Responders and non-responders to probiotic interventions: how can we improve the odds?

Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses

BACKGROUND

Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders.

RESULTS

Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial.

CONCLUSIONS

Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.

The Potential of Meta-Proteomics and Artificial Intelligence to Establish the Next Generation of Probiotics for Personalized Healthcare

The symbiosis of probiotic bacteria with humans has rendered various health benefits while providing nutrition and a suitable environment for their survival. However, the probiotics must survive unfavorable gut conditions to exert beneficial effects. The intrinsic resistance of probiotics to survive harsh conditions results from a myriad of proteins. Interaction of microbial proteins with the host is indispensable for modulating the gut microbiome, such as interaction with cell receptors and protective action against pathogens. The complex interplay of proteins should be unraveled by utilizing metaproteomic strategies. The contribution of probiotics to health is now widely accepted. However, due to the inconsistency of generalized probiotics, contemporary research toward precision probiotics has gained momentum for customized treatment. This review explores the application of metaproteomics and AI/ML algorithms in resolving multiomics data analysis and in silico prediction of microbial features for screening specific beneficial probiotic organisms. Implementing these integrative strategies could augment the potential of precision probiotics for personalized healthcare.

Dysbiotic Gut Microbiota-Derived Metabolites and Their Role in Non-Communicable Diseases

Dysbiosis, generally defined as the disruption to gut microbiota composition or function, is observed in most diseases, including allergies, cancer, metabolic diseases, neurological disorders and diseases associated with autoimmunity. Dysbiosis is commonly associated with reduced levels of beneficial gut microbiota-derived metabolites such as short-chain fatty acids (SCFA) and indoles. Supplementation with these beneficial metabolites, or interventions to increase their microbial production, has been shown to ameliorate a variety of inflammatory diseases. Conversely, the production of gut 'dysbiotic' metabolites or by-products by the gut microbiota may contribute to disease development. This review summarizes the various 'dysbiotic' gut-derived products observed in cardiovascular diseases, cancer, inflammatory bowel disease, metabolic diseases including non-alcoholic steatohepatitis and autoimmune disorders such as multiple sclerosis. The increased production of dysbiotic gut microbial products, including trimethylamine, hydrogen sulphide, products of amino acid metabolism such as p-Cresyl sulphate and phenylacetic acid, and secondary bile acids such as deoxycholic acid, is commonly observed across multiple diseases. The simultaneous increased production of dysbiotic metabolites with the impaired production of beneficial metabolites, commonly associated with a modern lifestyle, may partially explain the high prevalence of inflammatory diseases in western countries.

Experimental diets dictate the metabolic benefits of probiotics in obesity

Growing evidence supports the use of probiotics to prevent or mitigate obesity-related dysmetabolism and non-alcoholic fatty liver disease (NAFLD). However, frequent reports of responders versus non-responders to probiotic treatment warrant a better understanding of key modifiers of host-microbe interactions. The influence of host diet on probiotic efficacy, in particular against metabolic diseases, remains elusive. We fed C57BL6/J mice a low fat reference diet or one of two energy-matched high fat and high sucrose diets for 12 weeks; a classical high fat diet (HFD) and a customized fast food-mimicking diet (FFMD). During the studies, mice fed either obesogenic diet were gavaged daily with one of two probiotic lactic acid bacteria (LAB) strains previously classified as Lactobaccillus, namely Limosilactobacillus reuteri (L. reuteri)or Lacticaseibacillus paracaseisubsp. paracasei (L. paracasei), or vehicle. The tested probiotics exhibited a reproducible efficacy but dichotomous response according to the obesogenic diets used. Indeed, L. paracaseiprevented weight gain, improved insulin sensitivity, and protected against NAFLD development in mice fed HFD, but not FFMD. Conversely, L. reuteri improved glucoregulatory capacity, reduced NAFLD development, and increased distal gut bile acid levels associated with changes in predicted functions of the gut microbiota exclusively in the context of FFMD-feeding. We found that the probiotic efficacy of two LAB strains is highly dependent on experimental obesogenic diets. These findings highlight the need to carefully consider the confounding impact of diet in order to improve both the reproducibility of preclinical probiotic studies and their clinical research translatability.

Microbiome engineering: engineered live biotherapeutic products for treating human disease

The human microbiota is implicated in many disease states, including neurological disorders, cancer, and inflammatory diseases. This potentially huge impact on human health has prompted the development of microbiome engineering methods, which attempt to adapt the composition and function of the human host-microbiota system for a therapeutic purpose. One promising method is the use of engineered microorganisms that have been modified to perform a therapeutic function. The majority of these products have only been demonstrated in laboratory models; however, in recent years more concepts have reached the translational stage. This has led to an increase in the number of clinical trials, which are designed to assess the safety and efficacy of these treatments in humans. Within this review, we highlight the progress of some of these microbiome engineering clinical studies, with a focus on engineered live biotherapeutic products.

Near transfer to an unrelated N-back task mediates the effect of N-back working memory training on matrix reasoning

The extent to which working memory training improves performance on untrained tasks is highly controversial. Here we address this controversy by testing the hypothesis that far transfer may depend on near transfer using mediation models in three separate randomized controlled trials (RCTs). In all three RCTs, totalling 460 individuals, performance on untrained N-back tasks (near transfer) mediated transfer to Matrix Reasoning (representing far transfer) despite the lack of an intervention effect in RCTs 2 and 3. Untrained N-back performance also mediated transfer to a working memory composite, which showed a significant intervention effect (RCT 3). These findings support a model of N-back training in which transfer to untrained N-back tasks gates further transfer (at least in the case of working memory at the construct level) and Matrix Reasoning. This model can help adjudicate between the many studies and meta-analyses of working memory training that have provided mixed results but have not examined the relationship between near and far transfer on an individual-differences level.

Review article: the future of microbiome-based therapeutics

BACKGROUND

From consumption of fermented foods and probiotics to emerging applications of faecal microbiota transplantation, the health benefit of manipulating the human microbiota has been exploited for millennia. Despite this history, recent technological advances are unlocking the capacity for targeted microbial manipulation as a novel therapeutic.

AIM

This review summarises the current developments in microbiome-based medicines and provides insight into the next steps required for therapeutic development.

METHODS

Here we review current and emerging approaches and assess the capabilities and weaknesses of these technologies to provide safe and effective clinical interventions. Key literature was identified through Pubmed searches with the following key words, 'microbiome', 'microbiome biomarkers', 'probiotics', 'prebiotics', 'synbiotics', 'faecal microbiota transplant', 'live biotherapeutics', 'microbiome mimetics' and 'postbiotics'.

RESULTS

Improved understanding of the human microbiome and recent technological advances provide an opportunity to develop a new generation of therapies. These therapies will range from dietary interventions, prebiotic supplementations, single probiotic bacterial strains, human donor-derived faecal microbiota transplants, rationally selected combinations of bacterial strains as live biotherapeutics, and the beneficial products or effects produced by bacterial strains, termed microbiome mimetics.

CONCLUSIONS

Although methods to identify and refine these therapeutics are continually advancing, the rapid emergence of these new approaches necessitates accepted technological and ethical frameworks for measurement, testing, laboratory practices and clinical translation.

Host Species Adaptation of Obligate Gut Anaerobes Is Dependent on Their Environmental Survival

The gut microbiota of warm-blooded vertebrates consists of bacterial species belonging to two main phyla; Firmicutes and Bacteroidetes. However, does it mean that the same bacterial species are found in humans and chickens? Here we show that the ability to survive in an aerobic environment is central for host species adaptation. Known bacterial species commonly found in humans, pigs, chickens and Antarctic gentoo penguins are those capable of extended survival under aerobic conditions, i.e., either spore-forming, aerotolerant or facultatively anaerobic bacteria. Such bacteria are ubiquitously distributed in the environment, which acts as the source of infection with similar probability in humans, pigs, chickens, penguins and likely any other warm-blooded omnivorous hosts. On the other hand, gut anaerobes with no specific adaptation for survival in an aerobic environment exhibit host adaptation. This is associated with their vertical transmission from mothers to offspring and long-term colonisation after administration of a single dose. This knowledge influences the design of next-generation probiotics. The origin of aerotolerant or spore-forming probiotic strains may not be that important. On the other hand, if Bacteroidetes and other host-adapted species are used as future probiotics, host preference should be considered.

Why Are Bifidobacteria Important for Infants?

The presence of Bifidobacterium species in the maternal vaginal and fecal microbiota is arguably an evolutionary trait that allows these organisms to be primary colonizers of the newborn intestinal tract. Their ability to utilize human milk oligosaccharides fosters their establishment as core health-promoting organisms throughout life. A reduction in their abundance in infants has been shown to increase the prevalence of obesity, diabetes, metabolic disorder, and all-cause mortality later in life. Probiotic strains have been developed as supplements for premature babies and to counter some of these ailments as well as to confer a range of health benefits. The ability to modulate the immune response and produce short-chain fatty acids, particularly acetate and butyrate, that strengthen the gut barrier and regulate the gut microbiome, makes Bifidobacterium a core component of a healthy infant through adulthood.

Probiotic Lactobacilli Do Not Protect Chickens against Salmonella Enteritidis Infection by Competitive Exclusion in the Intestinal Tract but in Feed, Outside the Chicken Host

Lactobacilli are commonly used as probiotics in poultry to improve production parameters and to increase chicken resistance to enteric infections. However, lactobacilli do not efficiently colonise the chicken intestinal tract, and also, their anti-infection effect in vivo is sometimes questionable. In this study, we therefore evaluated the potential of a mixture of four Lactobacillus species (L. salivarius, L. reuteri, L. ingluviei and L. alvi) for the protection of chickens against Salmonella Enteritidis infection. Whenever the chickens were inoculated by lactobacilli and S. Enteritidis separately, there was no protective effect of lactobacilli. This means that when lactobacilli and S. Enteritidis are exposed to each other as late as in the crop of chickens, lactobacilli did not influence chicken resistance to S. Enteritidis at all. The only positive effect was recorded when the mixture of lactobacilli and S. Enteritidis was used for the inoculation of feed and the feed was anaerobically fermented for 1 to 5 days. In this case, chickens fed such a diet remained S. Enteritidis negative. In vitro experiments showed that the protective effect was caused by acidification of feed down to pH 4.6 due to lactobacilli fermentation and was associated with S. Enteritidis inactivation. The probiotic effect of lactobacilli was thus expressed in the feed, outside the chicken host.

Mechanisms of Cognitive Impairment in Depression. May Probiotics Help?

Depression is the major cause of disability globally. Apart from lowered mood and accompanying symptoms, it leads to cognitive impairment that altogether predicts disadvantaged social functioning. Reduced cognitive function in depression appears a bit neglected in the field of clinical and molecular psychiatry, while it is estimated to occur in two-thirds of depressed patients and persist in at least one third of remitted patients. This problem, therefore, requires elucidation at the biomolecular and system levels and calls for improvement in therapeutic approach. In this review study, we address the above-mentioned issues by discussing putative mechanisms of cognitive decline in depression: (1) increased oxidative stress and (2) inflammation, (3) disturbed hypothalamus-pituitary-adrenals axis, and (4) reduced monoamines functionality. Moreover, we acknowledge additional underpinnings of cognitive impairment in depressed elderly: (5) vascular-originated brain ischemia and (6) amyloid-beta plaque accumulation. Additionally, by reviewing molecular, pre-clinical and clinical evidence, we propose gut microbiota-targeted strategies as potential adjuvant therapeutics. The study provides a consolidated source of knowledge regarding mechanisms of cognitive impairment in depression and may path the way toward improved treatment options.

The potential role of adherence factors in probiotic function in the gastrointestinal tract of adults and pediatrics: a narrative review of experimental and human studies

Numerous studies point to the important role of probiotic bacteria in gastrointestinal health. Probiotics act through mechanisms affecting enteric pathogens, epithelial barrier function, immune signaling, and conditioning of indigenous microbiota. Once administered, probiotics reach the gastrointestinal tract and interact with the host through bacterial surface molecules, here called adhesion factors, which are either strain- or specie-specific. Probiotic adhesion, through structural adhesion factors, is a mechanism that facilitates persistence within the gastrointestinal tract and triggers the initial host responses. Thus, an understanding of specific probiotic adhesion mechanisms could predict how specific probiotic strains elicit benefits and the potential of adherence factors as a proxy to predict probiotic function. This review summarizes the present understanding of probiotic adherence in the gastrointestinal tract. It highlights the bacterial adhesion structure types, their molecular communication with the host and the consequent impact on intestinal diseases in both adult and pediatric populations. Finally, we discuss knockout/isolation studies as direct evidence for adhesion factors conferring anti-inflammatory and pathogen inhibition properties to a probiotic.What is known: Probiotics can be used to treat clinical conditions.Probiotics improve dysbiosis and symptoms.Clinical trials may not confirm in vitro and animal studies.What is new: Adhesion structures may be important for probiotic function.Need to systematically determine physical characteristics of probiotics before selecting for clinical trials.Probiotics may be genetically engineered to add to clinical efficacy.

The rising dominance of microbiology: what to expect in the next 15 years?

What microbiology beholds after a decade and a half in the future requires a vision based on the facts and ongoing trends in research and technological advancements. While the latter, assisted by microbial dark matter, presents a greater potential of creating an upsurge in in-situ and ex-situ rapid microbial detection techniques, this anticipated change will also set forth a revolution in microbial cultivation and diversity analyses. The availability of a microbial genetic toolbox at the expanse will help complement the current understanding of the microbiome and assist in real-time monitoring of the dynamics for detecting the health status of the host with utmost precision. Alongside, in light of the emerging infectious diseases, antimicrobial resistance (AMR) and social demands for safer and better health care alternatives, microbiology laboratories are prospected to drift in terms of the volume and nature of research and outcomes. With today's microbiological lens, one can predict with certainty that in the years to come, microbes will play a significant role in therapeutic treatment and the designing of novel diagnostic techniques. Another area where the scope of microbial application seems to be promising is the use of novel probiotics as a method to offer health benefits whilst promoting metabolic outputs specific for microbiome replenishment. Nonetheless, the evolution of extraterrestrial microbes or the adaptation of earth microbes as extraterrestrial residents are also yet another prominent microbial event one may witness in the upcoming years. But like the two sides of the coin, there is also an urgent need to dampen the bloom of urbanization, overpopulation and global trade and adopting sustainable approaches to control the recurrence of epidemics and pandemics.

Ecological Adaptations of Gut Microbiota Members and Their Consequences for Use as a New Generation of Probiotics

In this review, we link ecological adaptations of different gut microbiota members with their potential for use as a new generation of probiotics. Gut microbiota members differ in their adaptations to survival in aerobic environments. Interestingly, there is an inverse relationship between aerobic survival and abundance or potential for prolonged colonization of the intestinal tract. Facultative anaerobes, aerotolerant Lactobacilli and endospore-forming Firmicutes exhibit high fluctuation, and if such bacteria are to be used as probiotics, they must be continuously administered to mimic their permanent supply from the environment. On the other hand, species not expressing any form of aerobic resistance, such as those from phylum Bacteroidetes, commonly represent host-adapted microbiota members characterized by vertical transmission from mothers to offspring, capable of long-term colonization following a single dose administration. To achieve maximal probiotic efficacy, the mode of their administration should thus reflect their natural ecology.

Shaping the Future of Probiotics and Prebiotics

Recent and ongoing developments in microbiome science are enabling new frontiers of research for probiotics and prebiotics. Novel types, mechanisms, and applications currently under study have the potential to change scientific understanding as well as nutritional and healthcare applications of these interventions. The expansion of related fields of microbiome-targeted interventions, and an evolving landscape for implementation across regulatory, policy, prescriber, and consumer spheres, portends an era of significant change. In this review we examine recent, emerging, and anticipated trends in probiotic and prebiotic science, and create a vision for broad areas of developing influence in the field.

Novel Resistant Starch Type 4 Products of Different Starch Origins, Production Methods, and Amounts Are Not Equally Fermented when Fed to Sprague-Dawley Rats

SCOPE

The possible mechanisms of production of four novel resistant starch type 4 (RS4) products for total cecal fermentation in an in vivo rodent model are evaluated.

METHODS AND RESULTS

Forty weanling rats are randomly assigned to five groups (n = 8) for a 3-week study. Starches are the RS type 4 products, as 10% of weight of RS diets (RSA-RSD), and AMIOCA starch (100% amylopectin) comprises 53.6% weight of control (CON) and 43.6% weight of RS diets. The RS products vary by percent purity and origin (potato, corn, tapioca). At euthanasia, cecal contents, serum, GI tract, and abdominal fat are collected. RSB, RSC, and RSD fed rats have greater empty cecum weights, lower cecal content pH, higher cecal content wet weight, and higher total cecal content acetate and propionate than the CON and RSA fed rats. Two other indicators of fermentation, total cecal contents butyrate and glucagon-like peptide 1, do not have significant ANOVA F values, which require more subjects for 80% power.

CONCLUSION

RS4 products that are produced from different starch origins with varying amounts of RS4 content and different methods of production are not uniformly fermented in an in vivo model.

An In Vitro Enrichment Strategy for Formulating Synergistic Synbiotics

Research on the role of diet on gut and systemic health has led to considerable interest toward identifying novel therapeutic modulators of the gut microbiome, including the use of prebiotics and probiotics. However, various host responses have often been reported among many clinical trials. This is in part due to competitive exclusion as a result of the absence of ecological niches as well as host-mediated constraints via colonization resistance. In this research, we developed a novel in vitro enrichment (IVE) method for isolating autochthonous strains that can function as synergistic synbiotics and overcome these constraints. The method relied on stepwise in vitro fecal fermentations to enrich for and isolate Bifidobacterium strains that ferment the prebiotic xylooligosaccharide (XOS). We subsequently isolated Bifidobacterium longum subsp. longum CR15 and then tested its establishment in 20 unique fecal samples with or without XOS. The strain was established in up to 18 samples but only in the presence of XOS. Our findings revealed that the IVE method is suitable for isolating potential synergistic probiotic strains that possess the genetic and biochemical ability to ferment specific prebiotic substrates. The IVE method can be used as an initial high-throughput screen for probiotic selection and isolation prior to further characterization and in vivo tests.IMPORTANCE This study describes an in vitro enrichment method to formulate synergistic synbiotics that have potential for establishing autochthonous strains across multiple individuals. The rationale for this approach-that the chance of survival of a bacterial strain is improved by providing it with its required resources-is based on classic ecological theory. From these experiments, a human-derived strain, Bifidobacterium longum subsp. longum CR15, was identified as a xylooligosaccharide (XOS) fermenter in fecal environments and displayed synergistic effects in vitro The high rate of strain establishment observed in this study provides a basis for using synergistic synbiotics to overcome the responder/nonresponder phenomenon that occurs frequently in clinical trials with probiotic and prebiotic interventions. In addition, this approach can be applied in other protocols that require enrichment of specific bacterial populations prior to strain isolation.

Effects of long-term administration of Lactobacillus reuteri DSM-17938 on circulating levels of 5-HT and BDNF in adults with functional constipation

Accumulated evidence shows that some probiotic strains ameliorate functional constipation (FC) via the modulation of specific gastrointestinal peptide pathways. The aims of this study were to investigate: (1) the effects of long-term administration of Lactobacillus reuteri (LR) DSM 17938 on the serum levels of serotonin (5-HT) and brain-derived neurotrophic factor (BDNF); (2) the possible link between 5-HT, BDNF, and specific constipation-related symptoms; (3) whether genetic variability at the 5-HTT gene-linked polymorphic region (5-HTTLPR) and BDNF Val66Met loci could be associated with serum 5-HT and BDNF variations. LR DSM 17938 was administered to 56 FC patients for 105 days in a randomised, double-blind manner. The fasting blood samples were collected during the randomisation visit (V₁), at day 15 (induction period, V₂), day 60 (intermediate evaluation, V₃), and day 105 (V₄) and the Constipaq questionnaire (the sum of Constipation Scoring System (CSS) and patient assessment constipation quality of life (PAC-QoL)) was administered. A group of healthy subjects was enrolled as controls (HC). At V1, the mean serum 5-HT level in the whole patient group was significantly higher (P=0.027) than in HC subjects, while serum BDNF did not. At the end of probiotic administration (V4), 5-HT and BDNF levels were significantly lower than the initial values (V1) (P=0.008 and P=0.015, respectively). 5-HT and BDNF serum concentration were significantly associated (r=0.355; P=0.007). Neither 5-HT nor BDNF serum levels correlated with the CSS item scores and with the PAC-QoL. Lastly, the regression analysis demonstrated that the presence of the S allele of the 5-HTTLPR accounted for the reduction in the 5-HT concentration at V4. In conclusion, the long-term administration of LR DSM 17938 demonstrated that such a probiotic strain could improve FC by affecting 5-HT and BDNF serum concentrations.

Perspective: Fundamental Limitations of the Randomized Controlled Trial Method in Nutritional Research: The Example of Probiotics

Studies on the relation between health and nutrition are often inconclusive. There are concerns about the validity of many research findings, and methods that can deliver high-quality evidence-such as the randomized controlled trial (RCT) method-have been embraced by nutritional researchers. Unfortunately, many nutritional RCTs also yield ambiguous results. It has been argued that RCTs are ill-suited for certain settings, including nutritional research. In this perspective, we investigate whether there are fundamental limitations of the RCT method in nutritional research. To this end, and to limit the scope, we use probiotic studies as an example. We use an epistemological approach and evaluate the presuppositions that underlie the RCT method. Three general presuppositions are identified and discussed. We evaluate whether these presuppositions can be considered true in probiotic RCTs, which appears not always to be the case. This perspective concludes by exploring several alternative study methods that may be considered for future probiotic or nutritional intervention trials.

Comparative study of probiotic effects of Lactobacillus and Bifidobacteria strains on cholesterol levels, liver morphology and the gut microbiota in obese mice

BACKGROUND

Microbiome-modulating interventions are promising for treatment and prevention of metabolic syndrome. The number of probiotic strains demonstrated ability to decrease cholesterol level in vivo, however, it was poorly confirmed in a clinical setting. The aim was to study the effects of L. acidophilus IMV B-7279, L. casei IMV B-7280, B. animalіs VKL and B. animalіs VKB separately and in various compositions on the level of serum cholesterol, gut microbiota contents and liver morphology on a high-calorie-induced obesity model in BALB/c mice.

MATERIALS AND METHODS

We used for the study female BALB/c mice 6-8 weeks old (18-24 g). Experimental animals were fed by a fat-enriched diet (FED), and 8 experimental groups were formed (12 mice in each group) to test strains of probiotic bacteria L. delbrueckii subsp. bulgaricus IMV B-7281, L. casei IMV B-7280, B. animalіs VKL and B. animalіs VKB and compositions. We used ultrasound for in vivo assessment of the liver and visceral (mesenteric) fat size. In the blood serum of the obese mice, the level of cholesterol was estimated. The liver morphology and gut microbiota of obese mice were studied.

RESULTS

We revealed that after treatment with all of the studied probiotic bacteria and compositions of B. animalis VKL/B. animalis VKB/L. casei IMV B-7280, the weight of obese mice decreased, and cholesterol and its fraction levels in serum were reduced. The size of the liver slightly decreased after treatment with L. delbrueckii subsp. bulgaricus IMV B-7281, B. аnimalis VKB or probiotic compositions; we observed reduction of the mesenteric fat size after injection of all these probiotic bacteria (separately) and probiotic compositions. We defined the strain-dependent effects on serum lipid profiles, liver morphology and the gut microbiota. The B. animalis VKL/B. animalis VKB/L. casei IMV B-7280 composition effectively recovered the liver morphological structure of obese mice. The number of Lactobacillus spp., Bifidobacterium spp. and coliform bacteria increased, the number of staphylococci and streptococci reduced, and the number of microscopic fungi significantly decreased in the gut of obese mice after treatment with L. casei IMV B-7280, L. delbrueckii subsp. bulgaricus IMV B-7281, B. animalis (separately) or their compositions.

CONCLUSION

L. casei IMV B-7280 (separately) and a composition of B. animalis VKL/B. animalis VKB/L. casei IMV B-7280 are effective at decreasing the weight of obese mice, decreasing cholesterol level, restoring the liver morphology and beneficially modulating the gut microbiome in high-calorie-induced obesity.

Transmission of the gut microbiota: spreading of health

Transmission of commensal intestinal bacteria between humans could promote health by establishing, maintaining and replenishing microbial diversity in the microbiota of an individual. Unlike pathogens, the routes of transmission for commensal bacteria remain unappreciated and poorly understood, despite the likely commonalities between both. Consequently, broad infection control measures that are designed to prevent pathogen transmission and infection, such as oversanitation and the overuse of antibiotics, may inadvertently affect human health by altering normal commensal transmission. In this Review, we discuss the mechanisms and factors that influence host-to-host transmission of the intestinal microbiota and examine how a better understanding of these processes will identify new approaches to nurture and restore transmission routes that are used by beneficial bacteria.

The effects of a multispecies probiotic on migraine and markers of intestinal permeability-results of a randomized placebo-controlled study

BACKGROUND/OBJECTIVES

Migraine, associated with several gastrointestinal disorders, may result from increased intestinal permeability, allowing endotoxins to enter the bloodstream. We tested whether probiotics could reduce migraine through an effect on intestinal permeability and inflammation.

SUBJECTS/METHODS

In total, 63 patients were randomly allocated to the probiotic (n=31) or the placebo group (n=32). Participants ingested a multispecies probiotic (5x10⁹ colony-forming units) or placebo daily for 12 weeks. Migraine was assessed with the Migraine Disability Assessment Scale (MIDAS), the Headache Disability Inventory (HDI) and headache diaries. At baseline and 12 weeks, intestinal permeability was measured with the urinary lactulose/mannitol test and fecal and serum zonulin; inflammation was measured from interleukin (IL) -6, IL-10, tumor necrosis factor-α and C-reactive protein in serum.

RESULTS

The MIDAS migraine intensity score significantly decreased in both groups (P<0.001) and the HDI score significantly decreased in the probiotic group (P=0.032) and borderline in the placebo group (P=0.053). In the probiotics group, patients had a median of 6 migraine days in the first month, 4 in the second month (P=0.002) and 5 in the last month, which was not significantly different from the 5, 4, and 4 days in the placebo group. A ⩾2day reduction in migraine days was seen in 12/31 patients in the probiotics group versus 7/29 in the placebo group (ns). Probiotic use did not significantly affect medication use, intestinal permeability or inflammation compared to placebo.

CONCLUSIONS

In this study, we could not confirm significant benefit from a multispecies probiotic compared to a placebo on the outcome parameters of migraine and intestinal integrity.

Probiotic use in an infectious disease setting

INTRODUCTION

The lethality of infectious diseases and deep concern over growing antimicrobial resistance make it essential that alternative or adjunct therapies be developed. Areas covered: Using papers published in PubMed, a case is presented to consider beneficial microbes as a means to improve management of infectious diseases. Clinical evidence is mounting that certain probiotic microbes can contribute to this armamentarium. These could have an immediate effect against necrotizing enterocolitis, pre- and post-surgical procedures, antibiotic-associated infections, urogenital infections in women and for reducing the severity and duration of respiratory infections. While further studies will always be warranted irrespective of the intervention, and quality assurance and patient safety must remain a priority, the main barrier to implementation may well be unwarranted hesitation amongst physicians, healthcare administrators and regulators. Meanwhile, patients are already taking things into their own hands at a time when their knowledge of product selection is poor and clinical guidance is invariably missing. Expert commentary: Until vaccines and other alternatives emerge, it would be foolhardy to not use best practices to bring probiotics into mainstream infectious disease management. Our ability to manipulate microbial-host interactions offers hope before the last antibiotic stops being effective.

Geriatric Respondents and Non-Respondents to Probiotic Intervention Can be Differentiated by Inherent Gut Microbiome Composition

Scope

Probiotic interventions are known to have been shown to influence the composition of the intestinal microbiota in geriatrics. The growing concern is the apparent variation in response to identical strain dosage among human volunteers. One factor that governs this variation is the host gut microbiome. In this study, we attempted to define a core gut metagenome, which could act as a predisposition signature marker of inherent bacterial community that can help predict the success of a probiotic intervention.

Methods and results

To characterize the geriatric gut microbiome, we designed primers targeting the 16S rRNA hypervariable region V2–V3 followed by semiconductor sequencing using Ion Torrent PGM. Among respondents and non-respondents, the chief genera of phylum Firmicutes that showed significant differences are Lactobacillus, Clostridium, Eubacterium, and Blautia (q < 0.002), while in the genera of phylum Proteobacteria included Shigella, Escherichia, Burkholderia and Camphylobacter (q < 0.002).

Conclusion

We have identified potential microbial biomarkers and taxonomic patterns that correlate with a positive response to probiotic intervention in geriatric volunteers. Future work with larger cohorts of geriatrics with diverse dietary influences could reveal the potential of the signature patterns of microbiota for personalized nutrition.

The Probiotic Mixture VSL#3 Has Differential Effects on Intestinal Immune Parameters in Healthy Female BALB/c and C57BL/6 Mice

BACKGROUND

Probiotic bacteria may render mice resistant to the development of various inflammatory and infectious diseases.

OBJECTIVE

This study aimed to identify mechanisms by which probiotic bacteria may influence intestinal immune homeostasis in noninflammatory conditions.

METHODS

The effect of VSL#3, a mixture of 8 probiotic bacteria, on intestinal gene expression was studied in healthy female BALB/c and C57BL/6 mice after prolonged oral treatment (28 d, triweekly) with 3 × 10(8) colony-forming units of VSL#3. In a separate experiment in BALB/c mice, the effects of prolonged administration of VSL#3 and of phosphate-buffered saline (PBS), followed by 1 single dose of VSL#3, on innate and adaptive immune cells were evaluated.

RESULTS

Microarray analysis of the intestines of mice treated with PBS confirmed well-established differences in the expression of immune-related genes between C57BL/6 and BALB/c mice. Prolonged administration of VSL#3 was associated with downregulation of Il13 [fold change (FC) = 0.46] and Eosinophil peroxidase (Epx) (FC = 0.44) and upregulation of Il12rb1 (FC = 2.1), C-C chemokine receptor type 5 (Ccr5) (FC = 2.6), chemokine (C-X-C motif) receptor 3 (Cxcr3) (FC = 1.6), and C-X-C motif chemokine 10 (Cxcl10) (FC = 2.8) in BALB/c mice but not in C57BL/6 mice. In BALB/c mice, it was shown that 28 d of treatment with VSL#3 affected the Peyer's patches (PPs) and mesenteric lymph nodes (MLNs), which was evident from an increase in B cells (26% and 8%, respectively), a decrease in T cells (21% and 8%, respectively), and an increase in cluster of differentiation (CD) 11c(+) cells (57% in PPs) compared with PBS-treated mice. This treatment was also associated with increased frequencies of T helper 17 (13%) and regulatory T cells (11%) in the MLNs. Treatment with PBS followed by 1 single dose of VSL#3, 18 h before killing, was associated with a 2-fold increase in CD103(+)CD11c(+) dendritic cells in MLNs and PPs.

CONCLUSION

VSL#3 treatment mediates mouse strain-specific alterations in immunologic phenotype in conditions of homeostasis, suggesting that the effects of probiotic bacteria depend on the genetic background of the host.

The effects of the multispecies probiotic mixture Ecologic®Barrier on migraine: results of an open-label pilot study

Migraine prevalence is associated with gastrointestinal disorders. Possible underlying mechanisms could be increased gut permeability and inflammation. Probiotics may decrease intestinal permeability as well as inflammation, and therefore may reduce the frequency and/or intensity of migraine attacks. Therefore we assessed feasibility, possible clinical efficacy, and adverse reactions of probiotic treatment in migraine patients. 29 migraine patients took 2 g/d of a probiotic food supplement (Ecologic(®)Barrier, 2.5×10(9) cfu/g) during 12 weeks. Participants recorded frequency and intensity of migraine in a headache diary and completed the Migraine Disability Assessment Scale (MIDAS) and Henry Ford Hospital Headache Disability Inventory (HDI) at baseline and after 12 weeks of treatment. Compliance was measured every 4 weeks by counting the remaining sachets with probiotics. The study was completed by 27/29 (93%) patients who took 95% of the supplements. Obstipation was reported by 4 patients during the first 2 weeks of treatment only. The mean±standard deviation (SD) number of migraine days/month decreased significantly from 6.7±2.4 at baseline to 5.1±2.2 (P=0.008) in week 5-8 and 5.2±2.4 in week 9-12 (P=0.001). The mean±SD intensity of migraine decreased significantly from 6.3±1.5 at baseline to 5.5±1.9 after treatment (P=0.005). The MIDAS score improved from 24.8±25.5 to 16.6±13.5 (P=0.031). However, the mean HDI did not change significantly. In conclusion, probiotics may decrease migraine supporting a possible role for the intestine in migraine management. Feasibility and lack of adverse reactions justify further placebo-controlled studies.

The probiotic mixture VSL#3 mediates both pro- and anti-inflammatory responses in bone marrow-derived dendritic cells from C57BL/6 and BALB/c mice

Probiotic bacteria express a wide range of molecular structures that bind to receptors on innate immune cells and mediate health-promoting effects in the host. We have recently demonstrated in a colitis model that favourable effects of the probiotic mixture VSL#3 may in part be due to the suppression of intestinal chemokine expression. To obtain more insights into the underlying mechanisms, in the present study, we analysed the modulation of bone marrow-derived dendritic cells (BM-DC) from BALB/c (T helper (Th)2 biased) v. C57BL/6 (Th1 biased) mice. Our findings showed that VSL#3 differed from pure Toll-like receptor (TLR) ligands by inducing the production of various cytokines, including IL-12 p70 subunit (IL-12p70), IL-23 and IL-10. Dedicated TLR arrays were employed to profile mRNA from BM-DC cultured with lipopolysaccharide (LPS), VSL#3, or a combination of both. This approach led to the identification of (1) a cluster of genes that were up- or down-regulated, irrespective of the stimulus, (2) a cluster of genes that were synergistically up-regulated by LPS and VSL#3 in BM-DC from C57BL/6 mice, but not in those from BALB/c mice, and (3) a cluster of LPS-induced genes that were suppressed by VSL#3, in particular chemokine genes. These data show that this probiotic mixture has both pro- and anti-inflammatory effects on BM-DC and suggest that their immune-modulating properties in vivo may depend on the genetic background of the host.

A systems biology approach investigating the effect of probiotics on the vaginal microbiome and host responses in a double blind, placebo-controlled clinical trial of post-menopausal women

A lactobacilli dominated microbiota in most pre and post-menopausal women is an indicator of vaginal health. The objective of this double blinded, placebo-controlled crossover study was to evaluate in 14 post-menopausal women with an intermediate Nugent score, the effect of 3 days of vaginal administration of probiotic L. rhamnosus GR-1 and L. reuteri RC-14 (2.5×10⁹ CFU each) on the microbiota and host response. The probiotic treatment did not result in an improved Nugent score when compared to when placebo. Analysis using 16S rRNA sequencing and metabolomics profiling revealed that the relative abundance of Lactobacillus was increased following probiotic administration as compared to placebo, which was weakly associated with an increase in lactate levels. A decrease in Atopobium was also observed. Analysis of host responses by microarray showed the probiotics had an immune-modulatory response including effects on pattern recognition receptors such as TLR2 while also affecting epithelial barrier function. This is the first study to use an interactomic approach for the study of vaginal probiotic administration in post-menopausal women. It shows that in some cases multifaceted approaches are required to detect the subtle molecular changes induced by the host to instillation of probiotic strains.

Trial Registration

ClinicalTrials.gov NCT02139839

Effects of genetic, processing, or product formulation changes on efficacy and safety of probiotics

Commercial probiotic strains for food or supplement use can be altered in different ways for a variety of purposes. Production conditions for the strain or final product may be changed to address probiotic yield, functionality, or stability. Final food products may be modified to improve flavor and other sensory properties, provide new product formats, or respond to market opportunities. Such changes can alter the expression of physiological traits owing to the live nature of probiotics. In addition, genetic approaches may be used to improve strain attributes. This review explores whether genetic or phenotypic changes, by accident or design, might affect the efficacy or safety of commercial probiotics. We highlight key issues important to determining the need to re-confirm efficacy or safety after strain improvement, process optimization, or product formulation changes. Research pinpointing the mechanisms of action for probiotic function and the development of assays to measure them are greatly needed to better understand if such changes have a substantive impact on probiotic efficacy.

Can prebiotics and probiotics improve therapeutic outcomes for undernourished individuals?

It has become clear in recent years that the human intestinal microbiota plays an important role in maintaining health and thus is an attractive target for clinical interventions. Scientists and clinicians have become increasingly interested in assessing the ability of probiotics and prebiotics to enhance the nutritional status of malnourished children, pregnant women, the elderly, and individuals with non-communicable disease-associated malnutrition. A workshop was held by the International Scientific Association for Probiotics and Prebiotics (ISAPP), drawing on the knowledge of experts from industry, medicine, and academia, with the objective to assess the status of our understanding of the link between the microbiome and under-nutrition, specifically in relation to probiotic and prebiotic treatments for under-nourished individuals. These discussions led to four recommendations:   (1) The categories of malnourished individuals need to be differentiated To improve treatment outcomes, subjects should first be categorized based on the cause of malnutrition, additional health-concerns, differences in the gut microbiota, and sociological considerations. (2) Define a baseline "healthy" gut microbiota for each category Altered nutrient requirement (for example, in pregnancy and old age) and individual variation may change what constitutes a healthy gut microbiota for the individual. (3) Perform studies using model systems to test the effectiveness of potential probiotics and prebiotics against these specific categories These should illustrate how certain microbiota profiles can be altered, as members of different categories may respond differently to the same treatment. (4) Perform robust well-designed human studies with probiotics and/or prebiotics, with appropriate, defined primary outcomes and sample size These are critical to show efficacy and understand responder and non-responder outcomes. It is hoped that these recommendations will lead to new approaches that combat malnutrition. This report is the result of discussion during an expert workshop titled "How do the microbiota and probiotics and/or prebiotics influence poor nutritional status?" held during the 10th Meeting of the International Scientific Association for Probiotics and Prebiotics (ISAPP) in Cork, Ireland from October 1-3, 2012. The complete list of workshop attendees is shown in Table 1.

Longitudinal analysis of vaginal microbiome dynamics in women with recurrent bacterial vaginosis: recognition of the conversion process

Bacterial vaginosis (BV) affects ∼ 30% of women of reproductive age, has a high rate of recurrence, and is associated with miscarriage, preterm birth, and increased risk of acquiring other sexually transmitted infections, including HIV-1. Little is known of the daily changes in the vaginal bacterial composition as it progresses from treatment to recurrence, or whether any of these might be useful in its prediction or an understanding of its causes. We used phylogenetic branch-inclusive quantitative PCR (PB-qPCR) and Lactobacillus blocked/unblocked qPCR (Lb-qPCR) to characterize longitudinal changes in the vaginal microbiota in sequential vaginal self-swabs from five women with recurrent BV, from diagnosis through remission to recurrence. Both patients with acute BV samples dominated by G. vaginalis recurred during the study with similar profiles, whereas the three patients with acute BV samples dominated by other anaerobes did not recur or recurred to an intermediate Nugent score. L. iners dominated remission phases, with intermittent days of abnormal microbial profiles typically associated with menses. The exception was a newly discovered phenomenon, a sustained period of abnormal profiles, termed conversion, which preceded symptomatic acute BV. Species known to have antagonistic activity towards Lactobacillus were detected in pre-conversion samples, possibly contributing to the decline in Lactobacillus. Lb-qPCR scores define two categories of response in the initial post-treatment visit samples; scores <5 may correspond with poor response to treatment or rapid recurrence, whereas scores >8 may predict delayed or no recurrence. Amsel criteria or Nugent scores did not have this potential predictive capability. Larger studies are warranted to evaluate the prognostic potential of detecting conversion and poor Lb-qPCR scores at the post-treatment visit of recurrent BV patients.

Probiotics in inflammatory bowel disease: Pathophysiological background and clinical applications

Ulcerative colitis and Crohn’s disease, collectively termed the inflammatory bowel diseases (IBD), are chronic inflammatory disorders of the gastrointestinal tract. A “dysbiotic” relationship between the commensal gut flora and the intestinal mucosa-associated immune system has been at the core of the pathogenesis of these conditions. Probiotics are “good bacteria” with the ability to benefit the health of the host and their therapeutic application has been studied in IBD. The theoretical basis for such utilization relies upon the ability of probiotic microorganisms to interfere with the dysregulated homeostasis that takes place in IBD and restore the immune-bacterial interaction at the intestinal mucosa. Proposed mechanisms of action include the reconstitution of altered flora composition, enhancement of the integrity of the epithelial barrier, promotion of tolerogenic action by dendritic cells, strengthening of the defensive mechanisms of the innate immunity, and the suppression of pro-inflammatory adaptive immune responses. Despite this abundance of supporting experimental evidence, clinical application of probiotics in IBD has been disappointing. Possible explanations for such discrepancy include the great diversity of microorganisms that fall under the definition of probiotics, the lack of standardization of dosages and administration schemes, the heterogeneity between clinical trials, and the inclusion in the treatment arms of patients with a large variety of clinical phenotypes. Addressing these important issues will be critical for the optimal usage of probiotic-based therapies for patients with IBD.

High fat diet partially attenuates fermentation responses in rats fed resistant starch from high-amylose maize

OBJECTIVE

The effects of type 2 resistant starch from high-amylose maize (HAM-RS2) in rodents fed with low-fat diets were demonstrated in previous studies. Fish oil is also reported to reduce body fat. In the current study, the effects of high fat and fish oil on HAM-RS2 feeding in rats were investigated.

DESIGN AND METHODS

Rats were fed 0 or 27% (weight) HAM-RS2 with low (15% energy) or high fat (42% energy) diets that included 0 or 10% (energy) tuna oil to test the effect of HAM-RS2 in diet-induced obesity and effects of tuna oil. Data were analyzed as 2 × 2 × 2 factorial.

RESULTS

Rats fed HAM-RS2 had decreased cecal contents pH, increased cecal and cecal contents weight, increased cecal contents acetate, propionate, and butyrate, increased GLP-1 and PYY, and decreased abdominal fat. However, high fat partially attenuated effects of HAM-RS2, but increased GLP-1 active. Dietary tuna oil had limited effects at concentration used.

CONCLUSIONS

Results demonstrated that a high fat diet partially attenuates the response to HAM-RS2. The mechanism may center on reduced levels of cecal contents propionate and butyrate and reduced serum PYY. This study demonstrated that with consumption of high fat, HAM-RS2 produces fermentation but results in partial attenuation of effects.

Adverse events associated with antiangiogenic agents in combination with cytotoxic chemotherapy in metastatic colorectal cancer and their management

Colorectal cancer (CRC) is the third most common cancer in men and women, and, despite advances in detection and treatment that result in a steadily decreasing incidence and mortality, remains a leading cause of death. The 5-year survival rate of persons with metastatic CRC (mCRC) is only 12%. With the recognition of vascularity as an important factor in tumor proliferation and growth, targeting angiogenesis pathways has been a major focus of research. The addition of bevacizumab, an inhibitor of the vascular endothelial growth factor (VEGF) pathway, to cytotoxic chemotherapy has improved response rates and survival of patients with mCRC. Aflibercept, a potent new multiple angiogenic factor trap that prevents not only VEGF-A but also VEGF-B and placental growth factor from activating their native receptors, has demonstrated efficacy in previously treated patients with mCRC. Phase I/II clinical trials and, more recently, a phase III clinical trial, have demonstrated effective antiangiogenic and cytotoxic activity with acceptable safety and tolerability. As is the case with bevacizumab, the optimal use of aflibercept requires appropriate management of the associated anti-VEGF adverse events and those associated with its use in combination with chemotherapy. These adverse events have previously been observed and are generally manageable with appropriate therapeutic intervention.

Unraveling how probiotic yogurt works

No matter what the advertisements are, or are not, allowed to say, it would be good to know if probiotic yogurt, in addition to its nutritional value, has a beneficial effect on the gut. In this issue, McNulty, Gordon and their colleagues describe a parallel series of human and animal studies designed to uncover the effects of probiotic yogurt on the gut microbiota. The intake of yogurt supplemented with five bacterial species, including the probiotic Bifidobacterium animalis, did not appreciably alter the composition of the human or mouse gut microbiota, but it did induce transcriptional and metabolic changes that reflected host bacterial responses to the arrival of the new species. This elegant study provides a strategy to delineate the precise effects exerted by probiotic foods on the human gut.

Gut microbiota and the role of probiotics in therapy

Thanks to rapid progress in the development and application of molecular techniques to the assessment of the human gut microbiome, the true nature, diversity and metabolic potential of this 'hidden organ' are being revealed. Simultaneously, the complex physiological, immunological and metabolic interactions between host and microbiome are being untangled. By contrast, the probiotic concept has been with us for decades and, while supported more by fad and folklore in the past, is now gaining support, not only from experimental work in animal models, but also by well-designed studies in human diseases, most notably infectious diarrheas, inflammatory bowel disease and the irritable bowel syndrome.