually administered, it is essential to monitor their safety features, though this is not yet systematically done when selecting strains to be used as food cultures and probiotic preparations.

This Special Issue aims at collecting original research or review articles regarding the possible risks related to LAB use and strategies to avoid the detrimental effects that can be caused by strains carrying harmful genetic characters through safety assessment. The need for caution in the administration of LAB probiotics to individuals with particular sensitivity to infection or predisposing factors should be clearly presented through the description of ascertained LAB infection cases and studies on the possession and expression of hazardous traits.

Dr. Franca Rossi
Guest Editor

Manuscript Submission Information

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Keywords

  • Lactic acid bacteria
  • Safety aspects
  • Infection case reports
  • Adhesion and translocation
  • Hazardous genetic traits
  • Biogenic amines
  • Host tissue degrading enzymes
  • Antibiotic resistance In vitro safety assessment
  • Genome sequence-based safety assessment
  • Evaluation in animal models

Published Papers (9 papers)

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Research

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Open AccessArticle
Whole-Genome Sequencing of Lactobacillus helveticus D75 and D76 Confirms Safety and Probiotic Potential
Microorganisms 2020, 8(3), 329; https://doi.org/10.3390/microorganisms8030329 - 26 Feb 2020
Cited by 2
Abstract
Whole-genome DNA sequencing of Lactobacillus D75 and D76 strains (Vitaflor, Russia) was determined using the PacBio RS II platform, which was followed by de novo assembly with SMRT Portal 2.3.0. The average nucleotide identity (ANI) test showed that both strains belong to the [...] Read more.
Whole-genome DNA sequencing of Lactobacillus D75 and D76 strains (Vitaflor, Russia) was determined using the PacBio RS II platform, which was followed by de novo assembly with SMRT Portal 2.3.0. The average nucleotide identity (ANI) test showed that both strains belong to the Lactobacillus helveticus, but not to the L. acidophilus, as previously assumed. In addition, 31 exopolysaccharide (EPS) production genes (nine of which form a single genetic cluster), 13 adhesion genes, 38 milk protein and 11 milk sugar utilization genes, 13 genes for and against specific antagonistic activity, eight antibiotic resistance genes, and also three CRISPR blocks and eight Cas I-B system genes were identified in the genomes of both strains. The expression of bacteriocin helveticin J genes was confirmed. In fact, the presence of identified genes suggests that L. helveticus D75 and D76 are able to form biofilms on the outer mucin layer, inhibit the growth of pathogens and pathobionts, utilize milk substrates with the formation of digestible milk sugars and bioactive peptides, resist bacteriophages, show some genome-determined resistance to antibiotics, and stimulate the host’s immune system. Pathogenicity genes have not been identified. The study results confirm the safety and high probiotic potential of the strains. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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Open AccessArticle
Transmission of Vancomycin-Resistant Enterococci in the Hospital Setting: Uncovering the Patient–Environment Interplay
Microorganisms 2020, 8(2), 203; https://doi.org/10.3390/microorganisms8020203 - 31 Jan 2020
Cited by 4
Abstract
Vancomycin-resistant enterococci (VRE) are relevant nosocomial pathogens with an increasing incidence in the last decades. Their transmission is optimal in the hospital setting, as it offers two potential, large reservoirs that are closely related: susceptible patients and their environment. Here we investigate the [...] Read more.
Vancomycin-resistant enterococci (VRE) are relevant nosocomial pathogens with an increasing incidence in the last decades. Their transmission is optimal in the hospital setting, as it offers two potential, large reservoirs that are closely related: susceptible patients and their environment. Here we investigate the role of the hospital environment in the nosocomial transmission of VRE by establishing concrete links between contaminated surfaces and colonized/infected patients in outbreak and non-outbreak settings. Environmental and patient VRE isolates were collected between 2013 and 2019 and analyzed by whole-genome sequencing (WGS), subsequent multilocus sequence typing (MLST), and core genome (cg) MLST. Pairs of isolates differing in <3 alleles were rated as closely related, making a transmission likely. Fifty-three environmental VRE isolates were analyzed. MLST sequence types (ST) ST203 (50.0%), ST192 (21.3%), ST117 (17.3%), ST721 (8.8%), ST80 (2%), and ST1489 (0.7%) were detected, carrying the resistance determinants vanA (72.7%), vanB (24%), or both (3.3%). Of the 53 environmental isolates, 51 were found to form five clusters with genetically related patient isolates (n = 97 isolates). WGS confirms the role of the environment in the transmission dynamics of VRE in both the outbreak and non-outbreak settings, highlighting the importance of prevention and control of VRE spread. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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Open AccessArticle
Risk Factors for Long-Term Vancomycin-Resistant Enterococci Persistence—A Prospective Longitudinal Study
Microorganisms 2019, 7(10), 400; https://doi.org/10.3390/microorganisms7100400 - 26 Sep 2019
Cited by 2
Abstract
Vancomycin-resistant enterococci (VRE) are important nosocomial pathogens that require effective infection control measures, representing a challenge for healthcare systems. This study aimed at identifying risk factors associated with prolonged VRE carriage and determining the rate of clearance that allows the discontinuation of contact [...] Read more.
Vancomycin-resistant enterococci (VRE) are important nosocomial pathogens that require effective infection control measures, representing a challenge for healthcare systems. This study aimed at identifying risk factors associated with prolonged VRE carriage and determining the rate of clearance that allows the discontinuation of contact precautions. During a 2-year study, screening was performed in patients with a history of VRE or at risk of becoming colonized. After bacterial identification and antibiotic susceptibility testing, glycopeptide resistance was confirmed by PCR. Isolates were compared via whole genome sequence-based typing. Risk factors were recorded, and follow-up screening was performed upon readmission, defining patients as long-term carriers if still colonized ≥10 weeks after first detection. Of 1059 patients positive for VRE, carriage status was assessed upon readmission in 463 patients. VRE was cleared in 56.4% of the cases. Risk factors associated with long-term persistence were hospital stays (frequency, length), hemato-oncological disease, systemic treatment with steroids, and use of antibiotics. No specific genotypic clustering was observed in patients with VRE clearance or persistence. VRE clearance is possibly underestimated. The identification of risk factors favoring long-term carriage may contribute to a targeted implementation of infection control measures upon readmission of patients with history of VRE. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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Open AccessCommunication
Large Plasmid Complement Resolved: Complete Genome Sequencing of Lactobacillus plantarum MF1298, a Candidate Probiotic Strain Associated with Unfavorable Effect
Microorganisms 2019, 7(8), 262; https://doi.org/10.3390/microorganisms7080262 - 14 Aug 2019
Cited by 2
Abstract
Considerable attention has been given to the species Lactobacillus plantarum regarding its probiotic potential. L. plantarum strains have shown health benefits in several studies, and even nonstrain-specific claims are allowed in certain markets. L. plantarum strain MF1298 was considered a candidate probiotic, demonstrating [...] Read more.
Considerable attention has been given to the species Lactobacillus plantarum regarding its probiotic potential. L. plantarum strains have shown health benefits in several studies, and even nonstrain-specific claims are allowed in certain markets. L. plantarum strain MF1298 was considered a candidate probiotic, demonstrating in vitro probiotic properties and the ability to survive passage through the human intestinal tract. However, the strain showed an unfavorable effect on symptoms in subjects with irritable bowel syndrome in a clinical trial. The properties and the genome of this strain are thus of general interest. Obtaining the complete genome of strain MF1298 proved difficult due to its large plasmid complement. Here, we exploit a combination of sequencing approaches to obtain the complete chromosome and plasmid assemblies of MF1298. The Oxford Nanopore Technologies MinION long-read sequencer was particularly useful in resolving the unusually large number of plasmids in the strain, 14 in total. The complete genome sequence of 3,576,440 basepairs contains 3272 protein-encoding genes, of which 315 are located on plasmids. Few unique regions were found in comparison with other L. plantarum genomes. Notably, however, one of the plasmids contains genes related to vitamin B12 (cobalamin) turnover and genes encoding bacterial reverse transcriptases, features not previously reported for L. plantarum. The extensive plasmid information will be important for future studies with this strain. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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Open AccessArticle
The Anti-Rotaviral Activity of Low Molecular Weight and Non-Proteinaceous Substance from Bifidobacterium longum BORI Cell Extract
Microorganisms 2019, 7(4), 108; https://doi.org/10.3390/microorganisms7040108 - 23 Apr 2019
Abstract
Rotavirus infection is the most common diarrheal disease worldwide in children under five years of age, and it often results in death. In recent years, research on the relationship between rotavirus and probiotics has shown that probiotics are effective against diarrhea. A clinical [...] Read more.
Rotavirus infection is the most common diarrheal disease worldwide in children under five years of age, and it often results in death. In recent years, research on the relationship between rotavirus and probiotics has shown that probiotics are effective against diarrhea. A clinical trial has reported that Bifidobacterium longum BORI reduced diarrhea induced by rotavirus. The present work investigated the anti-rotaviral effect of B. longum BORI by cytopathic effect observation and real time cell analyses. Our study found that B. longum BORI showed strong anti-rotaviral effect when incubated with MA104 cells prior to viral infection, suggesting that the probiotic does in fact interfere with the interaction of viruses and host cells. It is believed that the efficacy is due to low-molecular weight and non-protein components derived from B. longum BORI. This discovery can help broaden the industrial application of B. longum BORI, which has been proven to be a safe and effective probiotic. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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Review

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Open AccessReview
Safety Aspects of Genetically Modified Lactic Acid Bacteria
Microorganisms 2020, 8(2), 297; https://doi.org/10.3390/microorganisms8020297 - 21 Feb 2020
Cited by 5
Abstract
Lactic acid bacteria (LAB) have a long history of use in the food industry. Some species are part of the normal human microbiota and have beneficial properties for human health. Their long-standing use and considerable biotechnological potential have led to the development of [...] Read more.
Lactic acid bacteria (LAB) have a long history of use in the food industry. Some species are part of the normal human microbiota and have beneficial properties for human health. Their long-standing use and considerable biotechnological potential have led to the development of various systems for their engineering. Together with novel approaches such as CRISPR-Cas, the established systems for engineering now allow significant improvements to LAB strains. Nevertheless, genetically modified LAB (GM-LAB) still encounter disapproval and are under extensive regulatory requirements. This review presents data on the prospects for LAB to obtain ‘generally recognized as safe’ (GRAS) status. Genetic modification of LAB is discussed, together with problems that can arise from their engineering, including their dissemination into the environment and the spread of antibiotic resistance markers. Possible solutions that would allow the use of GM-LAB are described, such as biocontainment, alternative selection markers, and use of homologous DNA. The use of GM-LAB as cell factories in closed systems that prevent their environmental release is the least problematic aspect, and this is also discussed. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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Open AccessReview
Warding Off Recurrent Yeast and Bacterial Vaginal Infections: Lactoferrin and Lactobacilli
Microorganisms 2020, 8(1), 130; https://doi.org/10.3390/microorganisms8010130 - 17 Jan 2020
Cited by 4
Abstract
Vaginal infections are the most prevalent women’s health problem. Incompetent diagnosis, inappropriate treatments, and antibiotic resistance are the main causes of the unsatisfactory results of conventional, antimicrobic treatment for these infections. Research has thus been conducted to identify new treatments for these genital [...] Read more.
Vaginal infections are the most prevalent women’s health problem. Incompetent diagnosis, inappropriate treatments, and antibiotic resistance are the main causes of the unsatisfactory results of conventional, antimicrobic treatment for these infections. Research has thus been conducted to identify new treatments for these genital diseases. The significant enhancement in our knowledge of vaginal microbiota has permitted the development of new, nonpharmacological strategies for the treatment of vaginal infections that seek to restore the balance of vaginal microflora, as opposed to modifying its components. Among these approaches, bioactive compounds, such as probiotics and nutraceutical proteins (such as lactoferrin), deserve particular attention. The aim of this review is to examine the role of probiotics (mainly Lactobacillus spp.) and lactoferrin as new strategies for counteracting bacterial and fungal vaginal infections. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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Open AccessReview
Members of the Lactobacillus Genus Complex (LGC) as Opportunistic Pathogens: A Review
Microorganisms 2019, 7(5), 126; https://doi.org/10.3390/microorganisms7050126 - 10 May 2019
Cited by 8
Abstract
Microorganisms belonging to the Lactobacillus genus complex (LGC) are naturally associated or deliberately added to fermented food products and are widely used as probiotic food supplements. Moreover, these bacteria normally colonize the mouth, gastrointestinal (GI) tract, and female genitourinary tract of humans. They [...] Read more.
Microorganisms belonging to the Lactobacillus genus complex (LGC) are naturally associated or deliberately added to fermented food products and are widely used as probiotic food supplements. Moreover, these bacteria normally colonize the mouth, gastrointestinal (GI) tract, and female genitourinary tract of humans. They exert multiple beneficial effects and are regarded as safe microorganisms. However, infections caused by lactobacilli, mainly endocarditis, bacteremia, and pleuropneumonia, occasionally occur. The relevance of Lactobacillus spp. and other members of the LGC as opportunistic pathogens in humans and related risk factors and predisposing conditions are illustrated in this review article with more emphasis on the species L. rhamnosus that has been more often involved in infection cases. The methods used to identify this species in clinical samples, to distinguish strains and to evaluate traits that can be associated to pathogenicity, as well as future perspectives for improving the identification of potentially pathogenic strains, are outlined. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
Open AccessReview
Probiotics: If It Does Not Help It Does Not Do Any Harm. Really?
Microorganisms 2019, 7(4), 104; https://doi.org/10.3390/microorganisms7040104 - 11 Apr 2019
Cited by 22
Abstract
Probiotics per definition should have beneficial effects on human health, and their consumption has tremendously increased in the last decades. In parallel, the amount of published material and claims for their beneficial efficacy soared continuously. Recently, multiple systemic reviews, meta-analyses, and expert opinions [...] Read more.
Probiotics per definition should have beneficial effects on human health, and their consumption has tremendously increased in the last decades. In parallel, the amount of published material and claims for their beneficial efficacy soared continuously. Recently, multiple systemic reviews, meta-analyses, and expert opinions expressed criticism on their claimed effects and safety. The present review describes the dark side of the probiotics, in terms of problematic research design, incomplete reporting, lack of transparency, and under-reported safety. Highlighted are the potential virulent factors and the mode of action in the intestinal lumen, risking the physiological microbiome equilibrium. Finally, regulatory topics are discussed to lighten the heterogeneous guidelines applied worldwide. The shift in the scientific world towards a better understanding of the human microbiome, before consumption of the probiotic cargo, is highly endorsed. It is hoped that better knowledge will extend the probiotic repertoire, re-confirm efficacy or safety, establish their efficacy and substantiate their beneficial effects. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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