Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

Utilization of the microbiome in personalized medicine

Inter-individual human variability, driven by various genetic and environmental factors, complicates the ability to develop effective population-based early disease detection, treatment and prognostic assessment. The microbiome, consisting of diverse microorganism communities including viruses, bacteria, fungi and eukaryotes colonizing human body surfaces, has recently been identified as a contributor to inter-individual variation, through its person-specific signatures. As such, the microbiome may modulate disease manifestations, even among individuals with similar genetic disease susceptibility risks. Information stored within microbiomes may therefore enable early detection and prognostic assessment of disease in at-risk populations, whereas microbiome modulation may constitute an effective and safe treatment tailored to the individual. In this Review, we explore recent advances in the application of microbiome data in precision medicine across a growing number of human diseases. We also discuss the challenges, limitations and prospects of analysing microbiome data for personalized patient care.

Effects of OsomeFood Clean Label plant-based meals on the gut microbiome

BACKGROUND

Plant-based diets offer more beneficial microbes and can modulate gut microbiomes to improve human health. We evaluated the effects of the plant-based OsomeFood Clean Label meal range ('AWE' diet), on the human gut microbiome.

METHODS

Over 21 days, ten healthy participants consumed OsomeFood meals for five consecutive weekday lunches and dinners and resumed their regular diets for other days/meals. On follow-up days, participants completed questionnaires to record satiety, energy and health, and provided stool samples. To document microbiome variations and identify associations, species and functional pathway annotations were analyzed by shotgun sequencing. Shannon diversity and regular diet calorie intake subsets were also assessed.

RESULTS

Overweight participants gained more species and functional pathway diversity than normal BMI participants. Nineteen disease-associated species were suppressed in moderate-responders without gaining diversity, and in strong-responders with diversity gains along with health-associated species. All participants reported improved short-chain fatty acids production, insulin and γ-aminobutyric acid signaling. Moreover, fullness correlated positively with Bacteroides eggerthii; energetic status with B. uniformis, B. longum, Phascolarctobacterium succinatutens, and Eubacterium eligens; healthy status with Faecalibacterium prausnitzii, Prevotella CAG 5226, Roseburia hominis, and Roseburia sp. CAG 182; and overall response with E. eligens and Corprococcus eutactus. Fiber consumption was negatively associated with pathogenic species.

CONCLUSION

Although the AWE diet was consumed for only five days a week, all participants, especially overweight ones, experienced improved fullness, health status, energy and overall responses. The AWE diet benefits all individuals, especially those of higher BMI or low-fiber consumption.

The Microbiome and Its Impact on Allogeneic Hematopoietic Cell Transplantation

ABSTRACT

Allogeneic hematopoietic cell transplantation (alloHCT) is a standard curative therapy for a variety of benign and malignant hematological diseases. Previously, patients who underwent alloHCT were at high risk for complications with potentially life-threatening toxicities, including a variety of opportunistic infections as well as acute and chronic manifestations of graft-versus-host disease (GVHD), where the transplanted immune system can produce inflammatory damage to the patient. With recent advances, including newer conditioning regimens, advances in viral and fungal infection prophylaxis, and novel GVHD prophylactic and treatment strategies, improvements in clinical outcomes have steadily improved. One modality with great potential that has yet to be fully realized is targeting the microbiome to further improve clinical outcomes.In recent years, the intestinal microbiota, which includes bacteria, fungi, viruses, and other microbes that reside within the intestinal tract, has become established as a potent modulator of alloHCT outcomes. The composition of intestinal bacteria, in particular, has been found in large multicenter prospective studies to be strongly associated with GVHD, treatment-related mortality, and overall survival. Murine studies have demonstrated a causal relationship between intestinal microbiota injury and aggravated GVHD, and more recently, clinical interventional studies of repleting the intestinal microbiota with fecal microbiota transplantation have emerged as effective therapies for GVHD. How the composition of the intestinal bacterial microbiota, which is often highly variable in alloHCT patients, can modulate GVHD and other outcomes is not fully understood. Recent studies, however, have begun to make substantial headway, including identifying particular bacterial subsets and/or bacterial-derived metabolites that can mediate harm or benefit. Here, the authors review recent studies that have improved our mechanistic understanding of the relationship between the microbiota and alloHCT outcomes, as well as studies that are beginning to establish strategies to modulate the microbiota with the hope of optimizing clinical outcomes.

The microbiome's fiber degradation profile and its relationship with the host diet

BACKGROUND

The relationship between the gut microbiome and diet has been the focus of numerous recent studies. Such studies aim to characterize the impact of diet on the composition of the microbiome, as well as the microbiome's ability to utilize various compounds in the diet and produce metabolites that may be beneficial for the host. Consumption of dietary fibers (DFs)-polysaccharides that cannot be broken down by the host's endogenous enzymes and are degraded primarily by members of the microbiome-is known to have a profound effect on the microbiome. Yet, a comprehensive characterization of microbiome compositional and functional shifts in response to the consumption of specific DFs is still lacking.

RESULTS

Here, we introduce a computational framework, coupling metagenomic sequencing with careful annotation of polysaccharide degrading enzymes and DF structures, for inferring the metabolic ability of a given microbiome sample to utilize a broad catalog of DFs. We demonstrate that the inferred fiber degradation profile (IFDP) generated by our framework accurately reflects the dietary habits of various hosts across four independent datasets. We further demonstrate that IFDPs are more tightly linked to the host diet than commonly used taxonomic and functional microbiome-based profiles. Finally, applying our framework to a set of ~700 metagenomes that represents large human population cohorts from 9 different countries, we highlight intriguing global patterns linking DF consumption habits with microbiome capacities.

CONCLUSIONS

Combined, our findings serve as a proof-of-concept for the use of DF-specific analysis for providing important complementary information for better understanding the relationship between dietary habits and the gut microbiome.

Faecal microbiota transplantation in patients with haematological malignancies undergoing cellular therapies: from translational research to routine clinical practice

The effect of the gut microbiota on patients' outcomes after allogeneic haematopoietic cell transplantation (HCT) is now well established. In particular, gut microbiota dysbiosis has been associated with acute graft-versus-host disease (GVHD). Furthermore, increasing data also suggest an effect of the gut microbiota on outcome after autologous HCT and CAR T cells. In fact, the bacterial gut microbiota interplays with the immune system and contributes to immunological complication and antitumour response to treatment. Therefore, faecal microbiota transplantation has been evaluated in patients with haematological malignancies for various indications, including Clostridioides difficile infection, eradication of multidrug-resistant bacteria, and steroid refractory acute GVHD. In addition, use of prophylactic faecal microbiota transplantation to restore the gut microbiota and improve patients' outcomes is being developed in the setting of allogeneic HCT, but also probably very soon in patients receiving autologous HCT or CAR T cells.

Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions

Humans often show variable responses to dietary, prebiotic, and probiotic interventions. Emerging evidence indicates that the gut microbiota is a key determinant for this population heterogeneity. Here, we provide an overview of some of the major computational and experimental tools being applied to critical questions of microbiota-mediated personalized nutrition and health. First, we discuss the latest advances in in silico modeling of the microbiota-nutrition-health axis, including the application of statistical, mechanistic, and hybrid artificial intelligence models. Second, we address high-throughput in vitro techniques for assessing interindividual heterogeneity, from ex vivo batch culturing of stool and continuous culturing in anaerobic bioreactors, to more sophisticated organ-on-a-chip models that integrate both host and microbial compartments. Third, we explore in vivo approaches for better understanding of personalized, microbiota-mediated responses to diet, prebiotics, and probiotics, from nonhuman animal models and human observational studies, to human feeding trials and crossover interventions. We highlight examples of existing, consumer-facing precision nutrition platforms that are currently leveraging the gut microbiota. Furthermore, we discuss how the integration of a broader set of the tools and techniques described in this piece can generate the data necessary to support a greater diversity of precision nutrition strategies. Finally, we present a vision of a precision nutrition and healthcare future, which leverages the gut microbiota to design effective, individual-specific interventions.

Microbiome-based therapeutics

Symbiotic microorganisms inhabiting the gastrointestinal tract promote health by decreasing susceptibility to infection and enhancing resistance to a range of diseases. In this Review, we discuss our increasing understanding of the impact of the microbiome on the mammalian host and recent efforts to culture and characterize intestinal symbiotic microorganisms that produce or modify metabolites that impact disease pathology. Manipulation of the intestinal microbiome has great potential to reduce the incidence and/or severity of a wide range of human conditions and diseases, and the biomedical research community now faces the challenge of translating our understanding of the microbiome into beneficial medical therapies. Our increasing understanding of symbiotic microbial species and the application of ecological principles and machine learning are providing exciting opportunities for microbiome-based therapeutics to progress from faecal microbiota transplantation to the administration of precisely defined and clinically validated symbiotic microbial consortia that optimize disease resistance.

Glutamic acid reshapes the plant microbiota to protect plants against pathogens

BACKGROUND

Plants in nature interact with other species, among which are mutualistic microorganisms that affect plant health. The co-existence of microbial symbionts with the host contributes to host fitness in a natural context. In turn, the composition of the plant microbiota responds to the environment and the state of the host, raising the possibility that it can be engineered to benefit the plant. However, technology for engineering the structure of the plant microbiome is not yet available.

RESULTS

The loss of diversity and reduction in population density of Streptomyces globisporus SP6C4, a core microbe, was observed coincident with the aging of strawberry plants. Here, we show that glutamic acid reshapes the plant microbial community and enriches populations of Streptomyces, a functional core microbe in the strawberry anthosphere. Similarly, in the tomato rhizosphere, treatment with glutamic acid increased the population sizes of Streptomyces as well as those of Bacillaceae and Burkholderiaceae. At the same time, diseases caused by species of Botrytis and Fusarium were significantly reduced in both habitats. We suggest that glutamic acid directly modulates the composition of the microbiome community.

CONCLUSIONS

Much is known about the structure of plant-associated microbial communities, but less is understood about how the community composition and complexity are controlled. Our results demonstrate that the intrinsic level of glutamic acid in planta is associated with the composition of the microbiota, which can be modulated by an external supply of a biostimulant. Video Abstract.

Functional heterogeneity in the fermentation capabilities of the healthy human gut microbiota

The human gut microbiota is known for its highly heterogeneous composition across different individuals. However, relatively little is known about functional differences in its ability to ferment complex polysaccharides. Through ex vivo measurements from healthy human donors, we show that individuals vary markedly in their microbial metabolic phenotypes (MMPs), mirroring differences in their microbiota composition, and resulting in the production of different quantities and proportions of Short Chain Fatty Acids (SCFAs) from the same inputs. We also show that aspects of these MMPs can be predicted from composition using 16S rRNA sequencing. From experiments performed using the same dietary fibers in vivo, we demonstrate that an ingested bolus of fiber is almost entirely consumed by the microbiota upon passage. We leverage our ex vivo data to construct a model of SCFA production and absorption in vivo, and argue that inter-individual differences in quantities of absorbed SCFA are directly related to differences in production. Though in vivo studies are required to confirm these data in the context of the gut, in addition to in vivo read outs of SCFAs produced in response to specific fiber spike-ins, these data suggest that optimizing SCFA production in a given individual through targeted fiber supplementation requires quantitative understanding of their MMP.

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity

BACKGROUND

The maternal microbiome has emerged as an important factor in gestational health and outcome and is associated with risk of preterm birth and offspring morbidity. Epidemiological evidence also points to successive pregnancies-referred to as maternal parity-as a risk factor for preterm birth, infant mortality, and impaired neonatal growth. Despite the fact that both the maternal microbiome and parity are linked to maternal-infant health, the impact of parity on the microbiome remains largely unexplored, in part due to the challenges of studying parity in humans.

RESULTS

Using synchronized pregnancies and dense longitudinal monitoring of the microbiome in pigs, we describe a microbiome trajectory during pregnancy and determine the extent to which parity modulates this trajectory. We show that the microbiome changes reproducibly during gestation and that this remodeling occurs more rapidly as parity increases. At the time of parturition, parity was linked to the relative abundance of several bacterial species, including Treponema bryantii, Lactobacillus amylovorus, and Lactobacillus reuteri. Strain tracking carried out in 18 maternal-offspring "quadrads"-each consisting of one mother sow and three piglets-linked maternal parity to altered levels of Akkermansia muciniphila, Prevotella stercorea, and Campylobacter coli in the infant gut 10 days after birth.

CONCLUSIONS

Collectively, these results identify parity as an important environmental factor that modulates the gut microbiome during pregnancy and highlight the utility of a swine model for investigating the microbiome in maternal-infant health. In addition, our data show that the impact of parity extends beyond the mother and is associated with alterations in the community of bacteria that colonize the offspring gut early in life. The bacterial species we identified as parity-associated in the mother and offspring have been shown to influence host metabolism in other systems, raising the possibility that such changes may influence host nutrient acquisition or utilization. These findings, taken together with our observation that even subtle differences in parity are associated with microbiome changes, underscore the importance of considering parity in the design and analysis of human microbiome studies during pregnancy and in infants. Video abstract.

Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome

BACKGROUND

While several studies have documented associations between dietary habits and microbiota composition and function in healthy individuals, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially with symptoms.

METHODS

Here, we used a novel approach that combined data from a 4-day food diary, integrated into a food tree, together with gut microbiota (shotgun metagenomic) for individuals with IBS (N = 149) and healthy controls (N = 52). Paired microbiota and food-based trees allowed us to detect new associations between subspecies and diet. Combining co-inertia analysis and linear regression models, exhaled gas levels and symptom severity could be predicted from metagenomic and dietary data.

RESULTS

We showed that individuals with severe IBS are characterized by a higher intake of poorer-quality food items during their main meals. Our analysis suggested that covariations between gut microbiota at subspecies level and diet could be explained with IBS symptom severity, exhaled gas, glycan metabolism, and meat/plant ratio. We provided evidence that IBS severity is associated with altered gut microbiota hydrogen function in correlation with microbiota enzymes involved in animal carbohydrate metabolism.

CONCLUSIONS

Our study provides an unprecedented resolution of diet-microbiota-symptom interactions and ultimately guides new interventional studies that aim to identify gut microbiome-based nutritional recommendations for the management of gastrointestinal symptoms.

TRIAL REGISTRATION

This trial was registered on the ClinicalTrials.gov, with the registration number NCT01252550 , on 3rd December 2010. Video abstract.

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria

Interest in preventive or therapeutic strategies targeting gut microbiota is increasing. Such strategies may involve the direct replenishment of the gut microbiota with single strains or strain mixtures, or the manipulation of strain abundance through dietary intervention, including lactic acid bacteria. A few candidate species associated with health benefits have been identified, including Faecalibacterium prausnitzii. Given its growth requirements, modulation of this bacterium has not been extensively studied. In this investigation, we explored the capacity of cell-free supernatants of different Lactobacillus, Streptococcus, Lactococcus, and Bifidobacterium strains to stimulate the growth of F. prausnitzii A2-165. Modulation by four strains with the greatest capacity to stimulate growth or delay lysis, Lactococcus lactis subsp. lactis CNCM I-1631, Lactococcus lactis subsp. cremoris CNCM I-3558, Lactobacillus paracasei CNCM I-3689, and Streptococcus thermophilus CNCM I-3862, was further characterized by transcriptomics. The response of F. prausnitzii to cell-free supernatants from these four strains revealed several shared characteristics, in particular, upregulation of carbohydrate metabolism and cell wall-related genes and downregulation of replication and mobilome genes. Overall, this study suggests differential responses of F. prausnitzii to metabolites produced by different strains, providing protection against cell death, with an increase in peptidoglycan levels for cell wall formation, and reduced cell mobilome activity.

Exploiting the gut microbiota's fermentation capabilities towards disease prevention

One of the crucial roles played in the context of human physiology by the human gut microbiota is to ferment resistant polysaccharides and dietary fibres in the colon. Even though it has long been presumed that these processes play fundamental roles in regulating human health, we remain unable to treat or even diagnose deficiencies in microbial fermentation. In part, this relatively slow progress can be attributed to the fact that studying the gut microbiota and its metabolic properties has until now heavily relied on next generation sequencing and case-control cohorts to identify differentially abundant genes, pathways or organisms in the context of a particular clinical indication. Unfortunately, these methods and studies do not allow us to rigorously probe the functional and metabolic phenotype of a microbiota, or for elucidating its mechanisms of action on the host. To improve our clinical control over these fermentation processes, it is critical that we improve our quantitative, mechanistic understanding of their impact on host physiology. In this review, we provide an overview of our current understanding of the roles microbial fermentation processes play in human health in the context of disease prevention. We then describe the evidence linking these processes with depression and anxiety-related conditions, and use these complex disorders as a framework for illustrating the fact that achieving a clinical vision that exploits microbial fermentation towards human health will depend on thoughtful multi-disciplinary collaboration between clinical research, systems biology, and the pharmaceutical and analytical sciences.

Prebiotics and Community Composition Influence Gas Production of the Human Gut Microbiota

Prebiotics confer benefits to human health, often by promoting the growth of gut bacteria that produce metabolites valuable to the human body, such as short-chain fatty acids (SCFAs). While prebiotic selection has strongly focused on maximizing the production of SCFAs, less attention has been paid to gases, a by-product of SCFA production that also has physiological effects on the human body. Here, we investigate how the content and volume of gas production by human gut microbiota are affected by the chemical composition of the prebiotic and the community composition of the microbiota. We first constructed a linear system model based on mass and electron balance and compared the theoretical product ranges of two prebiotics, inulin and pectin. Modeling shows that pectin is more restricted in product space, with less potential for H2 but more potential for CO2 production. An ex vivo experimental system showed pectin degradation produced significantly less H2 than inulin, but CO2 production fell outside the theoretical product range, suggesting fermentation of fecal debris. Microbial community composition also impacted results: methane production was dependent on the presence of Methanobacteria, while interindividual differences in H2 production during inulin degradation were driven by a Lachnospiraceae taxon. Overall, these results suggest that both the chemistry of the prebiotic and the composition of the microbiota are relevant to gas production. Metabolic processes that are relatively prevalent in the microbiome, such as H2 production, will depend more on substrate, while rare metabolisms such as methanogenesis depend more strongly on microbiome composition.IMPORTANCE Prebiotic fermentation in the gut often leads to the coproduction of short-chain fatty acids (SCFAs) and gases. While excess gas production can be a potential problem for those with functional gut disorders, gas production is rarely considered during prebiotic design. In this study, we combined the use of theoretical models and an ex vivo experimental platform to illustrate that both the chemical composition of the prebiotic and the community composition of the human gut microbiota can affect the volume and content of gas production during prebiotic fermentation. Specifically, more prevalent metabolic processes such as hydrogen production were strongly affected by the oxidation state of the probiotic, while rare metabolisms such as methane production were less affected by the chemical nature of the substrate and entirely dependent on the presence of Methanobacteria in the microbiota.

A Guide to Diet-Microbiome Study Design

Intense recent interest in understanding how the human gut microbiome influences health has kindled a concomitant interest in linking dietary choices to microbiome variation. Diet is known to be a driver of microbiome variation, and yet the precise mechanisms by which certain dietary components modulate the microbiome, and by which the microbiome produces byproducts and secondary metabolites from dietary components, are not well-understood. Interestingly, despite the influence of diet on the gut microbiome, the majority of microbiome studies published to date contain little or no analysis of dietary intake. Although an increasing number of microbiome studies are now collecting some form of dietary data or even performing diet interventions, there are no clear standards in the microbiome field for how to collect diet data or how to design a diet-microbiome study. In this article, we review the current practices in diet-microbiome analysis and study design and make several recommendations for best practices to provoke broader discussion in the field. We recommend that microbiome studies include multiple consecutive microbiome samples per study timepoint or phase and multiple days of dietary history prior to each microbiome sample whenever feasible. We find evidence that direct effects of diet on the microbiome are likely to be observable within days, while the length of an intervention required for observing microbiome-mediated effects on the host phenotype or host biomarkers, depending on the outcome, may be much longer, on the order of weeks or months. Finally, recent studies demonstrating that diet-microbiome interactions are personalized suggest that diet-microbiome studies should either include longitudinal sampling within individuals to identify personalized responses, or should include an adequate number of participants spanning a range of microbiome types to identify generalized responses.

Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships

The current understanding of inflammatory bowel disease (IBD) pathogenesis implicates a complex interaction between host genetics, host immunity, microbiome, and environmental exposures. Mechanisms gleaned from genetics and molecular pathogenesis offer clues to the critical triggers of mucosal inflammation and guide the development of therapeutic interventions. A complex network of interactions between host genetic factors, microbes, and microbial metabolites governs intestinal homeostasis, making classification and mechanistic dissection of involved pathways challenging. In this Review, we discuss these challenges, areas of active translation, and opportunities for development of next-generation therapies.

Diet, nutrients and the microbiome

Although there is associative evidence linking fecal microbiome profile to health and disease, many studies have not considered the confounding effects of dietary intake. Consuming food provides fermentable substrate which sustains the microbial ecosystem that resides with most abundance in the colon. Western, Mediterranean and vegetarian dietary patterns have a role in modulating the gut microbiota, as do trending restrictive diets such the paleolithic and ketogenic. Altering the amount or ratio of carbohydrate, protein and fat, particularly at the extremes of intake, impacts the microbiome. Diets high in fermentable carbohydrates support the relative abundance of Bifidobacterium, Prevotella, Ruminococcus, Dorea and Roseburia, among others, capable of degrading polysaccharides, oligosaccharides and sugars. Conversely, very high fat diets increase bile-resistant organisms such as Bilophila and Bacteroides. Food form, whole foods vs. ultra-processed, alters the provision of macronutrient substrate to the colon due to differing digestibility, and thereby may impact the microbiota and its metabolic activity. In addition, phytochemicals in plant-based foods have specific and possibly prebiotic effects on the microbiome. Further, food ingredients such as certain low-calorie sweeteners enhance Bifidobacterium spp. The weight of evidence to date suggests a high level of interindividual variability in the human microbiome vs. clearly defined, dietary-induced profiles. Healthful dietary patterns, emphasizing plant foods high in microbial-available carbohydrate, support favorable microbiome profiles active in saccharolytic fermentation. Future research into diet and microbiome should consider the balance of gut microbial-generated metabolites, an important link between microbiome profile and human health.

Macroecological dynamics of gut microbiota

The gut microbiota is now widely recognized as a dynamic ecosystem that plays an important role in health and disease. Although current sequencing technologies make it possible to explore how relative abundances of host-associated bacteria change over time, the biological processes governing microbial dynamics remain poorly understood. Therefore, as in other ecological systems, it is important to identify quantitative relationships describing various aspects of gut microbiota dynamics. In the present study, we use multiple high-resolution time series data obtained from humans and mice to demonstrate that, despite their inherent complexity, gut microbiota dynamics can be characterized by several robust scaling relationships. Interestingly, the observed patterns are highly similar to those previously identified across diverse ecological communities and economic systems, including the temporal fluctuations of animal and plant populations and the performance of publicly traded companies. Specifically, we find power-law relationships describing short- and long-term changes in gut microbiota abundances, species residence and return times, and the correlation between the mean and the temporal variance of species abundances. The observed scaling laws are altered in mice receiving different diets and are affected by context-specific perturbations in humans. We use the macroecological relationships to reveal specific bacterial taxa, the dynamics of which are substantially perturbed by dietary and environmental changes. Overall, our results suggest that a quantitative macroecological framework will be important for characterizing and understanding the complex dynamics of diverse microbial communities.

Marine Microalgae, Spirulina maxima-Derived Modified Pectin and Modified Pectin Nanoparticles Modulate the Gut Microbiota and Trigger Immune Responses in Mice

This study evaluated the modulation of gut microbiota, immune responses, and gut morphometry in C57BL/6 mice, upon oral administration of S. maxima-derived modified pectin (SmP, 7.5 mg/mL) and pectin nanoparticles (SmPNPs; 7.5 mg/mL). Metagenomics analysis was conducted using fecal samples, and mice duodenum and jejunum were used for analyzing the immune response and gut morphometry, respectively. The results of metagenomics analysis revealed that the abundance of Bacteroidetes in the gut increased in response to both modified SmP and SmPNPs (75%) as compared with that in the control group (66%), while that of Firmicutes decreased in (20%) as compared with that in the control group (30%). The mRNA levels of mucin, antimicrobial peptide, and antiviral and gut permeability-related genes in the duodenum were significantly (p < 0.05) upregulated (> 2-fold) upon modified SmP and SmPNPs feeding. Protein level of intestinal alkaline phosphatase was increased (1.9-fold) in the duodenum of modified SmPNPs feeding, evidenced by significantly increased goblet cell density (0.5 ± 0.03 cells/1000 µm2) and villi height (352 ± 10 µm). Our results suggest that both modified SmP and SmPNPs have the potential to modulate gut microbial community, enhance the expression of immune related genes, and improve gut morphology.

Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration

The human gut is inhabited by trillions of microorganisms composing a dynamic ecosystem implicated in health and disease. The composition of the gut microbiota is unique to each individual and tends to remain relatively stable throughout life, yet daily transient fluctuations are observed. Diet is a key modifiable factor influencing the composition of the gut microbiota, indicating the potential for therapeutic dietary strategies to manipulate microbial diversity, composition, and stability. While diet can induce a shift in the gut microbiota, these changes appear to be temporary. Whether prolonged dietary changes can induce permanent alterations in the gut microbiota is unknown, mainly due to a lack of long-term human dietary interventions, or long-term follow-ups of short-term dietary interventions. It is possible that habitual diets have a greater influence on the gut microbiota than acute dietary strategies. This review presents the current knowledge around the response of the gut microbiota to short-term and long-term dietary interventions and identifies major factors that contribute to microbiota response to diet. Overall, further research on long-term diets that include health and microbiome measures is required before clinical recommendations can be made for dietary modulation of the gut microbiota for health.

Demystifying the manipulation of host immunity, metabolism, and extraintestinal tumors by the gut microbiome

The trillions of microorganisms in the gut microbiome have attracted much attention recently owing to their sophisticated and widespread impacts on numerous aspects of host pathophysiology. Remarkable progress in large-scale sequencing and mass spectrometry has increased our understanding of the influence of the microbiome and/or its metabolites on the onset and progression of extraintestinal cancers and the efficacy of cancer immunotherapy. Given the plasticity in microbial composition and function, microbial-based therapeutic interventions, including dietary modulation, prebiotics, and probiotics, as well as fecal microbial transplantation, potentially permit the development of novel strategies for cancer therapy to improve clinical outcomes. Herein, we summarize the latest evidence on the involvement of the gut microbiome in host immunity and metabolism, the effects of the microbiome on extraintestinal cancers and the immune response, and strategies to modulate the gut microbiome, and we discuss ongoing studies and future areas of research that deserve focused research efforts.

Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids

BACKGROUND

The microbiome has been implicated in the initiation and persistence of inflammatory bowel disease. Despite the fact that diet is one of the most potent modulators of microbiome composition and function and that dietary intervention is the first-line therapy for treating pediatric Crohn's disease, the relationships between diet-induced remission, enteropathy, and microbiome are poorly understood. Here, we leverage a naturally-occurring canine model of chronic inflammatory enteropathy that exhibits robust remission following nutritional therapy, to perform a longitudinal study that integrates clinical monitoring, 16S rRNA gene amplicon sequencing, metagenomic sequencing, metabolomic profiling, and whole genome sequencing to investigate the relationship between therapeutic diet, microbiome, and disease.

RESULTS

We show that remission induced by a hydrolyzed protein diet is accompanied by alterations in microbial community structure marked by decreased abundance of pathobionts (e.g., Escherichia coli and Clostridium perfringens), reduced severity of dysbiosis, and increased levels of the secondary bile acids, lithocholic and deoxycholic acid. Physiologic levels of these bile acids inhibited the growth of E. coli and C. perfringens isolates, in vitro. Metagenomic analysis and whole genome sequencing identified the bile acid producer Clostridium hiranonis as elevated after dietary therapy and a likely source of secondary bile acids during remission. When C. hiranonis was administered to mice, levels of deoxycholic acid were preserved and pathology associated with DSS colitis was ameliorated. Finally, a closely related bile acid producer, Clostridium scindens, was associated with diet-induced remission in human pediatric Crohn's disease.

CONCLUSIONS

These data highlight that remission induced by a hydrolyzed protein diet is associated with improved microbiota structure, an expansion of bile acid-producing clostridia, and increased levels of secondary bile acids. Our observations from clinical studies of exclusive enteral nutrition in human Crohn's disease, along with our in vitro inhibition assays and in vivo studies in mice, suggest that this may be a conserved response to diet therapy with the potential to ameliorate disease. These findings provide insight into diet-induced remission of gastrointestinal disease and could help guide the rational design of more effective therapeutic diets.

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.

Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome

Perturbations in natural systems generally are the combination of multiple interactions among individual stressors. However, methods to interpret the effects of interacting stressors remain challenging and are biased to identifying synergies which are prioritized in conservation. Therefore we conducted a multiple stressor experiment (no stress, single, double, triple) on the coral Pocillopora meandrina to evaluate how its microbiome changes compositionally with increasing levels of perturbation. We found that effects of nutrient enrichment, simulated predation, and increased temperature are antagonistic, rather than synergistic or additive, for a variety of microbial community diversity measures. Importantly, high temperature and scarring alone had the greatest effect on changing microbial community composition and diversity. Using differential abundance analysis, we found that the main effects of stressors increased the abundance of opportunistic taxa, and two-way interactions among stressors acted antagonistically on this increase, while three-way interactions acted synergistically. These data suggest that: (1) multiple statistical analyses should be conducted for a complete assessment of microbial community dynamics, (2) for some statistical metrics multiple stressors do not necessarily increase the disruption of microbiomes over single stressors in this coral species, and (3) the observed stressor-induced community dysbiosis is characterized by a proliferation of opportunists rather than a depletion of a proposed coral symbiont of the genus Endozoicomonas.

Endophytic bacterial communities in peels and pulp of five root vegetables

Plants contain endophytic bacteria, whose communities both influence plant growth and can be an important source of probiotics. Here we used deep sequencing of a 16S rRNA gene fragment and bacterial cultivation to independently characterize the microbiomes of five plant species from divergent taxonomic orders—potato (Solanum tuberosum), carrot (Daucus sativus), beet (Beta vulgaris), neep (Brassica napus spp. napobrassica), and topinambur (Helianthus tuberosus). We found that both species richness and diversity tend to be higher in the peel, where Alphaproteobacteria and Actinobacteria dominate, while Gammaproteobacteria and Firmicutes dominate in the pulp. A statistical analysis revealed that the main characteristic features of the microbiomes of plant species originate from the peel microbiomes. Topinambur pulp displayed an interesting characteristic feature: it contained up to 10⁸ CFUs of lactic acid bacteria, suggesting its use as a source of probiotic bacteria. We also detected Listeria sp., in topinambur pulps, however, the 16S rRNA gene fragment is unable to distinguish between pathogenic versus non-pathogenic species, so the evaluation of this potential health risk is left to a future study.