Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features

Infant Complementary Feeding of Prebiotics for theMicrobiome and Immunity

Complementary feeding transitions infants from a milk-based diet to solid foods, providing essential nutrients to the infant and the developing gut microbiome while influencing immune development. Some of the earliest microbial colonisers readily ferment select oligosaccharides, influencing the ongoing establishment of the microbiome. Non-digestible oligosaccharides in prebiotic-supplemented formula and human milk oligosaccharides promote commensal immune-modulating bacteria such as Bifidobacterium, which decrease in abundance during weaning. Incorporating complex, bifidogenic, non-digestible carbohydrates during the transition to solid foods may present an opportunity to feed commensal bacteria and promote balanced concentrations of beneficial short chain fatty acid concentrations and vitamins that support gut barrier maturation and immunity throughout the complementary feeding window.

Transforming medicine with the microbiome

Advances in microbiome research are spurring the development of new therapeutics for a variety of diseases, but translational challenges remain.

Role of Probiotics in Mycoplasma pneumoniae Pneumonia in Children: A Short-Term Pilot Project

Mycoplasma pneumoniae is one of the most common pathogens causing community-acquired pneumonia in children. Mycoplasma pneumoniae pneumonia (MPP) can be successfully treated with azithromycin; however, antibiotic-associated diarrhea (AAD) is a common adverse effect. Increasing evidence suggests that some probiotics may prevent the development of AAD. The present study determined the effects of probiotics (live Clostridium butyricum plus Bifidobacterium infantis) on the prevention and treatment of AAD in children with MPP when co-administered with intravenous azithromycin. Fifty-five children with MPP were enrolled and received azithromycin (10 mg/kg/day; once daily for 7 days) combined with probiotics (starting on the third day of azithromycin treatment; 1,500 mg three times daily); 50 healthy children served as controls. At the end of the trial, the incidence of AAD, fecal microbiota, intestinal mucosal barriers, and systemic inflammation were analyzed using recommended systems biology techniques. No cases of AAD or other adverse events occurred in children with MPP after co-administration of probiotics with azithromycin. A live C. butyricum plus B. infantis preparation partly reconstructed the gut microbiota, especially restoration of bacterial diversity. The indicators of intestinal mucosal barrier function, such as D-lactate, endotoxin, and diamine oxidase, were significantly improved and the systemic inflammation (interleukin 10) was attenuated after probiotic therapy. The present study indicated that co-administration of probiotics with azithromycin is a promising therapy for MPP treatment which could prevent and treat AAD effectively.

The gut microbiome: Relationships with disease and opportunities for therapy

Over the past decade, our view of human-associated microbes has expanded beyond that of a few species toward an appreciation of the diverse and niche-specialized microbial communities that develop in the human host with chronological age. The largest reservoir of microbes exists in the distal gastrointestinal tract, both in the lumen, where microbes facilitate primary and secondary metabolism, and on mucosal surfaces, where they interact with host immune cell populations. While local microbial-driven immunomodulation in the gut is well described, more recent studies have demonstrated a role for the gut microbiome in influencing remote organs and mucosal and hematopoietic immune function. Unsurprisingly, therefore, perturbation to the composition and function of the gut microbiota has been associated with chronic diseases ranging from gastrointestinal inflammatory and metabolic conditions to neurological, cardiovascular, and respiratory illnesses. Considerable effort is currently focused on understanding the natural history of microbiome development in humans in the context of health outcomes, in parallel with improving our knowledge of microbiome-host molecular interactions. These efforts ultimately aim to develop effective approaches to rehabilitate perturbed human microbial ecosystems as a means to restore health or prevent disease. This review details the role of the gut microbiome in modulating host health with a focus on immunomodulation and discusses strategies for manipulating the gut microbiome for the management or prevention of chronic inflammatory conditions.

Eran Elinav: Beyond the microbiome

Eran Elinav: Beyond the microbiome

Eran is the head of the microbiome-focused research group at the Weizmann Institute in Israel. He has published seminal work demonstrating the importance of the microbiota in many different systems, from post-dieting weight gain to circadian rhythms. Recent work from Eran and colleagues shows how probiotics perturb rather than aid the recovery of the microbiota following antibiotic treatment in humans. We contacted Eran to find out about his journey in science so far.

Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases

BACKGROUND

Inflammatory bowel diseases (IBD) are a group of complex and multifactorial disorders with unknown etiology. Chronic intestinal inflammation develops against resident intestinal bacteria in genetically susceptible hosts. We hypothesized that host intestinal immunoglobulin (Ig) G can be used to identify bacteria involved in IBD pathogenesis.

RESULTS

IgG-bound and -unbound microorganisms were collected from 32 pediatric terminal ileum aspirate washes during colonoscopy [non-IBD (n = 10), Crohn disease (n = 15), and ulcerative colitis (n = 7)], and composition was assessed using the Illumina MiSeq platform. In vitro analysis of invasive capacity was evaluated by fluorescence in situ hybridization and gentamicin invasion assay; immune activation was measured by qPCR. Despite considerable inter-individual variations, IgG binding favored specific and unique mucosa-associated species in pediatric IBD patients. Burkholderia cepacia, Flavonifractor plautii, and Rumminococcus sp. demonstrated increased IgG binding, while Pseudomonas ST29 demonstrated reduced IgG binding, in IBD. In vitro validation confirmed that B. cepacia, F. plautii, and Rumminococcus display invasive potential while Pseudomonas protogens did not.

CONCLUSION

Using IgG as a marker of pathobionts in larger patient cohorts to identify microbes and elucidate their role in IBD pathogenesis will potentially underpin new strategies to facilitate development of novel, targeted diagnostic, and therapeutic approaches. Interestingly, this method can be used beyond the scope of this manuscript to evaluate altered gut pathobionts in a number of diseases associated with altered microbiota including arthritis, obesity, diabetes mellitus, alcoholic liver disease, cirrhosis, metabolic syndrome, and carcinomas.

Microbial regulation of organismal energy homeostasis

The gut microbiome has emerged as a key regulator of host metabolism. Here we review the various mechanisms through which the gut microbiome influences the energy metabolism of its host, highlighting the complex interactions between gut microbes, their metabolites and host cells. Among the most important bacterial metabolites are short-chain fatty acids, which serve as a direct energy source for host cells, stimulate the production of gut hormones and act in the brain to regulate food intake. Other microbial metabolites affect systemic energy expenditure by influencing thermogenesis and adipose tissue browning. Both direct and indirect mechanisms of action are known for specific metabolites, such as bile acids, branched chain amino acids, indole propionic acid and endocannabinoids. We also discuss the roles of specific bacteria in the production of specific metabolites and explore how external factors, such as antibiotics and exercise, affect the microbiome and thereby energy homeostasis. Collectively, we present a large body of evidence supporting the concept that gut microbiota-based therapies can be used to modulate host metabolism, and we expect to see such approaches moving from bench to bedside in the near future.

Intestinal Sensing by Gut Microbiota: Targeting Gut Peptides

There are more than 2 billion overweight and obese individuals worldwide, surpassing for the first time, the number of people affected by undernutrition. Obesity and its comorbidities inflict a heavy burden on the global economies and have become a serious threat to individuals' wellbeing with no immediate cure available. The causes of obesity are manifold, involving several factors including physiological, metabolic, neural, psychosocial, economic, genetics and the environment, among others. Recent advances in genome sequencing and metagenomic profiling have added another dimension to this complexity by implicating the gut microbiota as an important player in energy regulation and the development of obesity. As such, accumulating evidence demonstrate the impact of the gut microbiota on body weight, adiposity, glucose, lipid metabolism, and metabolic syndrome. This also includes the role of microbiota as a modulatory signal either directly or through its bioactive metabolites on intestinal lumen by releasing chemosensing factors known to have a major role in controlling food intake and regulating body weight. The importance of gut signaling by microbiota signaling is further highlighted by the presence of taste and nutrient receptors on the intestinal epithelium activated by the microbial degradation products as well as their role in release of peptides hormones controlling appetite and energy homeostasis. This review present evidence on how gut microbiota interacts with intestinal chemosensing and modulates the release and activity of gut peptides, particularly GLP-1 and PYY.

Disentangling What We Know About Microbes and Mental Health

Much has been written in recent years about the gut-brain axis. Exciting pilot studies suggest probiotic applications to the gut can reduce anxiety and depression via the vagus nerve. But not to diminish such findings, much still needs to be considered, including the fact that the vagus nerve links to many other body sites that also host a microbiome. Questions remain that touch the core of being human: (i) Do our microbes influence happiness and to what extent? (ii) What components of the gut microbiota and their function, including as it relates to mental health, are critical and how do they differ between agile, fit hunter gatherers and obese westerners or Danes described as the happiest people on the planet? (iii) What role do environmental pollutants play in this microbes-host ecosystem? While approaching life from a reductionist perspective has a long history in science, we need to try to interrogate these health and disease issues from a wider perspective. For verification of a link between the gut microbiota and brain, and to test new therapies, human studies are needed, and are long overdue.

The Dimension of Time in Host-Microbiome Interactions

The intestinal microbiota contains trillions of commensal microorganisms that shape multiple aspects of host physiology and disease. In contrast to the host's genome, the microbiome is amenable to change over the course of an organism's lifetime, providing an opportunity to therapeutically modulate the microbiome's impact on human pathophysiology. In this Perspective, we highlight environmental factors that regulate the temporal dynamics of the intestinal microbiome, with a particular focus on the different time scales at which they act. We propose that the identification of transient and intermediate states of microbiome responses to perturbations is essential for understanding the rules that govern the behavior of this ecosystem. The delineation of microbiome dynamics is also helpful for distinguishing cause and effect in microbiome responses to environmental stimuli. Understanding the dimension of time in host-microbiome interactions is therefore critical for therapeutic strategies that aim at short-term or long-term engineering of the intestinal microbial community.

Cancer Immune Checkpoint Inhibitor Therapy and the Gut Microbiota

The past decade has seen tremendous advances in both our understanding of cancer immunosuppressive microenvironments and colonic bacteria facilitated by immune checkpoint inhibitor antibodies and next generation sequencing, respectively. Because an important role of the host immune system is to communicate with and regulate the gut microbial community, it should not come as a surprise that the behavior of one is coupled to the other. In this review, we will attempt to dissect some of the studies demonstrating cancer immunotherapy modulation by specific gut microbes and discuss possible molecular mechanisms for this effect.

Why don't probiotics work?

The conclusions reached by Hooks et al. urge the field to investigate the complex multipathway interactions between the microbiome and the gut-brain axis to understand the potential causal relationships involved. Claims in the field of microbiota-gut-brain research remain problematic without appropriate controls and adequate statistical power. A crucial question that follows from the authors' extensive review is: “Why don't probiotics work?”

Novel Personalized Dietary Treatment for Autism Based on the Gut-Immune-Endocrine-Brain Axis

Autism spectrum disorder (ASD) is a neurodevelopmental condition manifesting with impaired social interaction and communication, and restricted and repetitive behaviors and interests. In this perspective article, a more comprehensive approach than the gut-brain axis, hereby termed the "gut-immune-endocrine-brain" axis, is taken, based on which a personalized treatment plan for ASD is presented. ASD has no known etiology or cure, making desperate parents willing to try any treatment that worked for an individual with ASD, without much regard for its effectiveness, safety or side effects. This has been the case for restrictive dietary interventions as gluten-free/casein-free and ketogenic diets and recently, probiotics have emerged as the new such fad. One of the concerns about these dietary and probiotic treatments is their non-specificity: they may not be effective for all individuals with ASD, not all probiotic strains may have the beneficial qualities advertised indiscriminately for probiotics, and strains conferring benefits in one condition may not be probiotic in another. Not all children with ASD show immune reactivity to dietary proteins in wheat and milk, and wheat and milk may not be the only dietary elements to which reactivity is exhibited, where dietary aquaporins that resemble human aquaporins may elicit antibody reactivity in genetically susceptible individuals, which may include individuals with ASD. These observations are utilized to formulate a three-step plan to create effective, targeted, personalized treatments with as few side effects as possible, enabled by a systems approach connecting the various findings for dietary, immune, and neuroautoimmune reactivity in individuals with ASD.

A Review on Gut Remediation of Selected Environmental Contaminants: Possible Roles of Probiotics and Gut Microbiota

Various environmental contaminants including heavy metals, pesticides and antibiotics can contaminate food and water, leading to adverse effects on human health, such as inflammation, oxidative stress and intestinal disorder. Therefore, remediation of the toxicity of foodborne contaminants in human has become a primary concern. Some probiotic bacteria, mainly Lactobacilli, have received a great attention due to their ability to reduce the toxicity of several contaminants. For instance, Lactobacilli can reduce the accumulation and toxicity of selective heavy metals and pesticides in animal tissues by inhibiting intestinal absorption of contaminants and enhancing intestinal barrier function. Probiotics have also shown to decrease the risk of antibiotic-associated diarrhea possibly via competing and producing antagonistic compounds against pathogenic bacteria. Furthermore, probiotics can improve immune function by enhancing the gut microbiota mediated anti-inflammation. Thus, these probiotic bacteria are promising candidates for protecting body against foodborne contaminants-induced toxicity. Study on the mechanism of these beneficial bacterial strains during remediation processes and particularly their interaction with host gut microbiota is an active field of research. This review summarizes the current understanding of the remediation mechanisms of some probiotics and the combined effects of probiotics and gut microbiota on remediation of foodborne contaminants in vivo.

One Health, Fermented Foods, and Gut Microbiota

Changes in present-day society such as diets with more sugar, salt, and saturated fat, bad habits and unhealthy lifestyles contribute to the likelihood of the involvement of the microbiota in inflammatory diseases, which contribute to global epidemics of obesity, depression, and mental health concerns. The microbiota is presently one of the hottest areas of scientific and medical research, and exerts a marked influence on the host during homeostasis and disease. Fermented foods and beverages are generally defined as products made by microbial organisms and enzymatic conversions of major and minor food components. Further to the commonly-recognized effects of nutrition on the digestive health (e.g., dysbiosis) and well-being, there is now strong evidence for the impact of fermented foods and beverages (e.g., yoghurt, pickles, bread, kefir, beers, wines, mead), produced or preserved by the action of microorganisms, on general health, namely their significance on the gut microbiota balance and brain functionality. Fermented products require microorganisms, i.e., Saccharomyces yeasts and lactic acid bacteria, yielding alcohol and lactic acid. Ingestion of vibrant probiotics, especially those contained in fermented foods, is found to cause significant positive improvements in balancing intestinal permeability and barrier function. Our guts control and deal with every aspect of our health. How we digest our food and even the food sensitivities we have is linked with our mood, behavior, energy, weight, food cravings, hormone balance, immunity, and overall wellness. We highlight some impacts in this domain and debate calls for the convergence of interdisciplinary research fields from the United Nations’ initiative. Worldwide human and animal medicine are practiced separately; veterinary science and animal health are generally neither considered nor inserted within national or international Health discussions. The absence of a clear definition and subsequent vision for the future of One Health may act as a barrier to transdisciplinary collaboration. The point of this mini review is to highlight the role of fermented foods and beverages on gut microbiota and debate if the need for confluence of transdisciplinary fields of One Health is feasible and achievable, since they are managed by separate sectors with limited communication.

Gut Microbial Metabolism and Nonalcoholic Fatty Liver Disease

The gut microbiome, the multispecies community of microbes that exists in the gastrointestinal tract, encodes several orders of magnitude more functional genes than the human genome. It also plays a pivotal role in human health, in part due to metabolism of environmental, dietary, and host‐derived substrates, which produce bioactive metabolites. Perturbations to the composition and associated metabolic output of the gut microbiome have been associated with a number of chronic liver diseases, including nonalcoholic fatty liver disease (NAFLD). Here, we review the rapidly evolving suite of next‐generation techniques used for studying gut microbiome composition, functional gene content, and bioactive products and discuss relationships with the pathogenesis of NAFLD.

Lactobacillus rhamnosus GG versus Placebo for Acute Gastroenteritis in Children

BACKGROUND

Acute gastroenteritis develops in millions of children in the United States every year, and treatment with probiotics is common. However, data to support the use of probiotics in this population are limited.

METHODS

We conducted a prospective, randomized, double-blind trial involving children 3 months to 4 years of age with acute gastroenteritis who presented to one of 10 U.S. pediatric emergency departments. Participants received a 5-day course of Lactobacillus rhamnosus GG at a dose of 1×10¹⁰ colony-forming units twice daily or matching placebo. Follow-up surveys were conducted daily for 5 days and again 14 days after enrollment and 1 month after enrollment. The primary outcome was moderate-to-severe gastroenteritis, which was defined as an illness episode with a total score on the modified Vesikari scale of 9 or higher (scores range from 0 to 20, with higher scores indicating more severe disease), within 14 days after enrollment. Secondary outcomes included the duration and frequency of diarrhea and vomiting, the duration of day-care absenteeism, and the rate of household transmission (defined as the development of symptoms of gastroenteritis in previously asymptomatic household contacts).

RESULTS

Among the 971 participants, 943 (97.1%) completed the trial. The median age was 1.4 years (interquartile range, 0.9 to 2.3), and 513 participants (52.9%) were male. The modified Vesikari scale score for the 14-day period after enrollment was 9 or higher in 55 of 468 participants (11.8%) in the L. rhamnosus GG group and in 60 of 475 participants (12.6%) in the placebo group (relative risk, 0.96; 95% confidence interval, 0.68 to 1.35; P=0.83). There were no significant differences between the L. rhamnosus GG group and the placebo group in the duration of diarrhea (median, 49.7 hours in the L. rhamnosus GG group and 50.9 hours in the placebo group; P=0.26), duration of vomiting (median, 0 hours in both groups; P=0.17), or day-care absenteeism (median, 2 days in both groups; P=0.67) or in the rate of household transmission (10.6% and 14.1% in the two groups, respectively; P=0.16).

CONCLUSIONS

Among preschool children with acute gastroenteritis, those who received a 5-day course of L. rhamnosus GG did not have better outcomes than those who received placebo. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others; ClinicalTrials.gov number, NCT01773967 .).

A four-strain probiotic exerts positive immunomodulatory effects by enhancing colonic butyrate production in vitro

Poorly formulated probiotic supplements intended for oral administration often fail to protect bacteria from the challenges of human digestion, meaning bacteria do not reach the small intestine in a viable state. As a result, the ability of probiotics to influence the human gut microbiota has not been proven. Here we show how (i) considered formulation of an aqueous probiotic suspension can facilitate delivery of viable probiotic bacteria to the gut and (ii) quantitate the effect of colonisation and proliferation of specific probiotic species on the human gut microbiota, using an in-vitro gut model. Our data revealed immediate colonisation and growth of three probiotic species in the luminal and mucosal compartments of the proximal and distal colon, and growth of a fourth species in the luminal proximal colon, leading to higher proximal and distal colonic lactate concentrations. The lactate stimulated growth of lactate-consuming bacteria, altering the bacterial diversity of the microbiota and resulting in increased short-chain fatty acid production, especially butyrate. Additionally, an immunomodulatory effect of the probiotics was seen; production of anti-inflammatory cytokines (IL-6 and IL-10) was increased and production of inflammatory chemokines (MCP-1, CXCL 10 and IL-8.) was reduced. The results indicate that the probiotic species alone do not result in a clinical effect; rather, they facilitate modulation of the gut microbiota composition and metabolic activity thereby influencing the immune response.

Isolation and Characterization of Potentially Probiotic Bacterial Strains from Mice: Proof of Concept for Personalized Probiotics

Modulation of the gut microbiota through the use of probiotics has been widely used to treat or prevent several intestinal diseases. However, inconsistent results have compromised the efficacy of this approach, especially in severe conditions such as inflammatory bowel disease (IBD). The purpose of our study was to develop a personalized probiotic strategy and assess its efficacy in a murine model of intestinal inflammation. Commensal bacterial strains were isolated from the feces of healthy mice and then administered back to the host as a personalized treatment in dextran sodium sulfate (DSS)-induced colitis. Colonic tissues were collected for histological analysis and to investigate inflammatory markers such as Il-1β, Il-6, TGF-β, and Il-10, and the enzyme myeloperoxidase as a neutrophil marker. The group that received the personalized probiotic showed reduced susceptibility to DSS-colitis as compared to a commercial probiotic. This protection was characterized by a lower disease activity index and reduced histopathological damage in the colon. Moreover, the personalized probiotic was more effective in modulating the host immune response, leading to decreased Il-1β and Il-6 and increased TGF-β and Il-10 expression. In conclusion, our study suggests that personalized probiotics may possess an advantage over commercial probiotics in treating dysbiotic-related conditions, possibly because they are derived directly from the host's own microbiota.

Targeting the microbiome: from probiotics to fecal microbiota transplantation

The modern techniques of microbiome science can be applied to the development and evaluation of all microbiota-directed products, including probiotics and fecal microbiota transplantation.

With Probiotics, Resistance Is Not Always Futile

Probiotics and other bacteriotherapies are actively being explored and applied as symptom- and disease-modifying agents. In a recent issue of Cell, two papers contribute to our understanding of how live bacterial therapies variably affect individuals and the short- and longer-term impact of these therapies on colonization and host response.

Head and neck manifestations of neurofibromatosis

Neurofibromatosis is a neurocutaneous systemic disease that occurs in 1:2500 to 3300 live births. Prevalence figures have shown it to be as common as cystic fibrosis or Down's syndrome and more than twice as common as muscular dystrophy. In this study, our experience with 257 cases of neurofibromatosis seen since 1972 is reviewed. Intracranial, bony, and extracranial anomalies are described in the 223 patients (87%) who presented with, or ultimately developed, head and neck manifestations of the disease. The most common intracranial tumor was optic glioma, found in 35 patients (14%), 19 younger than 10 years of age. Acoustic neuromas were diagnosed in eight individuals (3%) and were bilateral in three. The most common skull anomaly was macrocephaly, noted 78 times (30%). Absence of the sphenoid wing occurred in 11 patients (4%) and 19 others (7%) had facial asymmetry due to other skull abnormalities. Extracranial manifestations included neurofibromas of the plexiform and nonplexiform type, Lisch nodules, and cafe-au-lait spots.