Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection

The dual action of probiotic lactobacilli in suppressing virulence and survival of Arcobacter butzleri

Arcobacter butzleri is a widely distributed foodborne and waterborne pathogen, increasingly recognized as an emerging enteropathogen. Understanding its survival mechanisms and interactions with probiotics is crucial for developing targeted intervention strategies. A. butzleri must withstand various hostile conditions to successfully colonize the gastrointestinal tract, including inhibition by probiotics, such as Limosilactobacillus reuteri, Lactobacillus acidophilus and Lactiplantibacillus plantarum. Thus, this study aimed to assess the survival of A. butzleri under acidic conditions and determine its minimum inhibitory concentration (MIC) for bile salts. Additionally, the antimicrobial potential of the lactobacilli strains was evaluated by analysing the effects of their culture-free supernatant (CFS) on A. butzleri growth, coculture interactions, and biofilm formation. The influence of lactobacilli on A. butzleri was further investigated through competition, displacement and exclusion assays using Caco-2 cell models. The results indicate that lactobacilli strains exhibit tolerance to acidic environments and physiological bile salt concentrations, whereas A. butzleri was more susceptible to acidic stress. The antagonistic effect of lactobacilli was evidenced by growth inhibition of A. butzleri in the presence of CFS or during coculture. However, CFS from certain lactobacilli strains was found to enhance biofilm formation, highlighting potential consequences. Furthermore, while lactobacilli did not demonstrate significant antagonistic effects in competition assays, they effectively displaced and excluded A. butzleri in the Caco-2 infection model. Overall, these findings suggest that probiotic lactobacilli can inhibit A. butzleri growth, yet their impact on its virulence remains uncertain. This underscores the need for strain-specific probiotic selection to effectively target this pathogen and emphasizes that not every probiotic contribute to the prevention of A. butzleri infections.

Prevention and treatment of antibiotics-associated adverse effects through the use of probiotics: A review

BACKGROUND

The human gut hosts a diverse microbial community, essential for maintaining overall health. However, antibiotics, commonly prescribed for infections, can disrupt this delicate balance, leading to antibiotic-associated diarrhea, inflammatory bowel disease, obesity, and even neurological disorders. Recognizing this, probiotics have emerged as a promising strategy to counteract these adverse effects.

AIM OF REVIEW

This review aims to offer a comprehensive overview of the latest evidence concerning the utilization of probiotics in managing antibiotic-associated side effects.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Probiotics play a crucial role in preserving gut homeostasis, regulating intestinal function and metabolism, and modulating the host immune system. These mechanisms serve to effectively alleviate antibiotic-associated adverse effects and enhance overall well-being.

Bioengineered Probiotics for Clostridioides difficile Infection: An Overview of the Challenges and Potential for This New Treatment Approach

The rapid increase in microbial antibiotic resistance in Clostridioides difficile (C. difficile) strains and the formation of hypervirulent strains have been associated with a global increase in the incidence of C. difficile infection (CDI) and subsequently, an increase in the rate of recurrence. These consequences have led to an urgent need to develop new and promising alternative strategies to control this pathogen. Engineered probiotics are exciting new bacterial strains produced by editing the genome of the original probiotics. Recently, engineered probiotics have been used to develop delivery vehicles for vaccines, diagnostics, and therapeutics. Recent studies have demonstrated engineered probiotics may potentially be an effective approach to control or treat CDI. This review provides a brief overview of the considerations for engineered probiotics for medicinal use, with a focus on recent preclinical research using engineered probiotics to prevent or treat CDI. We also address the challenges faced in the production of engineered strains and how they may be overcome in the application of these agents to meet patient needs in the future.

Probiotic use reduces the incidence of antibiotic-associated diarrhea among adult patients: a meta-analysis

Introduction

Probiotics potentially mitigate diarrhea incidence and severity, but their effectiveness in antibiotic-associated diarrhea (AAD) remains debated.

Aim

This meta-analysis aimed to enhance evidence on probiotic use for AAD.Methods: A systematic search of randomized controlled trials (RCTs) from 2010 to 2023 in PubMed, EMBASE, Scopus, and Google Scholar was conducted. Eligible studies underwent risk assessment with the RoB-2 tool and data extraction using the random effects model. Subgroup analyses evaluated age, sample size, and probiotic strains' influence.

Results

Fifteen trials with 7427 participants were included. Overall quality was moderate. Pooled analysis favored probiotics, reducing AAD incidence by 40% (RR = 0.60, 95% CI: 0.43-0.82). This effect was consistent across subgroup analyses. Multistrain probiotics showed superior protection (RR = 0.40 vs. 0.9 or 0.6 for dual or single strains).

Conclusions

This review suggests that probiotics, especially multistrain combinations, mitigate AAD incidence. Future large-scale RCTs will address heterogeneity.

Antibiotic-perturbed microbiota and the role of probiotics

The disruptive effect of antibiotics on the composition and function of the human microbiota is well established. However, the hypothesis that probiotics can help restore the antibiotic-disrupted microbiota has been advanced, with little consideration of the strength of evidence supporting it. Some clinical data suggest that probiotics can reduce antibiotic-related side effects, including Clostridioides difficile-associated diarrhoea, but there are no data that causally link these clinical effects to microbiota protection or recovery. Substantial challenges hinder attempts to address this hypothesis, including the absence of consensus on the composition of a 'normal' microbiota, non-standardized and evolving microbiome measurement methods, and substantial inter-individual microbiota variation. In this Review, we explore these complexities. First, we review the known benefits and risks of antibiotics, the effect of antibiotics on the human microbiota, the resilience and adaptability of the microbiota, and how microbiota restoration might be defined and measured. Subsequently, we explore the evidence for the efficacy of probiotics in preventing disruption or aiding microbiota recovery post-antibiotic treatment. Finally, we offer insights into the current state of research and suggest directions for future research.

Modulation of gut-microbiota through probiotics and dietary interventions to improve host health

Dietary patterns play an important role in regards to the modulation and control of the gut microbiome composition and function. The interaction between diet and microbiota plays an important role in order to maintain intestinal homeostasis, which ultimately affect the host's health. Diet directly impacts the microbes that inhabit the gastrointestinal tract (GIT), which then contributes to the production of secondary metabolites, such as short-chain fatty acids, neurotransmitters, and antimicrobial peptides. Dietary consumption with genetically modified probiotics can be the best vaccine delivery vector and protect cells from various illnesses. A holistic approach to disease prevention, treatment, and management takes these intrinsically linked diet-microbes, microbe-microbe interactions, and microbe-host interactions into account. Dietary components, such as fiber can modulate beneficial gut microbiota, and they have resulting ameliorative effects against metabolic disorders. Medical interventions, such as antibiotic drugs can conversely have detrimental effects on gut microbiota by disputing the balance between Bacteroides and firmicute, which contribute to continuing disease states. We summarize the known effects of various dietary components, such as fibers, carbohydrates, fatty acids, vitamins, minerals, proteins, phenolic acids, and antibiotics on the composition of the gut microbiota in this article in addition to the beneficial effect of genetically modified probiotics and consequentially their role in regards to shaping human health. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Gut Microbiota-Gut Metabolites and Clostridioides difficile Infection: Approaching Sustainable Solutions for Therapy

Clostridioides difficile (C. difficile) infection (CDI) is the most common hospital-acquired infection. With the combination of a high rate of antibiotic resistance and recurrence, it has proven to be a debilitating public health threat. Current treatments for CDI include antibiotics and fecal microbiota transplantation, which contribute to recurrent CDIs and potential risks. Therefore, there is an ongoing need to develop new preventative treatment strategies for CDI. Notably, gut microbiota dysbiosis is the primary risk factor for CDI and provides a promising target for developing novel CDI therapy approaches. Along with gut microbiota dysbiosis, a reduction in important gut metabolites like secondary bile acids and short-chain fatty acids (SCFAs) were also seen in patients suffering from CDI. In this review study, we investigated the roles and mechanisms of gut microbiota and gut microbiota-derived gut metabolites, especially secondary bile acids and SCFAs in CDI pathogenesis. Moreover, specific signatures of gut microbiota and gut metabolites, as well as different factors that can modulate the gut microbiota, were also discussed, indicating that gut microbiota modulators like probiotics and prebiotics can be a potential therapeutic strategy for CDI as they can help restore gut microbiota and produce gut metabolites necessary for a healthy gut. The understanding of the associations between gut microbiota-gut metabolites and CDI will allow for developing precise and sustainable approaches, distinct from antibiotics and fecal transplant, for mitigating CDI and other gut microbiota dysbiosis-related diseases.

Evidence of the Beneficial Impact of Three Probiotic-Based Food Supplements on the Composition and Metabolic Activity of the Intestinal Microbiota in Healthy Individuals: An Ex Vivo Study

Scientific evidence has increasingly supported the beneficial effects of probiotic-based food supplements on human intestinal health. This ex vivo study investigated the effects on the composition and metabolic activity of the intestinal microbiota of three probiotic-based food supplements, containing, respectively, (1) Bifidobacterium longum ES1, (2) Lactobacillus acidophilus NCFM®, and (3) a combination of L. acidophilus NCFM®, Lactobacillus paracasei Lpc-37™, Bifidobacterium lactis Bi-07™, and Bifidobacterium lactis Bl-04™. This study employed fecal samples from six healthy donors, inoculated in a Colon-on-a-plate® system. After 48 h of exposure or non-exposure to the food supplements, the effects were measured on the overall microbial fermentation (pH), changes in microbial metabolic activity through the production of short-chain and branched-chain fatty acids (SCFAs and BCFAs), ammonium, lactate, and microbial composition. The strongest effect on the fermentation process was observed for the combined formulation probiotics, characterized by the significant stimulation of butyrate production, a significant reduction in BCFAs and ammonium in all donors, and a significant stimulatory effect on bifidobacteria and lactobacilli growth. Our findings suggest that the combined formulation probiotics significantly impact the intestinal microbiome of the healthy individuals, showing changes in metabolic activity and microbial abundance as the health benefit endpoint.

Human Gut Microbiota in Heart Failure: Trying to Unmask an Emerging Organ

There is a bidirectional relationship between the heart and the gut. The gut microbiota, the community of gut micro-organisms themselves, is an excellent gut-homeostasis keeper since it controls the growth of potentially harmful bacteria and protects the microbiota environment. There is evidence suggesting that a diet rich in fatty acids can be metabolized and converted by gut microbiota and hepatic enzymes to trimethyl-amine N-oxide (TMAO), a product that is associated with atherogenesis, platelet dysfunction, thrombotic events, coronary artery disease, stroke, heart failure (HF), and, ultimately, death. HF, by inducing gut ischemia, congestion, and, consequently, gut barrier dysfunction, promotes the intestinal leaking of micro-organisms and their products, facilitating their entrance into circulation and thus stimulating a low-grade inflammation associated with an immune response. Drugs used for HF may alter the gut microbiota, and, conversely, gut microbiota may modify the pharmacokinetic properties of the drugs. The modification of lifestyle based mainly on exercise and a Mediterranean diet, along with the use of pre- or probiotics, may be beneficial for the gut microbiota environment. The potential role of gut microbiota in HF development and progression is the subject of this review.

Probiotic supplementation during antibiotic treatment is unjustified in maintaining the gut microbiome diversity: a systematic review and meta-analysis

BACKGROUND

Probiotics are often used to prevent antibiotic-induced low-diversity dysbiosis, however their effect is not yet sufficiently summarized in this regard. We aimed to investigate the effects of concurrent probiotic supplementation on gut microbiome composition during antibiotic therapy.

METHODS

We performed a systematic review and meta-analysis of randomized controlled trials reporting the differences in gut microbiome diversity between patients on antibiotic therapy with and without concomitant probiotic supplementation. The systematic search was performed in three databases (MEDLINE (via PubMed), Embase, and Cochrane Central Register of Controlled Trials (CENTRAL)) without filters on 15 October 2021. A random-effects model was used to estimate pooled mean differences (MD) with 95% confidence intervals (CI). This review was registered on PROSPERO (CRD42021282983).

RESULTS

Of 11,769 identified articles, 15 were eligible in the systematic review and 5 in the meta-analyses. Quantitative data synthesis for Shannon (MD = 0.23, 95% CI: [(-)0.06-0.51]), Chao1 (MD = 11.59 [(-)18.42-41.60]) and observed OTUs (operational taxonomic unit) (MD = 17.15 [(-)9.43-43.73]) diversity indices revealed no significant difference between probiotic supplemented and control groups. Lacking data prevented meta-analyzing other diversity indices; however, most of the included studies reported no difference in the other reported α- and ß-diversity indices between the groups. Changes in the taxonomic composition varied across the eligible studies but tended to be similar in both groups. However, they showed a potential tendency to restore baseline levels in both groups after 3-8 weeks. This is the first meta-analysis and the most comprehensive review of the topic to date using high quality methods. The limited number of studies and low sample sizes are the main limitations of our study. Moreover, there was high variability across the studies regarding the indication of antibiotic therapy and the type, dose, and duration of antimicrobials and probiotics.

CONCLUSIONS

Our results showed that probiotic supplementation during antibiotic therapy was not found to be influential on gut microbiome diversity indices. Defining appropriate microbiome diversity indices, their standard ranges, and their clinical relevance would be crucial.

Efficacy of Omadacycline or Vancomycin Combined With Germinants for Preventing Clostridioides difficile Relapse in a Murine Model

BACKGROUND

Clostridioides difficile infections (CDI) and recurrence (rCDI) are major health care burdens. Recurrence is likely caused by spores in the gastrointestinal tract that germinate after antibiotic therapy. This murine study explores germinant-antibiotic combinations for CDI.

METHODS

Previously described murine models were evaluated using C. difficile VPI 10463. The severe model compared omadacycline versus vancomycin in survival, weight loss, clinical scoring, and C. difficile toxin production. The nonsevere model compared these antibiotics with and without germinants (solution of sodium taurocholate, taurine, sodium docusate, calcium gluconate). Additionally, colon histopathology, bile acid analysis, environmental/spore shedding, and 16S sequencing was evaluated.

RESULTS

In the severe model, omadacycline-treated mice had 60% survival versus 13.3% with vancomycin (hazard ratio [HR], 0.327; 95% confidence interval [CI],.126-.848; P = .015) along with decreased weight loss, and disease severity. In the nonsevere model, all mice survived with antibiotic-germinant treatment versus 60% antibiotics alone (HR, 0.109; 95% CI, .02-.410; P = .001). Omadacycline resulted in less changes in bile acids and microbiota composition. Germinant-treated mice showed no signs of rCDI, spore shedding, or significant toxin production at 15 days.

CONCLUSIONS

In murine models of CDI, omadacycline improved survival versus vancomycin. Germinant-antibiotic combinations were more effective at preventing rCDI compared to antibiotics alone without inducing toxin production.

Recombinant Probiotic Preparations: Current State, Development and Application Prospects

The article is devoted to the latest achievements in the field of research, development, and implementation of various types of medicinal products based on recombinant probiotics. The benefits of probiotics, their modern use in medicine along with the most frequently used genera and species of probiotic microorganisms were highlighted. The medicinal and therapeutic activities of the studied probiotics were indicated. The review suggests various methods of creating recombinant probiotic microorganisms, including standard genetic engineering methods, as well as systems biology approaches and new methods of using the CRISPR-Cas system. The range of potential therapeutic applications of drugs based on recombinant probiotics was proposed. Special attention was paid to modern research on the creation of new, more effective recombinant probiotics that can be used for various therapeutic purposes. Considering the vast diversity of therapeutic applications of recombinant probiotics and ambiguous functions, their use for the potential treatment of various common human diseases (non-infectious and infectious diseases of the gastrointestinal tract, metabolic disorders, and allergic conditions) was investigated. The prospects for creating different types of vaccines based on recombinant probiotics together with the prospects for their implementation into medicine were considered. The possibilities of using recombinant probiotics in veterinary medicine, particularly for the prevention of domestic animal diseases, were reviewed. The prospects for the implementation of recombinant probiotics as vaccines and diagnostic tools for testing certain diseases as well as modeling the work of the human digestive system were highlighted. The risks of creation, application, including the issues related to the regulatory sphere regarding the use of new recombinant microorganisms, which can potentially enter the environment and cause unforeseen circumstances, were outlined.

Effect of adding probiotics to an antibiotic intervention on the human gut microbial diversity and composition: a systematic review

Introduction. Millions of antibiotic prescriptions are written annually in the USA.

Gap Statement. Probiotics reduce antibiotic-induced gastrointestinal side effects; however, the effect of probiotics on preserving gut microbial composition in response to antibiotics is not well understood.

Aim. To evaluate whether the addition of probiotics is capable of reverting the changes in alpha diversity and gut microbial composition commonly observed in adult participants receiving antibiotics.

Methodology. A search was conducted by two researchers following the PRISMA guidelines using PubMed, Science Direct, Cochrane and Embase from January to December 2021 with the following inclusion criteria: (i) randomized clinical trials assessing the effect of antibiotics, probiotics or antibiotics+probiotics; (ii) 16S rRNA; (iii) adult participants; and (iv) in English. Once data was extracted in tables, a third researcher compared, evaluated and merged the collected data. The National Institutes of Health (NIH) rating system was utilized to analyse risk of bias.

Results. A total of 29 articles (n=11 antibiotics, n=11 probiotics and n=7 antibiotics+probiotics) met the inclusion criteria. The lack of standardization of protocols to analyse the gut microbial composition and the wide range of selected antibiotics/probiotics complicated data interpretation; however, despite these discrepancies, probiotic co-administration with antibiotics seemed to prevent some, but not all, of the gut microbial diversity and composition changes induced by antibiotics, including restoration of health-related bacteria such as Faecalibacterium prausnitzii .

Conclusion. Addition of probiotics to antibiotic interventions seems to preserve alpha diversity and ameliorate the changes to gut microbial composition caused by antibiotic interventions.

The effect of probiotics on postsurgical complications in patients with colorectal cancer: a systematic review and meta-analysis

Context

Clinical trials have investigated the effect of probiotics on postsurgical complications in colorectal cancer (CRC). However, so far, there are no systematic reviews evaluating the effect of probiotics and synbiotics on the clinical or infectious postsurgical complications of colorectal cancer.

Objective

The objective of this review was to synthesize the best available evidence on the effects of the use of probiotics or synbiotics on pre-, peri-, and post-operative complications of CRC surgical resection.

Data Sources

A search of the PubMed, Embase, LILACS, Scopus, Cochrane, Web of Science, ProQuest, and Google Scholar databases was conducted for clinical trials published up until January 2022.

Data Extraction

The population characteristics, period and protocol of supplementation, and postoperative complications were extracted and reported. A random-effects model was used to estimate the effect of probiotic and synbiotic treatment on these variables.

Data Synthesis

In total, 2518 studies were identified, of which 16 were included in the qualitative synthesis and 13 in the meta-analysis. Overall, probiotic supplementation reduced the incidence of ileus (odds ratio [OR] = .13, 95% confidence interval [CI]: .02, .78), diarrhea (OR = .32, 95% CI: .15, .69), abdominal collection (OR: .35, 95% CI: .13, .92), sepsis (OR = .41, 95% CI: .22, .80), pneumonia (OR = .39, 95% CI: .19, .83), and surgical site infection (OR = .53, 95% CI: .36, .78). The results of the subgroup analysis indicated that lower dose (<109 colony-forming units), higher duration of supplementation (>14 days), and being administrated ≤5 days before and >10 days after surgery was more effective at reducing the incidence of surgical site infection.

Conclusion

Probiotics and synbiotics seem to be a promising strategy for the prevention of postoperative complications after CRC surgery. Larger, high-quality randomized controlled trials are needed to establish the optimal treatment protocol for the use of probiotics and synbiotics in preventing postoperative complications for CRC surgery.

Plasma Microbiome in COVID-19 Subjects: An Indicator of Gut Barrier Defects and Dysbiosis

The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) complications. We aimed to investigate whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n = 146) and healthy individuals (n = 47) were collected during hospitalization and routine visits. Plasma microbiome was analyzed using 16S rRNA sequencing and gut permeability markers including fatty acid binding protein 2 (FABP2), peptidoglycan (PGN), and lipopolysaccharide (LPS) in both patient cohorts. Plasma samples of both cohorts contained predominately Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria. COVID-19 subjects exhibit significant dysbiosis (p = 0.001) of the plasma microbiome with increased abundance of Actinobacteria spp. (p = 0.0332), decreased abundance of Bacteroides spp. (p = 0.0003), and an increased Firmicutes:Bacteroidetes ratio (p = 0.0003) compared to healthy subjects. The concentration of the plasma gut permeability marker FABP2 (p = 0.0013) and the gut microbial antigens PGN (p < 0.0001) and LPS (p = 0.0049) were significantly elevated in COVID-19 patients compared to healthy subjects. These findings support the notion that the intestine may represent a source for bacteremia and contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.

Probiotics or Synbiotics for Preventing Postoperative Infection in Hepatopancreatobiliary Cancer Patients: A Meta-Analysis of Randomized Controlled Trials

OBJECTIVE

Postoperative infection of hepatopancreatobiliary cancer (HPBC) is a major cause of morbidity and mortality. Probiotics and synbiotics are potential prevention strategies, but evidence on the efficacy of probiotics or synbiotics in the prevention of postoperative infection for HPBC remains controversial. This study aimed to define the impact of probiotics or synbiotics on the incidence of postoperative infection in HPBC patients.

METHODS

A systematic search of the Cochrane Library, PubMed, Embase, and Web of Science databases was conducted from inception to February 2, 2021 to identify randomized controlled trials (RCTs) evaluating the efficacy of probiotics or synbiotics in HPBC. Data were pooled and expressed as the risk ratio (RR) and mean difference (MD) with 95% confidence intervals.

RESULTS

Eight RCTs involving 445 participants were included. Supplementation with probiotics or synbiotics significantly reduced the incidence of postoperative infection (RR 0.55) in HPBC patients, and both probiotics (RR 0.68) and synbiotics (RR 0.41) were effective in reducing the incidence of postoperative infection. In addition, probiotics or synbiotics can reduce duration of antibiotic use (MD -3.52) and length of hospital stay (MD -4.21).

CONCLUSION

Probiotics or synbiotics are effective strategies for the prevention of postoperative infection in HPBC patients.

Translating Microbiome Research From and To the Clinic

Extensive research has elucidated the influence of the gut microbiota on human health and disease susceptibility and resistance. We review recent clinical and laboratory-based experimental studies associating the gut microbiota with certain human diseases. We also highlight ongoing translational advances that manipulate the gut microbiota to treat human diseases and discuss opportunities and challenges in translating microbiome research from and to the bedside.

Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Nutritional and therapeutic approaches for protecting human gut microbiota from psychotropic treatments

Emerging evidence highlighted the essential role played by the microbiota-gut-brain axis in maintaining human homeostasis, including nutrition, immunity, and metabolism. Much recent work has linked the gut microbiota to many psychiatric and neurodegenerative disorders such as depression, schizophrenia, and Alzheimer's disease. Shared gut microbiota alterations or dysbiotic microbiota have been identified in these separate disorders relative to controls. Much attention has focused on the bidirectional interplay between the gut microbiota and the brain, establishing gut dysbiotic status as a critical factor in psychiatric disorders. Still, the antibiotic-like effect of psychotropic drugs, medications used for the treatment of these disorders, on gut microbiota is largely neglected. In this review, we summarize the current findings on the impact of psychotropics on gut microbiota and how their antimicrobial potency can trigger dysbiosis. We also discuss the potential therapeutic strategies, including probiotics, prebiotics, and fecal transplantation, to attenuate the dysbiosis related to psychotropics intake.

Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus)

BACKGROUND

Acute hepatopancreatic necrosis disease (AHPND) is an important shrimp bacterial disease caused by some Vibrio species. The severity of the impact of this disease on aquaculture worldwide has made it necessary to develop alternatives to prophylactic antibiotics use, such as the application of probiotics. To assess the potential to use probiotics in order to limit the detrimental effects of AHNPD, we evaluated the effect of the ILI strain, a Vibrio sp. bacterium and efficient shrimp probiotic, using metabarcoding (16S rRNA gene) on the gastrointestinal microbiota of shrimp after being challenged with AHPND-causing V. parahaemolyticus.

RESULTS

We showed how the gastrointestinal microbiome of shrimp varied between healthy and infected organisms. Nevertheless, a challenge of working with AHPND-causing Vibrio pathogens and Vibrio-related bacteria as probiotics is the potential risk of the probiotic strain becoming pathogenic. Consequently, we evaluated whether ILI strain can acquire the plasmid pV-AHPND via horizontal transfer and further cause the disease in shrimp. Conjugation assays were performed resulting in a high frequency (70%) of colonies harboring the pv-AHPND. However, no shrimp mortality was observed when transconjugant colonies of the ILI strain were used in a challenge test using healthy shrimp. We sequenced the genome of the ILI strain and performed comparative genomics analyses using AHPND and non-AHPND Vibrio isolates. Using available phylogenetic and phylogenomics analyses, we reclassified the ILI strain as Vibrio diabolicus. In summary, this work represents an effort to study the role that probiotics play in the normal gastrointestinal shrimp microbiome and in AHPND-infected shrimp, showing that the ILI probiotic was able to control pathogenic bacterial populations in the host's gastrointestinal tract and stimulate the shrimp's survival. The identification of probiotic bacterial species that are effective in the host's colonization is important to promote animal health and prevent disease.

CONCLUSIONS

This study describes probiotic bacteria capable of controlling pathogenic populations of bacteria in the shrimp gastrointestinal tract. Our work provides new insights into the complex dynamics between shrimp and the changes in the microbiota. It also addresses the practical application of probiotics to solve problems with pathogens that cause high mortality-rate in shrimp farming around the world. Video Abstract.

Understanding the host-microbe interactions using metabolic modeling

The human gut harbors an enormous number of symbiotic microbes, which is vital for human health. However, interactions within the complex microbiota community and between the microbiota and its host are challenging to elucidate, limiting development in the treatment for a variety of diseases associated with microbiota dysbiosis. Using in silico simulation methods based on flux balance analysis, those interactions can be better investigated. Flux balance analysis uses an annotated genome-scale reconstruction of a metabolic network to determine the distribution of metabolic fluxes that represent the complete metabolism of a bacterium in a certain metabolic environment such as the gut. Simulation of a set of bacterial species in a shared metabolic environment can enable the study of the effect of numerous perturbations, such as dietary changes or addition of a probiotic species in a personalized manner. This review aims to introduce to experimental biologists the possible applications of flux balance analysis in the host-microbiota interaction field and discusses its potential use to improve human health. Video abstract.

The prophylactic effects of BIFICO on the antibiotic-induced gut dysbiosis and gut microbiota

Background

The aim of this study is to evaluate the prophylactic effects of probiotic mixture BIFICO on antibiotic-induced gut dysbiosis (AIGD) and the influence on the change of the gut microbiota.

Methods

We conducted a prospective, randomized, controlled study and divided 196 patients who required intravenous beta-lactam antibiotics into three groups: a control group (no probiotics), a regular group (840 mg of BIFICO), and a double-dosage group (1680 mg of BIFICO). The symptoms of antibiotic-related diarrhea, bloating and abdominal pain and the incidence of AIGD were evaluated 7 days and 8–14 days after antibiotic use, with 10 patients in each group. 16S rDNA sequencing was performed to detect changes of the gut microbiota.

Results

Within 7 days of the initiation of antibiotic treatment, the incidences of AIGD in the control group, regular group (840 mg of BIFICO), and double-dosage group (1680 mg of BIFICO) were 21.88%, 14.93%, and 6.15% respectively. On days of 8–14th, the incidences of AIGD in the control group, regular group, and double-dosage group were 25%, 14.93%, and 4.62%, respectively. The incidence of AIGD in the double-dosage group within 7 days and 14 days were both significantly lower than that in relevant control group (P < 0.05). On day 14, the incidence of AIGD in the double-dosage group was lower than that in the regular group (P < 0.05). The number of operational taxonomic units (OTUs) in the control group after antibiotic treatment was significantly reduced compared to that prior to treatment, while those of the regular and double-dosage groups were stable. The species abundance, especially Parabacteroides, Phascolarctobacterium and Roseburia, of the double-dosage group was greater than that of the regular group and the control group.

Conclusions

BIFICO may reduce the occurrence of AIGD in a dose-dependent manner and can stabilize the gut microbiota balance.

Gut microbiota remodeling reverses aging-associated inflammation and dysregulation of systemic bile acid homeostasis in mice sex-specifically

Aging is usually characterized with inflammation and disordered bile acids (BAs) homeostasis, as well as gut dysbiosis. The pathophysiological changes during aging are also sexual specific. However, it remains unclear about the modulating process among gut microbiota, BA metabolism, and inflammation during aging. In this study, we established a direct link between gut microbiota and BA profile changes in the liver, serum, and four intestinal segments of both sexes during aging and gut microbiota remodeling by co-housing old mice with young ones. We found aging reduced Actinobacteria in male mice but increased Firmicutes in female mice. Among the top 10 altered genera with aging, 4 genera changed oppositely between male and female mice, and most of the changes were reversed by co-housing in both sexes. Gut microbiota remodeling by co-housing partly rescued the systemically dysregulated BA homeostasis induced by aging in a sex- and tissue-specific manner. Aging had greater impacts on hepatic BA profile in females, but intestinal BA profile in males. In addition, aging increased hepatic and colonic deoxycholic acid in male mice, but reduced them in females. Moreover, muricholic acids shifted markedly in the intestine, especially in old male mice, and partially reversed by co-housing. Notably, the ratios of primary to secondary BAs in the liver, serum, and all four intestinal segments were increased in old mice and reduced by co-housing in both sexes. Together, the presented data revealed that sex divergent changes of gut microbiota and BA profile in multiple body compartments during aging and gut microbiota remodeling, highlighting the sex-specific prevention and treatment of aging-related disorders by targeting gut microbiota-regulated BA metabolism should particularly be given more attention.

Probiotics, Prebiotics, Synbiotics, Postbiotics, and Obesity: Current Evidence, Controversies, and Perspectives

PURPOSE OF REVIEW

In this review, we summarize current evidence on gut microbiome and obesity; we discuss the role of probiotics, prebiotics, synbiotics, and postbiotics in obesity prevention and management; and we highlight and analyze main limitations, challenges, and controversies of their use.

RECENT FINDINGS

Overall, the majority of animal studies and meta-analyses of human studies examining the use of probiotics and synbiotics in obesity has shown their beneficial effects on weight reduction and other metabolic parameters via their involvement in gut microbiota modulation. Bifidobacterium and Lactobacillus strains are still the most widely used probiotics in functional foods and dietary supplements, but next generation probiotics, such as Faecalibacterium prausnitzii, Akkermansia muciniphila, or Clostridia strains, have demonstrated promising results. On the contrary, meta-analyses of human studies on the use of prebiotics in obesity have yielded contradictory results. In animal studies, postbiotics, mainly short-chain fatty acids, may increase energy expenditure through induction of thermogenesis in brown adipose tissue as well as browning of the white adipose tissue. The main limitations of studies on biotics in obesity include the paucity of human studies; heterogeneity among the studied subgroups regarding age, gender, and lifestyle; and use of different agents with potential therapeutic effects in different formulations, doses, ratio and different pharmacodynamics/pharmacokinetics. In terms of safety, the supplementation with prebiotics, probiotics, and synbiotics has not been associated with serious adverse effects among immune-competent individuals, with the exception of the use of probiotics and synbiotics in immunocompromised patients. Further large-scale Randomized Controlled Trials (RCTs) in humans are required to evaluate the beneficial properties of probiotics, prebiotics, synbiotics, and postbiotics; their ideal dose; the duration of supplementation; and the durability of their beneficial effects as well as their safety profile in the prevention and management of obesity.

A prospective longitudinal study on the microbiota composition in amyotrophic lateral sclerosis

BACKGROUND

A connection between amyotrophic lateral sclerosis (ALS) and altered gut microbiota composition has previously been reported in animal models. This work is the first prospective longitudinal study addressing the microbiota composition in ALS patients and the impact of a probiotic supplementation on the gut microbiota and disease progression.

METHODS

Fifty patients and 50 matched controls were enrolled. The microbial profile of stool samples from patients and controls was analyzed via PCR-Denaturing Gradient Gel Electrophoresis, and the main microbial groups quantified via qPCR. The whole microbiota was then analyzed via next generation sequencing after amplification of the V3-V4 region of 16S rDNA. Patients were then randomized to receive probiotic treatment or placebo and followed up for 6 months with ALSFRS-R, BMI, and FVC%.

RESULTS

The results demonstrate that the gut microbiota of ALS patients is characterized by some differences with respect to controls, regardless of the disability degree. Moreover, the gut microbiota composition changes during the course of the disease as demonstrated by the significant decrease in the number of observed operational taxonomic unit during the follow-up. Interestingly, an unbalance between potentially protective microbial groups, such as Bacteroidetes, and other with potential neurotoxic or pro-inflammatory activity, such as Cyanobacteria, has been shown. The 6-month probiotic treatment influenced the gut microbial composition; however, it did not bring the biodiversity of intestinal microbiota of patients closer to that of control subjects and no influence on the progression of the disease measured by ALSFRS-R was demonstrated.

CONCLUSIONS

Our study poses the bases for larger clinical studies to characterize the microbiota changes as a novel ALS biomarker and to test new microbial strategy to ameliorate the health status of the gut.

TRIAL REGISTRATION

CE 107/14, approved by the Ethics Committee of the "Maggiore della Carità" University Hospital, Italy.

In Vitro Bactericidal Effects of Photodynamic Therapy Combined with Four Tetracyclines against Clostridioides difficile KCTC5009 in Planktonic Cultures

Surface disinfection in health-care facilities is critical to prevent dissemination of Clostridioides difficile (C. difficile). Tetracyclines (TCs) are broad-spectrum antibiotics that are associated with a low risk of development of C. difficile infection (CDI) and are used as photosensitizers (PS) in photodynamic therapy (PDT). We evaluated whether TCs may be useful environmental cleansing agents. We compared the in vitro ability to kill C. difficile of four TCs (TC, doxycycline, minocycline, and tigecycline) combined with PDT using ultraviolet A (UVA). We included chitosan, a cationic material, as a booster to increase the photodynamic bactericidal efficacy of TCs. PDT-induced bactericidal effects were assessed by the number of viable cells and the degree of DNA damage and membrane integrity. To avoid the intrinsic antibacterial activity of TCs at high concentrations, we used low concentrations of TCs (0.05 and 0.1 mg/mL). The bactericidal effect of treatment with chitosan plus PDT was over 100 times higher than that with PDT alone for each of the four TCs. DNA damage measured by ethidium bromide monoazide and real-time quantitative polymerase chain reaction was also greater for PDT plus chitosan treatment than for PDT alone or under control conditions: the threshold cycle (Ct) values for the control, PDT, and PDT plus chitosan were 14.67 ± 0.22, 20.46 ± 0.12, and 25.54 ± 0.17, respectively. All four TCs caused similar levels of severe cell membrane damage during PDT compared with control conditions. These data suggest that PDT combined with any of the four TCs plus chitosan might be an available tool to kill efficiently planktonic form of C. difficile.

Molecular mechanisms of probiotic prevention of antibiotic-associated diarrhea

Antibiotic-associated diarrhea (AAD) is a common and unintended adverse effect of antibiotic treatment. It is characterized by the disruption of the gut microbiota, decreased intestinal short chain fatty acid (SCFA) concentrations, accumulation of luminal carbohydrates and colonic bile acids, altered water absorption, and ultimately diarrhea. Probiotics were shown to prevent AAD in numerous clinical trials. This review examines what is currently known about how probiotics reduce the risk for AAD via modulating the gut microbiota, altering nutrient and bile acid metabolism, inducing epithelial solute transporter activity, supporting intestinal barrier function, and influencing the immune system. Although probiotics are frequently prescribed with antibiotic use, mechanistic evidence verifying how they confer protection against AAD is extremely limited. This information is urgently needed for improving recommendations for sustaining probiotic development and for implementing probiotics in clinical settings.

(Patho-)Physiology of Na+/H+ Exchangers (NHEs) in the Digestive System

Na⁺/H⁺ exchangers (NHEs) are expressed in virtually all human tissues and organs. Two major tasks of those NHE isoforms that are located in plasma membranes are cell volume control by Na⁺-uptake and cellular pH regulation by H⁺-extrusion. Several NHEs, particularly NHE 1–4 and 8, are involved in the pathogenesis of diseases of the digestive system such as inflammatory bowel disease (ulcerative colitis, Crohn’s disease) and gastric and colorectal tumorigenesis. In the present review, we describe the physiological purposes, possible malfunctions and pathophysiological effects of the different NHE isoforms along the alimentary canal from esophagus to colon, including pancreas, liver and gallbladder. Particular attention is paid to the functions of NHEs in injury repair and to the role of NHE1 in Barrett’s esophagus. The impact of NHEs on gut microbiota and intestinal mucosal integrity is also dealt with. As the hitherto existing findings are not always consistent, sometimes even controversial, they are compared and critically discussed.

Consortium of Probiotics Attenuates Colonization of Clostridioides difficile

Clostridioides difficile infection (CDI) is increasing morbidity and mortality rates globally. Fecal microbiota transplantation (FMT), an effective therapy for eliminating Clostridioides difficile (C. difficile), cannot be used extensive due to a range of challenges. Probiotics thus constitutes a promising alternative therapy. In our study, we evaluated the effect of consortium of probiotics including five Lactobacilli strains and two Bifidobacterium strains on the colonization of toxigenic BI/NAP1/027 C. difficile in a mouse model. The results of 16S rRNA sequencing and targeted metabolomics showed the consortium of probiotics effectively decreased the colonization of C. difficile, changed the α- and β-diversity of the gut microbiota, decreased the primary bile acids, and increased the secondary bile acids. Spearman’s correlation showed that some of the OTUs such as Akkermansia, Bacteroides, Blautia et al. were positively correlated with C. difficile numbers and the primary bile acids, and negatively correlated with the secondary bile acids. However, some of the OTUs, such as Butyricicoccus, Ruminococcus, and Rikenellaceae, were negatively correlated with C. difficile copies and the primary bile acids, and positively correlated with the secondary bile acids. In summary, the consortium of probiotics effectively decreases the colonization of C. difficile, probably via alteration of gut microbiota and bile acids. Our probiotics mixture thus offers a promising FMT alternative.

Probiotics and prebiotics in clinical tests: an update

Probiotics have been explored in an exponentially increasing number of clinical trials for their health effects. Drawing conclusions from the published literature for the medical practitioner is difficult since rarely more than two clinical trials were conducted with the same probiotic strain against the same medical condition. Consequently, the European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) made a few recommendations restricting it to probiotic use against acute gastroenteritis and antibiotic-associated diarrhea. Recent studies also made a strong case for probiotic use against sepsis in preterm and term infants from developing countries. Conclusions on the value of probiotics are best based on detailed meta-analyses (MA) of randomized controlled trials (RCT). Outcomes of MA are discussed in the present review for a number of gastroenterology conditions. Since these MA pool data from trials using different probiotic species, large RCT published sometimes come to different conclusions than MA including these studies. This is not necessarily a contradiction but may only mean that the specific probiotic species did not work under the specified conditions. Positive or negative generalization about probiotics and prebiotics should be avoided. Credible effects are those confirmed in independent trials with a specified probiotic strain or chemically defined prebiotic in a specified patient population under the specified treatment conditions. Even distinct technological preparations of the same probiotic strain might affect clinical outcomes if they alter bacterial surface structures. Underpowered clinical trials are another problem in the probiotic field. Data obtained with sophisticated omics technologies, but derived from less than ten human subjects should be interpreted with caution even when published in high impact journals.

Modified Mouse Model of Clostridioides difficile Infection as a Platform for Probiotic Efficacy Studies

Probiotics may represent a promising approach for reducing Clostridioides (Clostridium) difficile infections (CDIs). A clinical trial conducted by our group demonstrated that CDI patients undergoing adjunctive treatment with Lactobacillus and Bifidobacterium probiotics had a reduction in diarrheal duration and compositional changes in their stool microbiomes. Here, we modified a CDI mouse model to represent clinical outcomes observed in patients and employed this model to identify evidence for the prevention of primary CDI and relapse with the same probiotic. Mice (n = 80) were administered 0.25 mg/ml cefoperazone over 5 days and subsequently challenged with 10² C. difficile VPI 10463 spores. A subset of mice (n = 40) were administered 10⁸ CFU of probiotics daily alongside cefoperazone pretreatment and until experimental endpoints were reached. Clinical scoring was performed daily on mice and used to evaluate CDI onset and severity. Moderate CDI in mice was defined by survival beyond day 3 postinfection, while mice with severe CDI were those who succumbed to infection prior to day 3 postinfection. Sequencing and analysis of 16S rRNA from stool content were performed to determine compositional alterations to the microbiota. Using total clinical scores, we identified an association between probiotic treatment and delayed onset of primary CDI and relapse by approximately 12 to 24 h (P < 0.001). The stool microbiome of mice with moderate CDI receiving probiotic treatment was significantly enriched with Lachnospiraceae during primary CDI (P < 0.05). The outcomes observed present an opportunity to use this modified CDI mouse model to examine the efficacy of nonantibiotic options for CDI management.

Probiotics: Reiterating What They Are and What They Are Not

It has been over seventeen years since the scientific definition of probiotics was crafted, along with guidelines ensuring the appropriate use of the term. This definition is now used globally, yet on a consistent basis scientists, media and industry misrepresent probiotics or make generalized statements that illustrate a misunderstanding of their utility and limitations. The rate of discovery of novel organisms with potentially therapeutic benefit for both human and environmental health is progressing at an unprecedented rate. However, the term “probiotic” is often misapplied to describe any microbe with plausible therapeutic utility in the human host. It is argued that strict compliance to the scientific definition of the term “probiotic” and avoidance of generalizations to the whole field of probiotics based upon studies of one product, will help advance the development and validation of microbial therapies, and applications to improve human health.