Gut microbiome-host interactions in health and disease

Ageing and gut microbes: perspectives for health maintenance and longevity

The ageing process affects the human gut microbiota phylogenetic composition and its interaction with the immune system. Age-related gut microbiota modifications are associated with immunosenescence and inflamm-ageing in a sort of self-sustaining loop, which allows the placement of gut microbiota unbalances among both the causes and the effects of the inflamm-ageing process. Even if, up to now, the link between gut microbiota and the ageing process is only partially understood, the gut ecosystem shows the potential to become a promising target for strategies able to contribute to the health status of older people. In this context, the consumption of pro/prebiotics may be useful in both prevention and treatment of age-related pathophysiological conditions, such as recovery and promotion of immune functions, i.e. adjuvant effect for influenza vaccine, and prevention and/or alleviation of common "winter diseases", as well as constipation and Clostridium difficile-associated diarrhoea. Moreover, being involved in different mechanisms which concur in counteracting inflammation, such as down-regulation of inflammation-associated genes and improvement of colonic mucosa conditions, probiotics have the potentiality to be involved in the promotion of longevity.

Quantifying your body: a how-to guide from a systems biology perspective

During the coming decade we will see an accelerated digital transformation of healthcare. Leading this change within the institutional medical community are both the move to digital medical records and the use of digital biomedical measurement devices. In addition to this institutional evolution, there is a non-institutional, bottom-up, unorganized, highly idiosyncratic movement by early adopters to "quantify" their own bodies. In this article, I share my decade-long personal experience of tracking many blood and stool biomarkers, which provide insight into the health or disease of major subsystems of my body. These results are interpreted in the context of the genetics of my human DNA and that of the microbes in my gut. Even though I am a computer scientist and not a medical professional, by using commercially available tests and a systems biology integrative approach, I have become an early example of Leroy Hood's vision of the emergence of predictive, preventive, personalized, and participatory (P4) medicine. It is an individual's story illustrating how each of us can contribute to realizing this paradigm shift.

Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut

The human gut microbiota consists of ten times more microorganisms than there are cells in our body, processes otherwise indigestible nutrients, and produces important energy precursors, essential amino acids, and vitamins. In this study, we assembled and validated a genome-scale metabolic reconstruction of Bacteroides thetaiotaomicron (iAH991), a prominent representative of the human gut microbiota, consisting of 1488 reactions, 1152 metabolites, and 991 genes. To create a comprehensive metabolic model of host-microbe interactions, we integrated iAH991 with a previously published mouse metabolic reconstruction, which was extended for intestinal transport and absorption reactions. The two metabolic models were linked through a joint compartment, the lumen, allowing metabolite exchange and providing a route for simulating different dietary regimes. The resulting model consists of 7239 reactions, 5164 metabolites, and 2769 genes. We simultaneously modeled growth of mouse and B. thetaiotaomicron on five different diets varying in fat, carbohydrate, and protein content. The integrated model captured mutually beneficial cross-feeding as well as competitive interactions. Furthermore, we identified metabolites that were exchanged between the two organisms, which were compared with published metabolomics data. This analysis resulted for the first time in a comprehensive description of the co-metabolism between a host and its commensal microbe. We also demonstrate in silico that the presence of B. thetaiotaomicron could rescue the growth phenotype of the host with an otherwise lethal enzymopathy and vice versa. This systems approach represents a powerful tool for modeling metabolic interactions between a gut microbe and its host in health and disease.

Current nutritional recommendations and novel dietary strategies to manage sarcopenia

Sarcopenia, the loss of skeletal muscle mass and function that occurs with aging, is associated with increased risk for several adverse health outcomes, including frailty, disability, falls, loss of independent living, and mortality. At present, no pharmacological treatment exists that is able to definitely halt the progression of sarcopenia. Likewise, no pharmacological remedies are yet available to prevent the onset of age-related muscle wasting. In this scenario, the combination of nutritional interventions and physical exercise appears to be the most effective strategy presently available for the management of sarcopenia. The purposes of this review are to summarize the current knowledge on the role of nutrition as a countermeasure for sarcopenia, illustrate the mechanisms of action of relevant dietary agents on the aging muscle, and introduce novel nutritional strategies that may help preserve muscle mass and function into old age. Issues related to the identification of the optimal timing of nutritional interventions in the context of primary and secondary prevention are also discussed. Finally, the prospect of elaborating personalized dietary and physical exercise recommendations through the implementation of integrated, high-throughput analytic approaches is illustrated.

Dietary patterns and colorectal cancer recurrence and survival: a cohort study

OBJECTIVE

To examine the association between dietary patterns and colorectal cancer (CRC) survival.

DESIGN

Cohort study.

SETTING

A familial CRC registry in Newfoundland.

PARTICIPANTS

529 newly diagnosed CRC patients from Newfoundland. They were recruited from 1999 to 2003 and followed up until April 2010.

OUTCOME MEASURE

Participants reported their dietary intake using a food frequency questionnaire. Dietary patterns were identified with factor analysis. Multivariable Cox proportional hazards models were employed to estimate HR and 95% CI for association of dietary patterns with CRC recurrence and death from all causes, after controlling for covariates.

RESULTS

Disease-free survival (DFS) among CRC patients was significantly worsened among patients with a high processed meat dietary pattern (the highest vs the lowest quartile HR 1.82, 95% CI 1.07 to 3.09). No associations were observed with the prudent vegetable or the high-sugar patterns and DFS. The association between the processed meat pattern and DFS was restricted to patients diagnosed with colon cancer (the highest vs the lowest quartile: HR 2.29, 95% CI 1.19 to 4.40) whereas the relationship between overall survival (OS) and this pattern was observed among patients with colon cancer only (the highest vs the lowest quartile: HR 2.13, 95% CI 1.03 to 4.43). Potential effect modification was noted for sex (p value for interaction 0.04, HR 3.85 for women and 1.22 for men).

CONCLUSIONS

The processed meat dietary pattern prior to diagnosis is associated with higher risk of tumour recurrence, metastasis and death among patients with CRC.

'Someone should oversee it': patient perspectives on the ethical issues arising with the regulation of probiotics

BACKGROUND

Although many probiotic products are currently available in yogurt or pill form in the United States (US), there is uncertainty surrounding the structure of regulation of these products. As more therapeutic probiotics are developed, changes to existing regulatory process in the United States may be required to meet the needs of patients and users in the population.

OBJECTIVE

This study examined how patients with chronic gastrointestinal (GI) diseases view the regulation of probiotics.

DESIGN

We conducted a multi-site qualitative study consisting of focus groups of patients with chronic gastrointestinal diseases at three tertiary hospitals: at [institutions removed for blinded review].

RESULTS

We conducted 22 focus groups with 136 patients with major gastrointestinal (GI) diseases between March and August 2009. Participants were not familiar with the existing regulation of probiotic products but wanted assurances of accurate labelling of strain as well as safety. Participants raised concerns that regulation of probiotics might be accompanied by greater costs, reduced access and increased involvement of pharmaceutical companies. Although participants voiced significant doubt of government regulators, they felt that products containing genetically modified probiotic strains should have oversight comparable to that of pharmaceutical drugs.

DISCUSSION AND CONCLUSION

If GI patient perspectives are indicative of public perceptions of therapeutic probiotics in the United States, consumers may expect more rigorous regulation in the future while simultaneously wanting low costs, easy access and low involvement of pharmaceutical companies. Manufacturers, translational scientists, clinicians and regulators should be sensitive to consumer attitudes when designing, testing and regulating new therapeutic probiotics.

Integration of datasets from different analytical techniques to assess the impact of nutrition on human metabolome

Bacteria colonizing the human intestinal tract exhibit a high phylogenetic diversity that reflects their immense metabolic potentials. The catalytic activity of gut microbes has an important impact on gastrointestinal (GI) functions and host health. The microbial conversion of carbohydrates and other food components leads to the formation of a large number of compounds that affect the host metabolome and have beneficial or adverse effects on human health. Metabolomics is a metabolic-biology system approach focused on the metabolic responses understanding of living systems to physio-pathological stimuli by using multivariate statistical data on human body fluids obtained by different instrumental techniques. A metabolomic approach based on an analytical platform could be able to separate, detect, characterize and quantify a wide range of metabolites and its metabolic pathways. This approach has been recently applied to study the metabolic changes triggered in the gut microbiota by specific diet components and diet variations, specific diseases, probiotic and synbiotic food intake. This review describes the metabolomic data obtained by analyzing human fluids by using different techniques and particularly Gas Chromatography Mass Spectrometry Solid-phase Micro Extraction (GC-MS/SPME), Proton Nuclear Magnetic Resonance (¹H-NMR) Spectroscopy and Fourier Transform Infrared (FTIR) Spectroscopy. This instrumental approach has a good potential in the identification and detection of specific food intake and diseases biomarkers.

Unique secreted-surface protein complex of Lactobacillus rhamnosus, identified by phage display

Proteins are the most diverse structures on bacterial surfaces; hence, they are candidates for species- and strain-specific interactions of bacteria with the host, environment, and other microorganisms. Genomics has decoded thousands of bacterial surface and secreted proteins, yet the function of most cannot be predicted because of the enormous variability and a lack of experimental data that would allow deduction of function through homology. Here, we used phage display to identify a pair of interacting extracellular proteins in the probiotic bacterium Lactobacillus rhamnosus HN001. A secreted protein, SpcA, containing two bacterial immunoglobulin-like domains type 3 (Big-3) and a domain distantly related to plant pathogen response domain 1 (PR-1-like) was identified by screening of an L. rhamnosus HN001 library using HN001 cells as bait. The SpcA-"docking" protein, SpcB, was in turn detected by another phage display library screening, using purified SpcA as bait. SpcB is a 3275-residue cell-surface protein that contains general features of large glycosylated Serine-rich adhesins/fibrils from gram-positive bacteria, including the hallmark signal sequence motif KxYKxGKxW. Both proteins are encoded by genes within a L. rhamnosus-unique gene cluster that distinguishes this species from other lactobacilli. To our knowledge, this is the first example of a secreted-docking protein pair identified in lactobacilli.

Global metabolic profiling of animal and human tissues via UPLC-MS

Obtaining comprehensive, untargeted metabolic profiles for complex solid samples, e.g., animal tissues, requires sample preparation and access to information-rich analytical methodologies such as mass spectrometry (MS). Here we describe a practical two-step process for tissue samples that is based on extraction into 'aqueous' and 'organic' phases for polar and nonpolar metabolites. Separation methods such as ultraperformance liquid chromatography (UPLC) in combination with MS are needed to obtain sufficient resolution to create diagnostic metabolic profiles and identify candidate biomarkers. We provide detailed protocols for sample preparation, chromatographic procedures, multivariate analysis and metabolite identification via tandem MS (MS/MS) techniques and high-resolution MS. By using these optimized approaches, analysis of a set of samples using a 96-well plate format would take ~48 h: 1 h for system setup, 8-10 h for sample preparation, 34 h for UPLC-MS analysis and 2-3 h for preliminary/exploratory data processing, representing a robust method for untargeted metabolic screening of tissue samples.

Normal neonatal microbiome variation in relation to environmental factors, infection and allergy

PURPOSE OF REVIEW

Bacterial colonization of the infant intestinal tract begins at birth. We are at the forefront of understanding complex relationships between bacteria and multiple parameters of health of the developing infant. Moreover, the establishment of the microbiome in the critical neonatal period is potentially foundational for lifelong health and disease susceptibility. Recent studies utilizing state-of-the-art culture-independent technologies have begun to increase our knowledge about the gut microbiome in infancy, the impact of multiple exposures, and its effects on immune response and clinical outcomes such as allergy and infection.

RECENT FINDINGS

Postnatal exposures play a central role in the complex interactions between the nearly blank canvas of the neonatal intestine, whereas genetic factors do not appear to be a major factor. Infant microbial colonization is affected by delivery mode, dietary exposures, antibiotic exposure, and environmental toxicants. Successive microbiome acquisition in infancy is likely a determinant of early immune programming, subsequent infection, and allergy risk.

SUMMARY

The novel investigation of the neonatal microbiome is beginning to unearth substantial information, with a focus on immune programming that coevolves with the developing microbiome early in life. Several exposures common to neonatal and infant populations could exert pressure on the development of the microbiome and major diseases including allergy and infection in large populations.

Promise of personalized omics to precision medicine

The rapid development of high-throughput technologies and computational frameworks enables the examination of biological systems in unprecedented detail. The ability to study biological phenomena at omics levels in turn is expected to lead to significant advances in personalized and precision medicine. Patients can be treated according to their own molecular characteristics. Individual omes as well as the integrated profiles of multiple omes, such as the genome, the epigenome, the transcriptome, the proteome, the metabolome, the antibodyome, and other omics information are expected to be valuable for health monitoring, preventative measures, and precision medicine. Moreover, omics technologies have the potential to transform medicine from traditional symptom-oriented diagnosis and treatment of diseases toward disease prevention and early diagnostics. We discuss here the advances and challenges in systems biology-powered personalized medicine at its current stage, as well as a prospective view of future personalized health care at the end of this review.

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We applied this approach to an RNA mixture derived from three diverse cultured bacterial species and to RNA isolated from clinical stool samples. The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA.

Surgical systems biology and personalized longitudinal phenotyping in critical care

Systems-wide molecular analysis of the metabolic, inflammatory and immune response to surgical trauma has yet to be translated into the operating room. Surgical patients are exposed to a large number of heterogeneous environmental insults that cannot only be quantified by genome-orientated 'omics platforms. Furthermore, surgery demands rapid or near real-time analysis. Systems-level metabolic phenotyping provides a novel 'global' perspective of an organism's metabolic response to surgical injury and, therefore, serves as an ideal platform for the development of personalized therapies in surgery. This article reviews current personalized approaches to healthcare in surgery and explores future directions for personalized surgical biomarker discovery and therapeutics. In particular, this article discusses our vision of 'personalized metabolic phenotyping' in surgery, and outlines next-generation technologies that will make this approach a reality.

Systems biology: personalized medicine for the future?

Systems biology is actively transforming the field of modern health care from symptom-based disease diagnosis and treatment to precision medicine in which patients are treated based on their individual characteristics. Development of high-throughput technologies such as high-throughout sequencing and mass spectrometry has enabled scientists and clinicians to examine genomes, transcriptomes, proteomes, metabolomes, and other omics information in unprecedented detail. The combined 'omics' information leads to a global profiling of health and disease, and provides new approaches for personalized health monitoring and preventative medicine. In this article, we review the efforts of systems biology in personalized medicine in the past 2 years, and discuss in detail achievements and concerns, as well as highlights and hurdles for future personalized health care.

Microbial co-occurrence relationships in the human microbiome

The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the dental plaque) are more likely to co-occur in complementary niches. This approach thus serves to open new opportunities for future targeted mechanistic studies of the microbial ecology of the human microbiome.

The human body is a complex ecosystem where microbes compete, and cooperate. These interactions can support health or promote disease, e.g. in dental plaque formation. The Human Microbiome Project collected and sequenced ca. 5,000 samples from 18 different body sites, including the airways, gut, skin, oral cavity and vagina. These data allowed the first assessment of significant patterns of co-presence and exclusion among human-associated bacteria. We combined sparse regression with an ensemble of similarity measures to predict microbial relationships within and between body sites. This captured known relationships in the dental plaque, vagina, and gut, and also predicted novel interactions involving members of under-characterized phyla such as TM7. We detected relationships necessary for plaque formation and differences in community composition among dominant members of the gut and vaginal microbiomes. Most relationships were strongly niche-specific, with only a few hub microorganisms forming links across multiple body areas. We also found that phylogenetic distance had a strong impact on the interaction type: closely related microorganisms co-occurred within the same niche, whereas most exclusive relationships occurred between more distantly related microorganisms. This establishes both the specific organisms and general principles by which microbial communities associated with healthy humans are assembled and maintained.

Host-microbiota interactions in inflammatory bowel disease

The interaction of the host with its abundant intestinal microbiota is complex and engages most of the cells in the intestinal mucosa. The inflammatory bowel diseases appear to be disorders of the host immune response to the microbiota. This is supported by data from induced gene mutations in mice and more recently by the identification of gene variants in humans that result in IBD or IBD susceptibility. These genetic studies have provided insights into the cells and molecular pathways involved in the host-microbiota dialog. This review discusses the innate, adaptive, and regulatory immune response to the microbiota in the context of the mouse and human genes that are involved in maintaining intestinal homeostasis and preventing inflammation. These data continue to support the hypothesis that inflammatory bowel disease results from a dysregulated adaptive immune response, particularly a CD4 T-cell response, to the microbiota. The microbiota itself is an active participant in these homeostatic processes. The microbiota composition is perturbed during inflammation, resulting in a dysbiosis that may induce or perpetuate inflammation. However, host genotype and the environment have a major impact on the shape of such dysbiosis, as well as upon which members of the microbiota stimulate pathogenic immune responses.

'Omics' of the mammalian gut--new insights into function

To understand the role of gut microbes in host health, it is imperative to probe their genetic potential, expression, and ecological status. The current high-throughput sequencing revolution, in addition to advances in mass spectrometry-based proteomics, have recently enabled deep access to these complex environments, and are revealing important insights into the roles of the gastrointestinal (GI) microbiota in host physiology and health. This review discusses examples of how the integration of cutting-edge 'meta-omics' technologies are providing new knowledge about the relationships between host health status in mammals and the microbes inhabiting the GI tract. In addition, we address some promises that these techniques hold for future therapeutic and diagnostic applications.

Gut indigenous microbiota and epigenetics

This review introduces and discusses data regarding fundamental and applied investigations in mammalian epigenomics and gut microbiota received over the last 10 years. Analysis of these data enabled us first to come to the conclusion that the multiple low-molecular-weight substances of indigenous gut microbiota origin should be considered one of the main endogenous factors actively participating in epigenomic mechanisms that are responsible for the mammalian genome reprograming and post-translated modifications. Gut microecological imbalance caused by various biogenic and abiogenic agents and factors can produce different epigenetic abnormalities and the onset and progression of metabolic diseases associated. The authors substantiate the necessity to create an international project 'Human Gut Microbiota and Epigenomics' that facilitates interdisciplinary collaborations among scientists and clinicians engaged in host microbial ecology, nutrition, metagenomics, epigenomics, and metabolomics investigations as well as in disease prevention and treatment. Some priority scientific and applied directions in the current omic technologies coupled with gnotobiological approaches are suggested that can open a new era in characterizing the role of the symbiotic microbiota small metabolic and signal molecules in the host epigenomics. Although the discussed subject is only at an early stage its validation can open novel approaches in drug discovery studies.

Third-generation sequencing techniques and applications to drug discovery

INTRODUCTION

There is an immediate need for functional and molecular studies to decipher differences between disease and 'normal' settings to identify large quantities of validated targets with the highest therapeutic utilities. Furthermore, drug mechanism of action and biomarkers to predict drug efficacy and safety need to be identified for effective design of clinical trials, decreasing attrition rates, regulatory agency approval process and drug repositioning. By expanding the power of genetics and pharmacogenetics studies, next-generation nucleic acid sequencing technologies have started to play an important role in all stages of drug discovery.

AREAS COVERED

This article reviews the first- and second-generation sequencing technologies (SGSTs) and challenges they pose to biomedicine. The article then focuses on the emerging third-generation sequencing technologies (TGSTs), their technological foundations and potential contributions to drug discovery.

EXPERT OPINION

Despite the scientific and commercial success of SGSTs, the goal of rapid, comprehensive and unbiased sequencing of nucleic acids has not been achieved. TGSTs promise to increase sequencing throughput and read lengths, decrease costs, run times and error rates, eliminate biases inherent in SGSTs and offer capabilities beyond nucleic acid sequencing. Such changes will have positive impact on all sequencing applications to drug discovery.

Cell biology of ischemia/reperfusion injury

Disorders characterized by ischemia/reperfusion (I/R), such as myocardial infarction, stroke, and peripheral vascular disease, continue to be among the most frequent causes of debilitating disease and death. Tissue injury and/or death occur as a result of the initial ischemic insult, which is determined primarily by the magnitude and duration of the interruption in the blood supply, and then subsequent damage induced by reperfusion. During prolonged ischemia, ATP levels and intracellular pH decrease as a result of anaerobic metabolism and lactate accumulation. As a consequence, ATPase-dependent ion transport mechanisms become dysfunctional, contributing to increased intracellular and mitochondrial calcium levels (calcium overload), cell swelling and rupture, and cell death by necrotic, necroptotic, apoptotic, and autophagic mechanisms. Although oxygen levels are restored upon reperfusion, a surge in the generation of reactive oxygen species occurs and proinflammatory neutrophils infiltrate ischemic tissues to exacerbate ischemic injury. The pathologic events induced by I/R orchestrate the opening of the mitochondrial permeability transition pore, which appears to represent a common end-effector of the pathologic events initiated by I/R. The aim of this treatise is to provide a comprehensive review of the mechanisms underlying the development of I/R injury, from which it should be apparent that a combination of molecular and cellular approaches targeting multiple pathologic processes to limit the extent of I/R injury must be adopted to enhance resistance to cell death and increase regenerative capacity in order to effect long-lasting repair of ischemic tissues.

Experimental and analytical tools for studying the human microbiome

The human microbiome substantially affects many aspects of human physiology, including metabolism, drug interactions and numerous diseases. This realization, coupled with ever-improving nucleotide sequencing technology, has precipitated the collection of diverse data sets that profile the microbiome. In the past 2 years, studies have begun to include sufficient numbers of subjects to provide the power to associate these microbiome features with clinical states using advanced algorithms, increasing the use of microbiome studies both individually and collectively. Here we discuss tools and strategies for microbiome studies, from primer selection to bioinformatics analysis.

Metagenomics: key to human gut microbiota

The human gastrointestinal tract harbors the most complex human microbial ecosystem (intestinal microbiota). The comprehensive genome of these microbial populations (intestinal microbiome) is estimated to have a far greater genetic potential than the human genome itself. Correlations between changes in composition and activity of the gut microbiota and common disorders, such as inflammatory bowel diseases, obesity, diabetes, and atopic diseases, have been proposed, increasing the interest of the scientific community in this research field. In this perspective, a comprehensive and detailed view of the human gut microbiota, in terms of phylogenetic composition as well as genetic and metabolic potential, is essential to understand the dynamics and possible mechanisms of the cause/effect relationships between gut microbiota and pathology. Metagenomics has emerged as one of the most powerful sequence-driven approaches to study the composition and the genetic potential of this complex ecosystem, and efforts in this direction have been smoothed by the implementation of next generation sequencing platforms. Here, we highlight the potential of the newest high-throughput, culture-independent approaches for the characterization of the human gut microbiome in health and disease. Recent and promising results in this field are presented, underlining the perspectives and future research direction of human gut microbial ecology.

1H NMR-based metabonomic applications to decipher gut microbial metabolic influence on mammalian health

Recent advances in molecular biology and microbiology have increased awareness on the importance of the gut microbiota to the overall mammalian host's health status. There is therefore increasing interest in nutrition research to characterise the molecular foundations of the gut microbial mammalian crosstalk at both physiological and biochemical pathway levels. Tackling these challenges can be achieved through systems biology strategies based on the measurement of metabolites to assess the highly complex metabolic exchanges between diverse biological compartments, including organs, biofluids and microbial symbionts. By opening a direct biochemical window into the metabolome, metabonomics is uniquely suited for the identification of biomarkers providing better understanding of these complex metabolic processes. Recent applications of top-down system biology based on (1)H NMR spectroscopy coupled to advanced chemometric modelling approaches provided compelling evidence that system-wide and organ-specific changes in biochemical processes may be finely tuned by gut microbial activities. This review aims at describing current advances in NMR-based metabonomics where the main objective is to discern the molecular pathways and biochemical mechanisms under the influence of the gut microbiota. Furthermore, emphasis is given on nutritional approaches, where the quest for homeostatic balance is dependent not only on the host but also on the nutritional modulation of the gut microbiota-host metabolic interactions, using, for instance, probiotics and prebiotics.

Microbial symbionts: a resource for the management of insect-related problems

Microorganisms establish with their animal hosts close interactions. They are involved in many aspects of the host life, physiology and evolution, including nutrition, reproduction, immune homeostasis, defence and speciation. Thus, the manipulation and the exploitation the microbiota could result in important practical applications for the development of strategies for the management of insect-related problems. This approach, defined as 'Microbial Resource Management' (MRM), has been applied successfully in various environments and ecosystems, as wastewater treatments, prebiotics in humans, anaerobic digestion and so on. MRM foresees the proper management of the microbial resource present in a given ecosystem in order to solve practical problems through the use of microorganisms. In this review we present an interesting field for application for MRM concept, i.e. the microbial communities associated with arthropods and nematodes. Several examples related to this field of applications are presented. Insect microbiota can be manipulated: (i) to control insect pests for agriculture; (ii) to control pathogens transmitted by insects to humans, animals and plants; (iii) to protect beneficial insects from diseases and stresses. Besides, we prospect further studies aimed to verify, improve and apply MRM by using the insect-symbiont ecosystem as a model.

Low-abundance biofilm species orchestrates inflammatory periodontal disease through the commensal microbiota and complement

Porphyromonas gingivalis is a low-abundance oral anaerobic bacterium implicated in periodontitis, a polymicrobial inflammatory disease, and the associated systemic conditions. However, the mechanism by which P. gingivalis contributes to inflammation and disease has remained elusive. Here we show that P. gingivalis, at very low colonization levels, triggers changes to the amount and composition of the oral commensal microbiota leading to inflammatory periodontal bone loss. The commensal microbiota and complement were both required for P. gingivalis-induced bone loss, as germ-free mice or conventionally raised C3a and C5a receptor-deficient mice did not develop bone loss after inoculation with P. gingivalis. These findings demonstrate that a single, low-abundance species can disrupt host-microbial homeostasis to cause inflammatory disease. The identification and targeting of similar low-abundance pathogens with community-wide impact may be important for treating inflammatory diseases of polymicrobial etiology.

Enteric microbiome metabolites correlate with response to simvastatin treatment

Although statins are widely prescribed medications, there remains considerable variability in therapeutic response. Genetics can explain only part of this variability. Metabolomics is a global biochemical approach that provides powerful tools for mapping pathways implicated in disease and in response to treatment. Metabolomics captures net interactions between genome, microbiome and the environment. In this study, we used a targeted GC-MS metabolomics platform to measure a panel of metabolites within cholesterol synthesis, dietary sterol absorption, and bile acid formation to determine metabolite signatures that may predict variation in statin LDL-C lowering efficacy. Measurements were performed in two subsets of the total study population in the Cholesterol and Pharmacogenetics (CAP) study: Full Range of Response (FR), and Good and Poor Responders (GPR) were 100 individuals randomly selected from across the entire range of LDL-C responses in CAP. GPR were 48 individuals, 24 each from the top and bottom 10% of the LDL-C response distribution matched for body mass index, race, and gender. We identified three secondary, bacterial-derived bile acids that contribute to predicting the magnitude of statin-induced LDL-C lowering in good responders. Bile acids and statins share transporters in the liver and intestine; we observed that increased plasma concentration of simvastatin positively correlates with higher levels of several secondary bile acids. Genetic analysis of these subjects identified associations between levels of seven bile acids and a single nucleotide polymorphism (SNP), rs4149056, in the gene encoding the organic anion transporter SLCO1B1. These findings, along with recently published results that the gut microbiome plays an important role in cardiovascular disease, indicate that interactions between genome, gut microbiome and environmental influences should be considered in the study and management of cardiovascular disease. Metabolic profiles could provide valuable information about treatment outcomes and could contribute to a more personalized approach to therapy.

Vaccinia and other viruses with available vaccines show marked homology with the HIV-1 envelope glycoprotein: the prospect of using existing vaccines to stem the AIDS pandemic

Cross-reactive immunity occurs when infection with or vaccination against one virus protects against another related family member. A search for homologues of the HIV-1 envelope glycoprotein revealed that it is composed of thousands of intercalating and overlapping viral matches of pentapeptide or longer gapped consensi, belonging to over 70% of the currently sequenced virome, infecting all kingdoms from bacteria to man. It was also highly homologous to proteins from the Visna/Maedi and other ovine viruses, while other proteins (nef/tat/gag/pol) were homologous to proteins from the equine infectious anaemia virus and HTLV-2/HTLV-3 viruses. This phenomenon suggests that horizontal gene transfer from coinfecting RNA and DNA viruses to retroviruses is extensive, providing a route for the subsequent insertion of non-retroviral genes into human and other genomes via retroviral integration. This homology includes all viruses for which vaccines already exist. Cross-reactive immunity may be operative in AIDS, as Vaccinia vaccination decreases viral replication in HIV-1 infected patients' cells, for the CCR5 tropic form. Measles, Dengue virus, or GB virus C infections also decrease the HIV-1 viral load. A resumption of Vaccinia/smallpox vaccination might be expected to have a significant effect on the AIDS pandemic, and a careful study of the potential uses of other existing viral and bacterial vaccines merits close attention. This phenomenon may also be relevant to other recalcitrant viruses, bacteria, and parasites for which no vaccine exists and the armory of existing vaccines may have a role to play in diseases other than those for which they were designed.

The intestinal microbiota and chronic disorders of the gut

Mucosal surfaces of the gut are colonized by large numbers of heterogeneous bacteria that contribute to intestinal health and disease. In genetically susceptible individuals, a 'pathogenic community' may arise, whereby abnormal gut flora contributes to alterations in the mucosa and local immune system leading to gastrointestinal disease. These diseases include enteric infections, such as Clostridium difficile infection, small intestinal bacterial overgrowth, functional gastrointestinal disorders (including IBS), IBD and colorectal cancer. Prebiotics, probiotics and synbiotics (a combination of prebiotics and probiotics) have the capacity to reverse pathologic changes in gut flora and local immunity. Intestinal health and disease need to be thoroughly characterized to understand the interplay between the indigenous microbiota, the immune system and genetic host factors. This Review provides a broad overview of the importance of the intestinal microbiota in chronic disorders of the gut.

The intake of grain fibers modulates cytokine levels in blood

Dietary fiber may modulate the environment of the intestinal lumen, alter the intestinal microflora populations, and influence the immune response and disease risk. Epidemiological investigations have suggested that higher fiber intake is associated with lower overall mortality, in particular from cardiovascular and digestive tract diseases. Here a panel of 17 cytokines and chemokines were measured in plasma of 88 cancer-free subjects sampled within the Italian EPIC-Italy cohort. A statistically significant inverse association (p-trend = 0.01) was observed for cereal fiber and cytokines included in the main factor in factor analysis (IL-1β, IL-4, IL-5, IL-6, IL-13, and TNF-α), which alone explained 35.5% of variance. Our study suggests that fiber intake, especially cereal fiber, may be associated with a decreased level of pro-inflammatory cytokines.

Intestinal microbiota in human health and disease: the impact of probiotics

The complex communities of microorganisms that colonise the human gastrointestinal tract play an important role in human health. The development of culture-independent molecular techniques has provided new insights in the composition and diversity of the intestinal microbiota. Here, we summarise the present state of the art on the intestinal microbiota with specific attention for the application of high-throughput functional microbiomic approaches to determine the contribution of the intestinal microbiota to human health. Moreover, we review the association between dysbiosis of the microbiota and both intestinal and extra-intestinal diseases. Finally, we discuss the potential of probiotic microorganism to modulate the intestinal microbiota and thereby contribute to health and well-being. The effects of probiotic consumption on the intestinal microbiota are addressed, as well as the development of tailor-made probiotics designed for specific aberrations that are associated with microbial dysbiosis.

At least it won't hurt: the personal risks of antibiotic exposure

This review presents recent evidence regarding the adverse effects of antibiotic therapy mediated by collateral damage to commensal flora. Two major drivers have characterized recent research in this field: new perspectives into human microbiota afforded by next-generation DNA sequencing techniques and ongoing attention to antimicrobial resistance. New molecular techniques have illustrated that antibiotic therapy can disturb human microbiota, and that these changes are associated with infection. Concurrently, epidemiologic studies using patient-level data offer new insights into the role of antibiotics in the emergence, selection and spread of antimicrobial resistance, and Clostridium difficile infection (CDI).

Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward

In this commentary, we will review some of the early efforts aimed at understanding the role of the enteric microbiota in the causality of inflammatory bowel diseases. By examining these studies and drawing on our own experiences bridging clinical gastroenterology and microbial ecology as part of the NIH-funded Human Microbiome Project (Turnbaugh et al., 2007), we hope to help define some of the “growing pains” that have hampered these initial efforts. It is our sincere hope that this discussion will help advance future efforts in this area by identifying current challenges and limitations and by suggesting strategies to overcome these obstacles.