Choosing an appropriate probiotic product for your patient: An evidence-based practical guide

Enhanced Clostridioides difficile infection prevention with a pharmacy-controlled policy that adds a three-strain Lactobacillus probiotic concomitantly to antibiotic therapy

When 70% of antibiotic users took a 3-strain Lactobacillus probiotic preparation the hospital-wide rate of healthcare-associated Clostridioides difficile infection improved significantly. The incidence of C. difficile infection for those taking the probiotic along with multiple antibiotics or a single high-risk antibiotic was decreased by at least half.

Improving the drying of Propionibacterium freudenreichii starter cultures

Propionibacterium freudenreichii is a beneficial food-grade actinobacterium, widely implemented, and thus consumed, in various food products. As the main application, P. freudenreichii is used as a cheese-ripening starter, mostly in hard type cheeses. Indeed, during manufacture of "Swiss-type" cheeses (or opened-body cheeses), the technological process favors propionibacteria growth, as well as the corresponding propionic fermentation. This leads to the characteristic flavor of these cheeses, through the release of short chain fatty acids and through lipolysis, as well as to their specific texture. To fulfil this ripening, massive amounts of propionibacteria are industrially produced, dried and stored, prior to cheese making. Furthermore, P. freudenreichii is commercialized in various probiotic food supplements aiming at preserving intestinal health and comfort, in line with its ability to produce beneficial metabolites (short chain fatty acids, vitamins), as well as immunomodulatory compounds. Other industrial applications of P. freudenreichii include the production of food-grade vitamins of the B group, of trehalose, of conjugated linoleic acid, and of biopreservatives. For these different applications, maintaining survival and activity of propionibacteria during production, drying, storage and finally implementation, is crucial. More widely, maintaining live and active probiotic bacteria represents a challenge as the market for probiotic products increases. Probiotic bacteria are, for a bulk majority, freeze-dried, but spray drying is also more and more considered. Indeed, this process is both continuous and more cost-efficient, as it utilizes less energy compared to freeze-drying; on the other hand, it exposes bacteria to higher heat and oxidative stresses. Apart from process optimization and strain selection, it is possible to enhance the resistance of bacteria by taking advantage of their adaptation capacity. Indeed, P. freudenreichii stress tolerance can be boosted by different pretreatments applied before the drying step, thus considerably increasing its final survival. In particular, adaptation to hyperosmotic conditions improves stress tolerance, while the presence of osmoprotectants may mitigate this improvement. Thermal adaptation also modulates tolerance towards these technological challenges. The composition of the growth medium, including the ratio between the carbohydrates provided and the non-protein nitrogen, plays a key role in driving the accumulation of osmoprotectants. This, in turn, determines P. freudenreichii tolerance towards different stresses, and overall towards both freeze-drying and spray-drying. As an example, the accumulation of trehalose enhances its spray-drying survival, while the accumulation of glycine betaine enhances its freeze-drying survival. Growth of propionibacteria in hyperconcentrated whey was used to trigger multiple stress tolerance acquisition, underpinned by overexpression of key stress protein, accumulation of cytoplasmic storage compounds, and leading to enhanced spray-drying survival. A simplified process, from cultivation to atomization, was developed by using whey as a 2-in-1 medium in which propionibacteria were grown, protected and dried with minimal cell death. This innovative process was then subjected to scaling up at the industrial level. In this aim, a gentle multi-stage drying process offering mild drying conditions by coupling spray drying with belt drying, led to final probiotic survival close to 100% when stress tolerance acquisition was previously implemented. Such innovation opens new avenues for the efficient, cost-effective and sustainable development of new probiotic production technologies, as well as probiotic application in the context of food and feed. KEY POINTS: • Propionibacteria acquire multi-stress tolerance when grown in hyper-concentrated whey. • Spray drying of osmo-adapted probiotic bacteria is possible with limited cell death. • A two-in-one drying method is developed to grow and dry probiotic bacteria in the same matrix.

Potential Roles for Probiotics in the Treatment of COVID-19 Patients and Prevention of Complications Associated with Increased Antibiotic Use

Medical care for patients hospitalized with COVID-19 is an evolving process. Most COVID-19 inpatients (58-95%) received empiric antibiotics to prevent the increased mortality due to ventilator-associated pneumonia and other secondary infections observed in COVID-19 patients. The expected consequences of increased antibiotic use include antibiotic-associated diarrhea (AAD) and Clostridioides difficile infections (CDI). We reviewed the literature (January 2020-March 2021) to explore strategies to reduce these consequences. Antimicrobial stewardship programs were effective in controlling antibiotic use during past influenza epidemics and have also been shown to reduce healthcare-associated rates of CDI. Another potential strategy is the use of specific strains of probiotics shown to be effective for the prevention of AAD and CDI prior to the pandemic. During 2020, there was a paucity of published trials using these two strategies in COVID-19 patients, but trials are currently ongoing. A multi-strain probiotic mixture was found to be effective in reducing COVID-19-associated diarrhea in one trial. These strategies are promising but need further evidence from trials in COVID-19 patients.

Vaginal Probiotics for Reproductive Health and Related Dysbiosis: Systematic Review and Meta-Analysis

The use of probiotics in reproductive-related dysbiosis is an area of continuous progress due to the growing interest from clinicians and patients suffering from recurrent reproductive microbiota disorders. An imbalance in the natural colonization sites related to reproductive health—vaginal, cervicovaginal, endometrial, and pregnancy-related altered microbiota—could play a decisive role in reproductive outcomes. Oral and vaginal administrations are in continuous discussion regarding the clinical effects pursued, but the oral route is used and studied more often despite the need for further transference to the colonization site. The aim of the present review was to retrieve the standardized protocols of vaginal probiotics commonly used for investigating their microbiota modulation capacities. Most of the studies selected focused on treating bacterial vaginosis (BV) as the most common dysbiosis; a few studies focused on vulvovaginal candidiasis (VVC) and on pretreatment during in vitro fertilization (IVF). Vaginal probiotic doses administered were similar to oral probiotics protocols, ranging from ≥10⁷ CFU/day to 2.5 × 10¹⁰ CFU/day, but were highly variable regarding the treatment duration timing. Moderate vaginal microbiota modulation was achieved; the relative abundance of abnormal microbiota decreased and Lactobacillus species increased.

Perils and pitfalls of probiotic quasi-experimental studies for primary prevention of Clostridioides difficile infection: A review of the evidence

BACKGROUND

Primary prevention of Clostridioides (Clostridium) difficile infections (CDI) is an important but challenging infection control goal for hospitals and health care facilities. Enhanced infection control protocols have reduced CDI rates, but the problem persists and administration of probiotics to patients at risk could be very useful if shown to be safe and effective. Randomized controlled trials are largely impractical for primary prevention CDI trials due to large required study sizes and quasi-experimental studies are becoming more frequent as a method to assess this problem.

OBJECTIVE

Our goal is to review the published quasi-experimental studies adding probiotics to their infection control protocols to reduce CDI and determine the strengths and limitations for this type of study design.

METHODS

The literature was searched using PubMed, Google Scholar, Medline and Cochrane Databases and gastrointestinal meeting abstracts from January 2000 to January 2020 for quasi-experimental intervention studies testing various probiotics for the primary prevention of CDI.

RESULTS

We found 28 studies with 7 different types of probiotics (10 studies implementing a hospital-wide intervention, 6 studies targeting 1-3 wards, and 12 studies on either sustainability, cost-effectiveness or subgroup analysis). Some probiotics demonstrated a significant reduction in CDI rates; all four of the probiotic types given only on specific wards and 3 of the 4 probiotics given facility-wide. However, this type of study design was influenced by numerous factors which must be carefully accounted for in the analysis.

CONCLUSIONS

Some probiotics may be an effective addition to infection control protocols to prevent C. difficile infections, but careful study design considerations are needed.

Efficacy of Single-Strain Probiotics Versus Multi-Strain Mixtures: Systematic Review of Strain and Disease Specificity

The diversity of probiotic products makes choosing an appropriate probiotic challenging. One unanswered question is whether single-strain probiotics are more effective than multi-strain mixtures. The aim of this review is to account for both disease and strain specificity to determine whether single strains or multiple strains are equivalent or more effective. This literature review of randomized controlled trials from 1973 to 2019 was used to compare the pooled efficacy of trials with a single strain versus the probiotic mixture with same matched strain within the same type of disease indication. A total of 65 RCTs were included (41 with single strains, 22 multi-strain mixtures and 2 comparing single strain to mixture arms) for eight different disease indications (N = 10,863). Only three strains (L. rhamnosus GG, L. helveticus R52 and B. lactis Bb12) had corresponding trials with matching mixtures. Use of L. rhamnosus GG only was significantly more protective for necrotizing enterocolitis compared to two mixtures also containing different strains of B. lactis. The mixture of L. rhamnosus GG and B. lactis Bb12 was significantly more effective than L. rhamnosus GG alone for the eradication of H. pylori. In most cases, single strains were equivalent to mixtures. Choice of an appropriate probiotic should be based, not on the number of strains in the product, rather based on evidence-based trials of efficacy. In most cases, multi-strain mixtures were not significantly more effective than single-strain probiotics.

4-Vinylguaiacol, an Active Metabolite of Ferulic Acid by Enteric Microbiota and Probiotics, Possesses Significant Activities against Drug-Resistant Human Colorectal Cancer Cells

Ferulic acid, a hydroxycinnamic acid, is abundant in vegetables, grains, and medicinal plants. Emerging evidence suggests that ferulic acid may exert beneficial effects against colorectal cancer. However, the anticancer activity of ferulic acid is relatively low, and its metabolism after oral administration is largely unknown. In this study, mimicking the enteric environment, human intestinal microflora and commercial probiotics were used to metabolize ferulic acid to its metabolites, and their anticancer activities were evaluated. Ferulic acid can be biotransformed to 4-vinylguaiacol (2-methoxy-4-vinylphenol), and the contents of ferulic acid and 4-vinylguaiacol in bio-transformed extracts were determined by high-performance liquid chromatography (HPLC). Using the chemotherapy-sensitive cell line HCT-116 and the chemo-resistant cell line HT-29, the cell proliferation was determined by the modified trichrome stain assay. The cell cycle and induction of apoptosis were assayed using flow cytometry. HPLC data showed that there was a marked transformation from ferulic acid to 4-vinylguaiacol, and the conversion rates of intestinal microflora and four probiotics were from 1.3 to 36.8%. Both ferulic acid and 4-vinylguaiacol possessed dose- and time-related anticancer activities on the two cell lines, while 4-vinylguaiacol showed more potent effects than ferulic acid. Interestingly, 4-vinylguaiacol exhibited significantly higher antiproliferative effects on the HT-29 cell line than that on HCT-116. The IC50 of the metabolite 4-vinylguaiacol on HT-29 cells was 350 μM, 3.7-fold higher than its parent compound. The potential of cancer cell growth inhibition of 4-vinylguaiacol was mediated by cell cycle arrest at the G1 phase and induction of apoptosis. Data from this study indicate that the oral administration of ferulic acid offers a promising approach to increase its anticancer activity through gut microbial conversion to 4-vinylguaiacol, and the biotransformation could also be achieved by selected commercial probiotics. 4-Vinylguaiacol is a potential anticancer metabolite from ferulic acid for chemotherapy-resistant colon cancer cells.

Potential role of probiotics in reducing Clostridioides difficile virulence: Interference with quorum sensing systems

Opportunistic pathogenic bacteria may cause disease after the normally protective microbiome is disrupted (typically by antibiotic exposure). Clostridioides difficile is one such pathogen having a severe impact on healthcare facilities and increasing costs of medical care. The search for new therapeutic strategies that are not reliant on additional antibiotic exposures are currently being explored. One such strategy is to disrupt the production of C. difficile virulence factors by interfering with quorum sensing (QS) systems. QS has been well studied in other bacteria, but our understanding in C. difficile is not so well understood. Some probiotic strains or combinations of strains have been shown to be effective in the treatment or primary prevention of C. difficile infections and may possess multiple mechanisms of action. One mechanism of probiotics might be the inhibition of QS, but their role has not been clearly defined yet. A literature search was conducted using standard databases (PubMed, Google Scholar) from database inception to August 2020. The objective of this paper is to update our understanding of how QS leads to toxin production by C. difficile, which is important in pathogenesis, and how QS inhibitors or probiotics may disrupt this pathway. We found two main QS systems for C. difficile (Agr and Lux systems) that are involved in C. difficile pathogenesis by regulating toxin production, motility and adherence. Probiotics and other QS inhibitors targeting QS systems may represent important new directions of therapy and prevention of CDI.

Use of probiotics in clinical practice with special reference to diarrheal diseases: A position statement of the Malaysian Society of Gastroenterology and Hepatology

Probiotics comprise a large group of microorganisms, which have different properties and thus confer different benefits. The use of probiotics has shown promising results in the management of diarrheal diseases. While the availability of probiotic products has flourished in the marketplace, there is limited guidance on the selection of probiotics for clinical use. This position paper is aimed at informing clinicians about the proper selection criteria of probiotics based on current evidence on strain-specific efficacy and safety for the management of diarrheal diseases. Members of the working group discussed issues on probiotic use in clinical practice, which were then drafted into statements. Literature to support or refute the statements were gathered through a search of medical literature from 2011 to 2020. Recommendations were formulated based on the drafted statements and evidence gathered, revised as necessary, and finalized upon agreement of all members. Twelve statements and recommendations were developed covering the areas of quality control in the manufacturing of probiotics, criteria for selection of probiotics, and established evidence for use of probiotics in diarrheal diseases in adults and children. Recommendations for the use of specific probiotic strains in clinical practice were categorized as proven and probable efficacy based on strength of evidence. Robust evidence is available to support the use of probiotics for diarrheal diseases in clinical practice. Based on the results obtained, we strongly advocate the careful evaluation of products, including manufacturing practices, strain-specific evidence, and contraindications for at-risk populations when choosing probiotics for use in clinical practice.

Efficacy and safety of Bacillus coagulans LBSC in irritable bowel syndrome: A prospective, interventional, randomized, double-blind, placebo-controlled clinical study [CONSORT Compliant]

GOALS

To evaluate safety and efficacy of Bacillus coagulans LBSC [DSM17654] in irritable bowel syndrome (IBS) through a prospective, interventional, randomized, double-blind, and placebo-controlled, CONSORT compliant clinical trial.

BACKGROUND

Bacteriotherapy shows promising impact on alleviating clinical conditions of IBS and associated functional gastrointestinal disorders. B coagulans LBSC is a genetically and phenotypically safe probiotic strain used in this study to study its impact on ameliorating IBS symptoms and improving quality of life.

METHODS

In this interventional, randomized, double-blind, placebo-controlled clinical study, total 40 subjects (18-65 years) were screened through Rome IV criteria and randomized into 2 groups, that is, interventional and placebo arm (n = 20/arm). Similar dosages were received by both the arm, that is, placebo (vehicle) and interventional arm (B coagulans LBSC, 6 billion/d) for a period of 80 days. Study completed with per protocol subjects (n = 38) and results were considered to evaluate the primary and secondary endpoints.

RESULTS

Assessment through Digestive Symptom Frequency Questionnaire 5 point Likert scale showed significant improvement in interventional arm compared to placebo on symptoms such as bloating/cramping, abdominal pain, diarrhea, constipation, stomach rumbling, nausea, vomiting, headache, and anxiety. Maximum of "no symptoms" cases and mild to moderate gastrointestinal symptoms along with improved stool consistency were from interventional arm tested following IBS severity scoring system and Bristol stool form scale. Upper gastrointestinal endoscopy revealed no clinical difference of gastrointestinal mucosa between both the arms. B coagulans LBSC was well tolerated with no serious adverse events.

CONCLUSIONS

B coagulans LBSC was safe for human consumption and efficacious in alleviating overall pathophysiological symptoms of IBS and thereby improving inclusive quality of life evaluated.

Effectiveness of Probiotic, Prebiotic, and Synbiotic Supplementation to Improve Perinatal Mental Health in Mothers: A Systematic Review and Meta-Analysis

Introduction: There is an emerging interest in modulating the gut microbiota to target the gut-brain axis and improve maternal mental health in the perinatal period. This systematic review evaluated the effectiveness of prebiotics, probiotics, and synbiotics supplementation during pregnancy to reduce the risk of maternal mental health problems in the perinatal period. Methods: Electronic biomedical databases and clinical trial registries were searched from database inception through August 2020 to identify randomized controlled clinical trials (RCTs) evaluating the effect of probiotic, prebiotic, or synbiotic supplements administered to women during pregnancy on measures of perinatal depression, anxiety, and other mental health outcomes. Study selection, risk of bias appraisal, and data extraction were independently performed by two reviewers. Pooled mean differences (MD) and odds ratios (pOR) with 95% confidence intervals (CI) were calculated in random-effects meta-analyses for the outcomes of interest in the review. Results: From 3,868 studies identified through the search strategy, three RCTs of low risk of bias involving 713 participants were included, all three testing probiotics. There were no differences between probiotics and control groups in the mean depression scores (MD -0.46; 95% CI -2.16, 1.25) at end of follow-up. Although statistical significance was not achieved, probiotics showed an advantage in the proportion of participants scoring below an established cut-off for depression (pOR 0.68; 95% CI 0.43, 1.07). Compared to placebo, probiotics in pregnancy reduced anxiety symptoms (MD -0.99; 95% CI -1.80, -0.18); however, this advantage was not translated in a reduction in the proportion of participants scoring above an established cut-off for anxiety (pOR 0.65; 95% CI 0.23, 1.85). There were no differences between probiotics and control groups in global mental health scores at end of follow-up (MD 1.09; 95% CI -2.04, 4.22). Conclusion: There is limited but promising evidence about the effectiveness of probiotics during pregnancy to reduce anxiety symptoms and reduce the proportion of women scoring ABOVE a cut-off depression score. There is a lack of RCT evidence supporting prebiotics and synbiotics supplementation for similar purposes in the perinatal period. More research is needed before prebiotics, probiotics, and synbiotics are recommended to support maternal mental health and well-being in the perinatal period. Systematic Review Registration: PROSPERO, CRD42019137158.

Single and Multiple Inoculum of Lactiplantibacillus plantarum Strains in Table Olive Lab-Scale Fermentations

In order to improve the olives’ quality, and to reduce the de-bittering time during the table olive fermentation process, it is necessary to pilot the fermentation by inoculating the brine with selected cultures of microorganisms. Some probiotic tests, such as resistance/sensitivity to antibiotics, bile salt hydrolase (BSH) activity, growth at acidic pH, an auto-aggregation assay, and a test of the production of exopolysaccharides, were carried out in order to screen 35 oleuropeinolytic Lactiplantibacillus plantarum subsp. plantarum strains to be used in guided fermentations of table olives. On the basis of the technological and probiotic screening, we analyzed the progress of three different lab-scale fermentations of Olea europaea L. Itrana cv. olives inoculated with spontaneous, single, and multiple starters: jar A was left to ferment spontaneously; jar B was inoculated with a strongly oleuropeinolytic strain (L. plantarum B1); jar C was inoculated with a multiple inoculum (L. plantarum B1 + L. plantarum B51 + L. plantarum B124). The following parameters were monitored during the fermentation: pH, titratable acidity, NaCl concentration, the degradation of bio-phenols, and the enrichment rate of hydroxytyrosol and tyrosol in the olive’s flesh, oil and brine. The degradation of secoiridoid glucosides appeared to be faster in the inoculated jars than in the spontaneously-fermented jar. The production of hydroxytyrosol and ligstroside aglycons was high. This indicated a complete degradation of the oleuropein and a partial degradation of the ligstroside. The multiple inoculum ensured a complete debittering, and could give probiotic traits. The presence of L. plantarum B1 and B124 as a fermentation starter guarantees an optimal trend of de-bittering and fermentation variables, thus ensuring the production of a better final product. L. plantarum B51 could be considered to be a promising probiotic candidate for obtaining probiotic food of completely vegetable origin.

Probiotics for treating acute infectious diarrhoea

BACKGROUND

Probiotics may be effective in reducing the duration of acute infectious diarrhoea.

OBJECTIVES

To assess the effects of probiotics in proven or presumed acute infectious diarrhoea.

SEARCH METHODS

We searched the trials register of the Cochrane Infectious Diseases Group, MEDLINE, and Embase from inception to 17 December 2019, as well as the Cochrane Controlled Trials Register (Issue 12, 2019), in the Cochrane Library, and reference lists from studies and reviews. We included additional studies identified during external review.

SELECTION CRITERIA

Randomized controlled trials comparing a specified probiotic agent with a placebo or no probiotic in people with acute diarrhoea that is proven or presumed to be caused by an infectious agent.

DATA COLLECTION AND ANALYSIS

Two review authors independently applied inclusion criteria, assessed risk of bias, and extracted data. Primary outcomes were measures of diarrhoea duration (diarrhoea lasting ≥ 48 hours; duration of diarrhoea). Secondary outcomes were number of people hospitalized in community studies, duration of hospitalization in inpatient studies, diarrhoea lasting ≥ 14 days, and adverse events.

MAIN RESULTS

We included 82 studies with a total of 12,127 participants. These studies included 11,526 children (age < 18 years) and 412 adults (three studies recruited 189 adults and children but did not specify numbers in each age group). No cluster-randomized trials were included. Studies varied in the definitions used for "acute diarrhoea" and "end of the diarrhoeal illness" and in the probiotic(s) tested. A total of 53 trials were undertaken in countries where both child and adult mortality was low or very low, and 26 where either child or adult mortality was high. Risk of bias was high or unclear in many studies, and there was marked statistical heterogeneity when findings for the primary outcomes were pooled in meta-analysis. Effect size was similar in the sensitivity analysis and marked heterogeneity persisted. Publication bias was demonstrated from funnel plots for the main outcomes. In our main analysis of the primary outcomes in studies at low risk for all indices of risk of bias, no difference was detected between probiotic and control groups for the risk of diarrhoea lasting ≥ 48 hours (risk ratio (RR) 1.00, 95% confidence interval (CI) 0.91 to 1.09; 2 trials, 1770 participants; moderate-certainty evidence); or for duration of diarrhoea (mean difference (MD) 8.64 hours shorter, 95% CI 29.4 hours shorter to 12.1 hours longer; 6 trials, 3058 participants; very low-certainty evidence). Effect size was similar and marked heterogeneity persisted in pre-specified subgroup analyses of the primary outcomes that included all studies. These included analyses limited to the probiotics Lactobacillus rhamnosus GG and Saccharomyces boulardii. In six trials (433 participants) of Lactobacillus reuteri, there was consistency amongst findings (I² = 0%), but risk of bias was present in all included studies. Heterogeneity also was not explained by types of participants (age, nutritional/socioeconomic status captured by mortality stratum, region of the world where studies were undertaken), diarrhoea in children caused by rotavirus, exposure to antibiotics, and the few studies of children who were also treated with zinc. In addition, there were no clear differences in effect size for the primary outcomes in post hoc analyses according to decade of publication of studies and whether or not trials had been registered. For other outcomes, the duration of hospitalization in inpatient studies on average was shorter in probiotic groups than in control groups but there was marked heterogeneity between studies (I² = 96%; MD -18.03 hours, 95% CI -27.28 to -8.78, random-effects model: 24 trials, 4056 participants). No differences were detected between probiotic and control groups in the number of people with diarrhoea lasting ≥ 14 days (RR 0.49, 95% CI 0.16 to 1.53; 9 studies, 2928 participants) or in risk of hospitalization in community studies (RR 1.26, 95% CI 0.84 to 1.89; 6 studies, 2283 participants). No serious adverse events were attributed to probiotics.

AUTHORS' CONCLUSIONS

Probiotics probably make little or no difference to the number of people who have diarrhoea lasting 48 hours or longer, and we are uncertain whether probiotics reduce the duration of diarrhoea. This analysis is based on large trials with low risk of bias.

Intestinal microbiota: The hidden gems in the gut?

Within the last decade, our understanding of the role of the intestinal microbiota in health and disease has rapidly increased due to significant advances in next-generation sequencing technologies. Scientists have discovered more and more gut microbes with supposedly "beneficial" roles for human health and are starting to identify the underlying mechanisms. In this review, we summarize the latest knowledge about the human intestinal microbiota, including the intestinal bacteriome, virome and mycobiome. We discuss the function that recent studies attribute to the intestinal microbiota in preventing or controlling selected diseases and present recent research on biotherapeutic approaches to control these diseases.

Differential Adaptation of Propionibacterium freudenreichii CIRM-BIA129 to Cow's Milk Versus Soymilk Environments Modulates Its Stress Tolerance and Proteome

Propionibacterium freudenreichii is a beneficial bacterium that modulates the gut microbiota, motility and inflammation. It is traditionally consumed within various fermented dairy products. Changes to consumer habits in the context of food transition are, however, driving the demand for non-dairy fermented foods, resulting in a considerable development of plant-based fermented products that require greater scientific knowledge. Fermented soymilks, in particular, offer an alternative source of live probiotics. While the adaptation of lactic acid bacteria (LAB) to such vegetable substrates is well documented, little is known about that of propionibacteria. We therefore investigated the adaptation of Propionibacterium freudenreichii to soymilk by comparison to cow's milk. P. freudenreichii grew in cow's milk but not in soymilk, but it did grow in soymilk when co-cultured with the lactic acid bacterium Lactobacillus plantarum. When grown in soymilk ultrafiltrate (SUF, the aqueous phase of soymilk), P. freudenreichii cells appeared thinner and rectangular-shaped, while they were thicker and more rounded in cow's milk utltrafiltrate (MUF, the aqueous phase of cow milk). The amount of extractable surface proteins (SlpA, SlpB, SlpD, SlpE) was furthermore reduced in SUF, when compared to MUF. This included the SlpB protein, previously shown to modulate adhesion and immunomodulation in P. freudenreichii. Tolerance toward an acid and toward a bile salts challenge were enhanced in SUF. By contrast, tolerance toward an oxidative and a thermal challenge were enhanced in MUF. A whole-cell proteomic approach further identified differential expression of 35 proteins involved in amino acid transport and metabolism (including amino acid dehydrogenase, amino acid transporter), 32 proteins involved in carbohydrate transport and metabolism (including glycosyltransferase, PTS), indicating metabolic adaptation to the substrate. The culture medium also modulated the amount of stress proteins involved in stress remediation: GroEL, OpuCA, CysK, DnaJ, GrpE, in line with the modulation of stress tolerance. Changing the fermented substrate may thus significantly affect the fermentative and probiotic properties of dairy propionibacteria. This needs to be considered when developing new fermented functional foods.

Probiotics Modulate Intestinal Motility and Inflammation in Zebrafish Models

This study was aimed to assess effects of three strains of probiotics Lactobacillus acidophilus NCFM, Lactobacillus rhamnosus HN001, and Bifidobacterium animalis subsp. lactis Bi-07 on the intestinal motility and inflammation in the zebrafish models. The intestinal motility model was established using 5 days postfertilization (dpf) zebrafish administered with a fluorescent dye Nile red at 10 ng/mL for 16 h, followed by probiotics treatment for 24 h and the intestinal motility was inversely proportional to the intestinal fluorescence intensity that was quantitatively measured by image analysis. The intestinal inflammation was induced by treating 3 dpf neutrophil fluorescent zebrafish with 0.0125% of trinitrobenzenesulfonic acid for 48 h. Probiotics were administered at low, moderate, and high concentrations determined based on maximum tolerable concentration through soaking. All three strains of probiotics promoted intestinal movement, of which B. animalis subsp. lactis Bi-07 was most potent at lower concentrations. L. rhamnosus HN001 and B. animalis subsp. lactis Bi-07 had the therapeutic effects on the intestinal inflammation and the inflammation-associated mucosal damage recovery. The anti-inflammatory mechanisms of L. rhamnosus HN001 was related to both reduce inflammatory factor interleukin-6 (IL-6) and restored tissue repair factor transforming growth factor-β-1 (TGFβ-1); whereas B. animalis subsp. lactis Bi-07 was probably only associated with TGFβ-1 elevation. Using larval zebrafish models for probiotics screening and assessment would speed up product research and development and improve products' efficacy and quality.

Lactobacillus acidophilus LB: a useful pharmabiotic for the treatment of digestive disorders

Dysbiosis, a loss of balance between resident bacterial communities and their host, is associated with multiple diseases, including inflammatory bowel diseases (nonspecific chronic ulcerative colitis and Crohn's disease), and digestive functional disorders. Probiotics, prebiotics, synbiotic organisms and, more recently, pharmabiotics, have been shown to modulate the human microbiota. In this review, we provide an overview of the key concepts relating to probiotics, prebiotics, synbiotic organisms, and pharmabiotics, with a focus on available clinical evidence regarding the specific use of a unique pharmabiotic, the strain Lactobacillus acidophilus LB (Lactobacillus boucardii), for the management of gastrointestinal disorders. Since it does not contain living organisms, the administration of L. acidophilus LB is effective and safe as an adjuvant in the treatment of acute diarrhea, chronic diarrhea, and antibiotic-associated diarrhea, even in the presence of immunosuppression.

Sequential laxative-probiotic usage for treatment of irritable bowel syndrome: a novel method inspired by mathematical modelling of the microbiome

The gut microbiome plays an important role in human health. However, its response to external intervention is complex. A previous study showed that the response to Clostridium butyricum (CB) treatment of irritable bowel syndrome (IBS) is heterogeneous. We proposed that mathematical model simulation of the microbiota may help to optimize the management of IBS-associated microbiota. In this study, a novel mathematical non-extinction and defecation normalized (NEDN) model was generated for stable simulation of the dynamic nature of gut microbiota. In silico simulation revealed that a laxative may create a favourable opportunity for Clostridium cluster XIVa to shift the microbiota. An explorative clinical trial was conducted to compare three CB regimens in an IBS cohort: laxative, interval of 2 weeks and CB administration for 2 weeks (L2P); laxative immediately followed by CB administration (LP) for 2 weeks; and CB administration for 2 weeks (P). The LP regimen optimally relieved the IBS symptoms and shifted the microbiota closer to those of the healthy subjects during 2 weeks of CB intake. These results indicate that integration of biological/mathematical approaches and clinical scenarios is a promising method for management of microbiota. Additionally, the optimal effect of sequential laxative-CB usage for IBS treatment warrants further validation.

Clinical trial registration numbers: NCT02254629.

Date of registration: October 2, 2014.

Protective Role of Probiotic Supplements in Hepatic Steatosis: A Rat Model Study

Background

Treating nonalcoholic fatty liver disease (NAFLD) is considered one of the public health priorities in the past decade. So far, probiotics have represented promising results in controlling the signs and symptoms of NAFLD. However, attempts to find the ideal probiotic strain are still ongoing. The present study is designed to find the best strain amongst suitable probiotic strains according to their ability to ameliorate histopathological and oxidative stress biomarkers in hepatic steatosis-induced rats.

Methods

Initially, four probiotics species, including Lactobacillus (L.) acidophilus, L. casei, L. reuteri, and Bacillus coagulans, were cultured and prepared as a lyophilized powder for animals. The experiment lasted for fifty days. Initially, hepatic steatosis was induced by excessive ingestion of D-fructose in rats for eight weeks, followed by eight weeks of administering probiotics and D-fructose concurrently. Forty-two six-week-old male rats were alienated to different groups and were supplemented with different probiotics (1∗10⁹ CFU in 500 mL drinking water). After eight weeks, blood and liver samples were taken for further evaluation, and plasma and oxidative stress markers corresponding to liver injuries were examined.

Results

Administration of probiotics over eight weeks reversed hepatic and blood triglyceride concentration and blood glucose levels. Also, probiotics significantly suppressed markers of oxidative stress in the liver tissue.

Conclusions

Although some of the single probiotic formulations were able to mitigate oxidative stress markers, mixtures of probiotics significantly ameliorated more symptoms in the NAFLD animals. This enhanced effect might be due to probiotics' cumulative potential to maintain oxidative stress and deliver improved lipid profiles, liver function markers, and inflammatory markers.

Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial

Many clinical studies have evaluated the effect of probiotics, but only a few have assessed their dose effects on gut microbiota and host. We conducted a randomized, double-blind, controlled intervention clinical trial to assess the safety (primary endpoint) of and gut microbiota response (secondary endpoint) to the daily ingestion for 4 weeks of two doses (1 or 3 bottles/day) of a fermented milk product (Test) in 96 healthy adults. The Test product is a multi-strain fermented milk product, combining yogurt strains and probiotic candidate strains Lactobacillus paracasei subsp. paracasei CNCM I-1518 and CNCM I-3689 and Lactobacillus rhamnosus CNCM I-3690. We assessed the safety of the Test product on the following parameters: adverse events, vital signs, hematological and metabolic profile, hepatic, kidney or thyroid function, inflammatory markers, bowel habits and digestive symptoms. We explored the longitudinal gut microbiota response to product consumption and dose, by 16S rRNA gene sequencing and functional contribution by shotgun metagenomics. Safety results did not show any significant difference between the Test and Control products whatever the parameters assessed, at the two doses ingested daily over a 4-week-period. Probiotic candidate strains were detected only during consumption period, and at a significantly higher level for the three strains in subjects who consumed 3 products bottles/day. The global structure of the gut microbiota as assessed by alpha and beta-diversity, was not altered by consumption of the product for four weeks. A zero-inflated beta regression model with random effects (ZIBR) identified a few bacterial genera with differential responses to test product consumption dose compared to control. Shotgun metagenomics analysis revealed a functional contribution to the gut microbiome of probiotic candidates.

Therapeutic, Prophylactic, and Functional Use of Probiotics: A Current Perspective

Probiotics are considered as the twenty-first century panpharmacon due to their competent remedial power to cure from gastrointestinal dysbiosis, systematic metabolic diseases, and genetic impairments up to complicated neurodegenerative disorders. They paved the way for an innovative managing of various severe diseases through palatable food products. The probiotics' role as a "bio-therapy" increased their significance in food and medicine due to many competitive advantages over traditional treatment therapies. Their prophylactic and therapeutic potential has been assessed through hundreds of preclinical and clinical studies. In addition, the food industry employs probiotics as functional and nutraceutical ingredients to enhance the added value of food product in terms of increased health benefits. However, regardless of promising health-boosting effects, the probiotics' efficacy still needs an in-depth understanding of systematic mechanisms and factors supporting the healthy actions.

The Role of Probiotics, Prebiotics and Synbiotics in Combating Multidrug-Resistant Organisms

The prevalence of multidrug-resistant organisms is increasing worldwide, posing a unique challenge to global health care systems. Novel approaches are needed to combat the spread of infection with these organisms. The enteric microbiome, and in particular the resistome, offers a unique target in both the prevention of infection with these organisms and the acquisition and spread within the community. We highlight a novel approach to combat multidrug-resistant organisms: the use of prebiotics, probiotics, and synbiotics to manipulate the microbiome and resistome. This review summarizes the published literature and clinical trials related to these products to date, with a focus on efficacious trials. It highlights the probable mechanism of action for each product, as well as its safety profile in selective populations. Ultimately, although further research is needed before a definitive statement can be made on the efficacy of any of these 3 interventions, the literature to date offers new hope and a new tool in the arsenal in the fight against bacterial drug resistance.

Use of Probiotics for the Management of Acute Gastroenteritis in Children: An Update

Since the publication of the 2014 European Society for Paediatric Gastroenterology, Hepatology, and Nutrition Working Group (WG) on Probiotics and Prebiotics guidelines for the management of acute gastroenteritis (AGE), new evidence concerning the efficacy of probiotics has become available. This document provides updated recommendations on the use of probiotics for the treatment of AGE in previously presumed healthy infants and children. A systematic literature search was performed. All pooled analyses were explicitly performed for the current report. The WG graded the recommendations and assessed the certainty of the supporting evidence using the Grading of Recommendations, Assessment Development, and Evaluations tool. The recommendations were formulated if at least 2 randomized controlled trials that used a given probiotic were available. Despite the large number of identified trials, the WG could not identify 2 randomized controlled trial of high quality for any strain that provided benefit when used for treating AGE. The WG made weak recommendations for (in descending order in terms of the number of trials evaluating any given strain): Saccharomyces boulardii (low to very low certainty of evidence); Lactobacillus rhamnosus GG (very low certainty of evidence); L reuteri DSM 17938 (low to very low certainty of evidence); and L rhamnosus 19070-2 and L reuteri DSM 12246 (very low certainty of evidence). The WG made a strong recommendation against L helveticus R0052 and L rhamnosus R0011 (moderate certainty of evidence) and a weak recommendation against Bacillus clausii strains O/C, SIN, N/R, and T (very low certainty of evidence).

Evaluation of the Probiotic Properties and the Capacity to Form Biofilms of Various Lactobacillus Strains

Over the last 20 years, Lactobacillus species inhabiting the gastrointestinal tract (GIT) have received much attention, and their health-promoting properties are now well-described. Probiotic effects cannot be generalized, and their uses cover a wide range of applications. It is thus important to proceed to an accurate selection and evaluation of probiotic candidates. We evaluate the probiotic potential of six strains of Lactobacillus in different in vitro models representing critical factors of either survival, efficacy, or both. We characterized the strains for their ability to (i) modulate intestinal permeability using transepithelial electrical resistance (TEER), (ii) form biofilms and resist stressful conditions, and (iii) produce beneficial host and/or bacteria metabolites. Our data reveal the specificity of Lactobacillus strains to modulate intestinal permeability depending on the cell type. The six isolates were able to form spatially organized biofilms, and we provide evidence that the biofilm form is beneficial in a strongly acidic environment. Finally, we demonstrated the ability of the strains to produce γ-aminobutyric acid (GABA) that is involved in the gut-brain axis and beneficial enzymes that promote the bacterial tolerance to bile salts. Overall, our study highlights the specific properties of Lactobacillus strains and their possible applications as biofilms.

Clinical Trials of Probiotic Strains in Selected Disease Entities

Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. Although their mechanism of action is not clearly explained, it is known that they positively modulate the immune system, which leads to immunity potentiation. A number of studies prove that probiotics strengthen cognitive functions, reduce anxiety, and regulate the lipid metabolism in the human body. Probiotics used in humans are most often of the Lactobacillus and Bifidobacterium species. However, as more research is conducted, new species with beneficial, probiotic properties are being discovered. This paper provides a review of available information about the influence of probiotics on human health. It summarizes the current knowledge on the mechanism of action of probiotics as well as clinical trial results proving their efficacy in allergic, neurodegenerative, and cardiac diseases. This review also discusses the data concerning the safety of probiotics in clinical treatment.

Probiotics use for antibiotic-associated diarrhea: a pragmatic participatory evaluation in nursing homes

BACKGROUND

Antibiotic-associated diarrhea (AAD) occurs in 2-25% of nursing home residents, which may lead to dehydration, malnutrition, severe complications and hospitalizations. Research shows that probiotics can be effective and safe in reducing AAD. However, probiotics are not routinely used in Dutch nursing homes. The objectives of this evaluation were to develop a procedure for the implementation of probiotics to prevent AAD in nursing homes, to evaluate effects on AAD occurrence, and to evaluate the implementation process of probiotics in daily care.

METHODS

A pragmatic participatory evaluation (PPE) design was chosen, as it seemed a suitable approach for implementation of probiotics, as well as for evaluation of its effectiveness in daily nursing home practice. Probiotics administration was implemented in three nursing homes of the Rivas Zorggroep for residents with somatic and/or psychogeriatric conditions. Ninety-three residents provided data on 167 episodes of antibiotics use, of which 84 episodes that included supplementation with probiotics and 83 episodes with no probiotics supplementation. A multispecies probiotics was administered twice daily upon start of antibiotic treatment, up to 1 week after completing the antibiotics course. The occurrence of AAD was monitored and a process evaluation was conducted to assess facilitators and barriers of probiotics implementation.

RESULTS

The number of episodes with AAD when using probiotics was significantly lower than when no probiotics was used (20% vs 36%; p = 0,022, Chi-square). No significant differences in the occurrence of AAD were found between the residents taking amoxicillin/clavulanic acid or ciprofloxacin. Reported facilitators for implementation were perceived benefits of probiotics and prescription by medical staff. Reported challenges were probiotics intake by residents and individual decision-making as to which resident would benefit from it.

CONCLUSION

Successful implementation of probiotics demonstrated the prevention of AAD in nursing home residents.

TRIAL REGISTRATION

ISRCTN 94786163, retrospectively registered on 3 February 2020.

The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice

Background

Emergence of antibiotic resistance is a global public health concern. The relationships between antibiotic use, the gut community composition, normal physiology and metabolism, and individual and public health are still being defined. Shifts in composition of bacteria, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) after antibiotic treatment are not well-understood.

Methods

This project used next-generation sequencing, custom-built metagenomics pipeline and differential abundance analysis to study the effect of antibiotic monotherapy on resistome and taxonomic composition in the gut of Balb/c mice infected with E. coli via transurethral catheterization to investigate the evolution and emergence of antibiotic resistance.

Results

There is a longitudinal decrease of gut microbiota diversity after antibiotic treatment. Various ARGs are enriched within the gut microbiota despite an overall reduction of the diversity and total amount of bacteria after antibiotic treatment. Sometimes treatment with a specific class of antibiotics selected for ARGs that resist antibiotics of a completely different class (e.g. treatment of ciprofloxacin or fosfomycin selected for cepA that resists ampicillin). Relative abundance of some MGEs increased substantially after antibiotic treatment (e.g. transposases in the ciprofloxacin group).

Conclusions

Antibiotic treatment caused a remarkable reduction in diversity of gut bacterial microbiota but enrichment of certain types of ARGs and MGEs. These results demonstrate an emergence of cross-resistance as well as a profound change in the gut resistome following oral treatment of antibiotics.

Beneficial Propionibacteria within a Probiotic Emmental Cheese: Impact on Dextran Sodium Sulphate-Induced Colitis in Mice

BACKGROUNDS AND AIMS

Inflammatory Bowel Diseases (IBD), including Ulcerative Colitis (UC), coincide with alterations in the gut microbiota. Consumption of immunomodulatory strains of probiotic bacteria may induce or prolong remission in UC patients. Fermented foods, including cheeses, constitute major vectors for bacteria consumption. New evidences revealed anti-inflammatory effects in selected strains of Propionibacterium freudenreichii. We thus hypothesized that consumption of a functional cheese, fermented by such a strain, may exert a positive effect on IBD.

METHODS

We investigated the impact of cheese fermented by P. freudenreichii on gut inflammation. We developed an experimental single-strain cheese solely fermented by a selected immunomodulatory strain of P. freudenreichii, CIRM-BIA 129. We moreover produced, in industrial conditions, an Emmental cheese using the same strain, in combination with Lactobacillus delbrueckii CNRZ327 and Streptococcus thermophilus LMD-9, as starters. Consumption of both cheeses was investigated with respect to prevention of Dextran Sodium Sulphate (DSS)-induced colitis in mice.

RESULTS

Consumption of the single-strain experimental cheese, or of the industrial Emmental, both fermented by P. freudenreichii CIRM-BIA 129, reduced severity of subsequent DSS-induced colitis, weight loss, disease activity index and histological score. Both treatments, in a preventive way, reduced small bowel Immunoglobulin A (IgA) secretion, restored occludin gene expression and prevented induction of Tumor Necrosis Factor α (TNFα), Interferon γ (IFNγ) and Interleukin-17 (IL-17).

CONCLUSIONS

A combination of immunomodulatory strains of starter bacteria can be used to manufacture an anti-inflammatory cheese, as revealed in an animal model of colitis. This opens new perspectives for personalised nutrition in the context of IBD.

Systematic Review with Meta-Analysis: Lactobacillus reuteri DSM 17938 for Treating Acute Gastroenteritis in Children. An Update

The effectiveness of Lactobacillus reuteri DSM 17938 (L. reuteri) for the management of acute gastroenteritis (AGE) has been recently questioned. We performed a systematic review to update evidence on L. reuteri for treating AGE in children. We searched MEDLINE, EMBASE, the Cochrane Library databases, and additional data sources from January 2016 (end of search for our 2016 systematic review) to August 2019. The primary outcomes were stool volume and duration of diarrhea. Four RCTs were included. None of them evaluated stool volume. Compared with placebo or no treatment, L. reuteri reduced diarrhea duration (four RCTs, n = 347, mean difference, MD −0.87 days, 95% CI [−1.43, −0.31]). L. reuteri use was also associated with a reduced duration of hospitalization (three RCTs, n = 284, MD −0.54 days, 95% CI [−1.09, 0.0]). The small effect sizes of limited clinical relevance and methodological limitations of the included trials should be noted when interpreting these findings.

Propionibacterium freudenreichii CIRM-BIA 129 Osmoadaptation Coupled to Acid-Adaptation Increases Its Viability During Freeze-Drying

Propionibacterium freudenreichii is a beneficial bacterium with documented effects on the gut microbiota and on inflammation. Its presence within the animal and human intestinal microbiota was correlated with immunomodulatory effects, mediated by both propionibacterial surface components and by secreted metabolites. It is widely implemented, both in the manufacture of fermented dairy products such as Swiss-type cheeses, and in the production of probiotic food complements, under the form of freeze-dried powders. The bottleneck of this drying process consists in the limited survival of bacteria during drying and storage. Protective pre-treatments have been applied to other bacteria and may, in a strain-dependent manner, confer enhanced resistance. However, very little information was yet published on P. freudenreichii adaptation to freeze-drying. In this report, an immunomodulatory strain of this probiotic bacterium was cultured under hyperosmotic constraint in order to trigger osmoadaptation. This adaptation was then combined with acid or thermal pre-treatment. Such combination led to accumulation of key stress proteins, of intracellular compatible solute glycine betaine, to modulation of the propionibacterial membrane composition, and to enhanced survival upon freeze-drying. This work opens new perspectives for efficient production of live and active probiotic propionibacteria.

Benefits and drawbacks of osmotic adjustment in Propionibacterium freudenreichii

Propionibacterium freudenreichii is a beneficial bacterium used as a cheese starter and as a probiotic. Indeed, selected strains of P. freudenreichii combine both technological and health-promoting abilities. Moreover, during large-scale industrial production of dried bacteria and during consumption, P. freudenreichii may undergo different stressful processes. Osmotic adaptation was shown to enhance P. freudenreichii tolerance towards stresses, which are encountered during freeze-drying and during digestion. In this report, we compared the osmoadaptation molecular mechanisms of two P. freudenreichii strains. Both osmotolerance and osmoadaptation were strain-dependent and had different effects on multiple stress tolerance, depending on the presence of osmoprotectants. Availability of glycine betaine (GB) restored the growth of one of the two strains. In this strain, osmotic preadaptation enhanced heat, oxidative and acid stresses tolerance, as well as survival upon freeze-drying. However, addition of GB in the medium had deleterious effects on stress tolerance, while restoring optimal growth under hyperosmotic constraint. In the other strain, neither salt nor GB enhanced stress tolerance, which was constitutively low. Accordingly, whole cell proteomics revealed that mechanisms triggered by salt in the presence and in the absence of GB are different between strains. Osmotic adjustment may thus have deleterious effects on industrial abilities of P. freudenreichii. BIOLOGICAL SIGNIFICANCE: Propionibacteria are found in various niches including fodder, silage, rumen, milk and cheeses. This means adaptation towards different ecological environments with different physicochemical parameters. Propionibacterium freudenreichii, in particular, is furthermore used both as dairy starter and as probiotic and is thus submitted to high scale industrial production. Production and subsequent stabilization still need optimization. Drying processes like freeze-drying are stressful. Osmotic adjustments may modulated tolerance towards drying. However, they are strain-dependent, medium-dependent and may either reduce or increase stress tolerance. A case-by-case study, for each strain-medium thus seems necessary. In this work, we identify key proteins involved in osmoadaptation and give new insights into adaptation mechanisms in P. freudenreichii. This opens new perspectives for the selections of strains and for the choice of the growth medium composition.

Post-surgical intestinal dysbiosis: use of an innovative mixture (Lactobacillus plantarum LP01, Lactobacillus lactis subspecies cremoris LLC02, Lactobacillus delbrueckii LDD01)

Abdominal surgery represents a high risk for hospital-acquired infections and complication that may compromise the surgery outcome. Patients with recent abdominal surgery have an intestinal dysbiosis. There is evidence that probiotics may counterbalance the impaired microbiota. Therefore, the current survey evaluated the efficacy and safety of Abincol®, an oral nutraceutical containing a probiotic mixture with Lactobacillus plantarum LP01 (1 billion of living cells), Lactobacillus lactis subspecies cremoris LLC02 (800 millions of living cells), and Lactobacillus delbrueckii LDD01 (200 millions of living cells), in 612 outpatients (344 males and 268 females, mean age 58 years) undergoing digestive surgery. Patients took 1 stick/daily for 8 weeks. Abincol® significantly diminished the presence and the severity of intestinal symptoms and improved stool form. In conclusion, the current survey suggests that Abincol® may be considered an effective and safe therapeutic option in the management of patients undergoing digestivesurgery.

The Gut Microbiome in Inflammatory Bowel Disease: Lessons Learned From Other Immune-Mediated Inflammatory Diseases

There is a growing appreciation for the role of the gut microbiome in human health and disease. Aided by advances in sequencing technologies and analytical methods, recent research has shown the healthy gut microbiome to possess considerable diversity and functional capacity. Dysbiosis of the gut microbiota is believed to be involved in the pathogenesis of not only diseases that primarily affect the gastrointestinal tract but also other less obvious diseases, including neurologic, rheumatologic, metabolic, hepatic, and other illnesses. Chronic immune-mediated inflammatory diseases (IMIDs) represent a group of diseases that share many underlying etiological factors including genetics, aberrant immunological responses, and environmental factors. Gut dysbiosis has been reported to be common to IMIDs as a whole, and much effort is currently being directed toward elucidating microbiome-mediated disease mechanisms and their implications for causality. In this review, we discuss gut microbiome studies in several IMIDs and show how these studies can inform our understanding of the role of the gut microbiome in inflammatory bowel disease.

The Immunomodulatory Properties of Extracellular Vesicles Derived from Probiotics: A Novel Approach for the Management of Gastrointestinal Diseases

Probiotics, included in functional foods, nutritional supplements, or nutraceuticals, exhibit different beneficial effects on gut function. They are extensively used to improve the digestive processes as well as reduce the symptoms and progression of different diseases. Probiotics have shown to improve dysbiosis and modulate the immune response of the host by interacting with different cell types. Probiotics and the host can interact in a direct way, but it is becoming apparent that communication occurs also through extracellular vesicles (EVs) derived from probiotics. EVs are key for bacteria-bacteria and bacteria-host interactions, since they carry a wide variety of components that can modulate different signaling pathways, including those involved in the immune response. Interestingly, EVs are recently starting to be considered as an alternative to probiotics in those cases for which the use of live bacteria could be dangerous, such as immunocompromised individuals or situations where the intestinal barrier is impaired. EVs can spread through the mucus layer and interact with the host, avoiding the risk of sepsis. This review summarizes the existing knowledge about EVs from different probiotic strains, their properties, and their potential use for the prevention or treatment of different gastrointestinal diseases.

Probiotics in the next-generation sequencing era

Technological developments, including massively parallel DNA sequencing, gnotobiotics, metabolomics, RNA sequencing and culturomics, have markedly propelled the field of microbiome research in recent years. These methodologies can be harnessed to improve our in-depth mechanistic understanding of basic concepts related to consumption of probiotics, including their rules of engagement with the indigenous microbiome and impacts on the human host. We have recently demonstrated that even during probiotic supplementation, resident gut bacteria in a subset of individuals resist the mucosal presence of probiotic strains, limiting their modulatory effect on the microbiome and on the host gut transcriptional landscape. Resistance is partly alleviated by antibiotics treatment, which enables probiotics to interact with the host at the gut mucosal interface, although rather than promoting reconstitution of the indigenous microbiome and of the host transcriptional profile, they inhibit these components from returning to their naïve pre-antibiotic configurations. In this commentary, we discuss our findings in the context of previous and recent works, and suggest that incorporating the state-of-the-art methods currently utilized in microbiome research into the field of probiotics may lead to improved understanding of their mechanisms of activity, as well as their efficacy and long-term safety.

Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling

Probiotic products are becoming more prevalent as awareness of the role of beneficial microbes in health increases. Ingredient labels of these products often omit identifications at the strain level, making it difficult to track down applicable published research. In this study, we investigated whether products labeled with the same species name contained different strains of those species. From 21 commercially available probiotic supplements and beverages, we cultured five main species: Bacillus coagulans, Bacillus subtilis, Lactobacillus plantarum, Lactobacillus rhamnosus, and the yeast Saccharomyces boulardii. To confirm the identity of each bacterial isolate, we applied standard molecular approaches: 16S rRNA gene sequencing and Matrix Assisted Laser Desorption Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS). Phenotypic profiling and identification were performed with the Biolog Microbial Identification system. All of the bacterial isolates were correctly identified by at least one approach. Sequencing the 16S rRNA gene led to 82% of species identifications matching the product label, with 71% of isolates identified by MALDI-TOF MS and 60% identified correctly with the Biolog system. Analysis of the Biolog phenotypic profiles revealed different patterns of carbon source usage by each species, with sugars preferentially utilized by all except B. subtilis. To assess the strain-level differences, we compared strains of the same species and found variability in carbohydrate utilization and tolerance to environmental stressors (salt, acidity, antibiotics). By demonstrating that products listing the same species often contain strains with different 16S sequences and phenotypes, this study highlights that current labels of probiotic supplements do not sufficiently convey the strain diversity in these products.