The fecal metabolome as a functional readout of the gut microbiome

Integrative analysis of the intestinal metabolome of childhood asthma

BACKGROUND

The intestinal metabolome reflects the biological consequences of diverse exposures and might provide insight into asthma pathophysiology.

OBJECTIVE

We sought to perform an untargeted integrative analysis of the intestinal metabolome of childhood asthma in this ancillary study of the Vitamin D Antenatal Asthma Reduction Trial.

METHODS

Metabolomic profiling was performed by using mass spectrometry on fecal samples collected from 361 three-year-old subjects. Adjusted logistic regression analyses identified metabolites and modules of highly correlated metabolites associated with asthma diagnosis by age 3 years. Sparse canonical correlation analysis identified associations relevant to asthma between the intestinal metabolome and other "omics": the intestinal microbiome as measured by using 16S rRNA sequencing, the plasma metabolome as measured by using mass spectrometry, and diet as measured by using food frequency questionnaires.

RESULTS

Several intestinal metabolites were associated with asthma at age 3 years, including inverse associations between asthma and polyunsaturated fatty acids (adjusted logistic regression β = -6.3; 95% CI, -11.3 to -1.4; P = .01) and other lipids. Asthma-associated intestinal metabolites were significant mediators of the inverse relationship between exclusive breast-feeding for the first 4 months of life and asthma (P for indirect association = .04) and the positive association between a diet rich in meats and asthma (P = .03). Specific intestinal bacterial taxa, including the family Christensenellaceae, and plasma metabolites, including γ-tocopherol/β-tocopherol, were positively associated with asthma and asthma-associated intestinal metabolites.

CONCLUSION

Integrative analyses revealed significant interrelationships between the intestinal metabolome and the intestinal microbiome, plasma metabolome, and diet in association with childhood asthma. These findings require replication in future studies.

The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens

The gut microbiota has an important role in animal health and performance, but its contribution is difficult to determine, in particular given the effects of host genetic factors. Here, whole-genome sequencing of the hosts and 16S rRNA gene sequencing of the microbiota were performed to separate the effects between host genetics and the microbiota in the duodenum, jejunum, ileum, caecum and faeces on fat deposition in 206 yellow broilers reared under identical conditions. Despite the notable spatial variation in the diversity, composition and potential function of the gut microbiota, host genetics exerted limited effects on the gut microbial community. The duodenal and caecal microbiota made greater contributions to fat deposition and could separately account for 24% and 21% of the variance in the abdominal fat mass after correcting for host genetic effects. We further identified two caecal microbial taxa, Methanobrevibacter and Mucispirillum schaedleri, which were significantly correlated with fat deposition. Chickens with a lower Methanobrevibacter abundance had significantly lower abdominal fat content than those with a higher abundance of Methanobrevibacter (35.51 vs. 55.59 g), and the body weights of these chickens did not notably differ. Chickens with a higher M. schaedleri abundance exhibited lower abdominal fat accumulation (39.88 vs. 55.06 g) and body weight (2.23 vs. 2.41 kg) than those with a lower abundance of this species. These findings may aid the development of strategies for altering the gut microbiota to control fat deposition during broiler production.

Host and microbiome multi-omics integration: applications and methodologies

The study of the microbial community-the microbiome-associated with a human host is a maturing research field. It is increasingly clear that the composition of the human's microbiome is associated with various diseases such as gastrointestinal diseases, liver diseases and metabolic diseases. Using high-throughput technologies such as next-generation sequencing and mass spectrometry-based metabolomics, we are able to comprehensively sequence the microbiome-the metagenome-and associate these data with the genomic, epigenomics, transcriptomic and metabolic profile of the host. Our review summarises the application of integrating host omics with microbiome as well as the analytical methods and related tools applied in these studies. In addition, potential future directions are discussed.

Recent advances and perspectives of metabolomics-based investigations in Parkinson's disease

Parkinson's disease (PD) is the second most prevalent neurodegenerative disease of the central nervous system (CNS), which affects mostly older adults. In recent years, the incidence of PD has been dramatically increasing with the aging population expanding. Due to the lack of effective biomarkers, the accurate diagnosis and precise treatment of PD are currently compromised. Notably, metabolites have been considered as the most direct reflection of the physiological and pathological conditions in individuals and represent attractive candidates to provide deep insights into disease phenotypes. By profiling the metabolites in biofluids (cerebrospinal fluid, blood, urine), feces and brain tissues, metabolomics has become a powerful and promising tool to identify novel biomarkers and provide valuable insights into the etiopathogenesis of neurological diseases. In this review, we will summarize the recent advancements of major analytical platforms implemented in metabolomics studies, dedicated to the improvement and extension of metabolome coverage for in-depth biological research. Based on the current metabolomics studies in both clinical populations and experimental PD models, this review will present new findings in metabolomics biomarkers research and abnormal metabolic pathways in PD, and will discuss the correlation between metabolomic changes and clinical conditions of PD. A better understanding of the biological underpinning of PD pathogenesis might offer novel diagnostic, prognostic, and therapeutic approaches to this devastating disease.

Pathobiont release from dysbiotic gut microbiota biofilms in intestinal inflammatory diseases: a role for iron?

Gut microbiota interacting with an intact mucosal surface are key to the maintenance of homeostasis and health. This review discusses the current state of knowledge of the biofilm mode of growth of these microbiota communities, and how in turn their disruptions may cause disease. Beyond alterations of relative microbial abundance and diversity, the aim of the review is to focus on the disruptions of the microbiota biofilm structure and function, the dispersion of commensal bacteria, and the mechanisms whereby these dispersed commensals may become pathobionts. Recent findings have linked iron acquisition to the expression of virulence factors in gut commensals that have become pathobionts. Causal studies are emerging, and mechanisms common to enteropathogen-induced disruptions, as well as those reported for Inflammatory Bowel Disease and colo-rectal cancer are used as examples to illustrate the great translational potential of such research. These new observations shed new light on our attempts to develop new therapies that are able to protect and restore gut microbiota homeostasis in the many disease conditions that have been linked to microbiota dysbiosis.

The Gut Microbiome in Pancreatic Disease

The gut microbiome increasingly is recognized for its role in human health and disease. Initial evidence has indicated that gut microbial dysbiosis is associated with several pancreatic diseases. Although it is not known if these associations are causative, gut dysbiosis is hypothesized to mediate chronic proinflammatory changes in the pancreas. Further mechanistic and epidemiologic studies of the microbiome are needed. Ultimately, targeted modulation of the microbiota could have therapeutic value.

The fecal metabolome is associated with gestational diabetes mellitus

Dysbiosis of gut microbiota has been linked to gestational diabetes mellitus (GDM), and grows as a resource for GDM biomarkers. However, the contributions of gut microbiota to GDM remain incompletely understood. Metabolites are key messengers in the interactions between gut microbiota and the host. Metabolomics is emerging as an essential tool in exploring the contributions of gut microbiota to diseases. In this study, we performed ¹H-NMR based metabolomics on the feces of 62 pregnant women, including 31 women with GDM, and 31 women as the non-diabetes (NDM) control. Using Principle Component Analysis (PCA) and Orthogonal Projection to Latent Structures Discrimination Analysis (OPLS-DA), we observed clear cluster separation of the fecal metabolome between women with GDM and the NDM control. We further applied several feature selection methods to find five fecal metabolites contributing to the cluster separation of the fecal metabolome. These five metabolites, namely dibutyl decanedioate, N-acetylgalactosamine-4-sulphate, homocysteine, l-malic acid, and butanone, were significantly correlated with the clinical indices of GDM. Metabolite enrichment and pathway analysis on the five metabolites suggested that the fecal citrate cycle and sulfur metabolism were correlated with GDM. The results of this study demonstrated that disorders in the fecal metabolome are associated with GDM.

Fecal metabolome could separate women with GDM from the non-diabetic control.

The Equine Gastrointestinal Microbiome: Impacts of Age and Obesity

Gastrointestinal microbial communities are increasingly being implicated in host susceptibilities to nutritional/metabolic diseases; such conditions are more prevalent in obese and/or older horses. This controlled study evaluated associations between host-phenotype and the fecal microbiome / metabolome. Thirty-five, Welsh Mountain pony mares were studied across 2 years (Controls, n = 6/year, 5–15 years, Body Condition Score (BCS) 4.5–6/9; Obese, n = 6/year, 5–15 years, BCS > 7/9; Aged, n = 6 Year 1; n = 5 Year 2, ≥19 years old). Animals were individually fed the same hay to maintenance (2% body mass as daily dry matter intake) for 2 (aged / obese) or 4 (control), 4-week periods in a randomized study. Outset phenotype was determined (body fat%, markers of insulin sensitivity). Feces were sampled on the final 3 days of hay feeding-periods and communities determined using Next Generation Sequencing of amplified V1–V2 hypervariable regions of bacterial 16S rRNA. Copy numbers for fecal bacteria, protozoa and fungi were similar across groups, whilst bacterial diversity was increased in the obese group. Dominant bacterial phyla in all groups were Bacteroidetes > Firmicutes > Fibrobacter. Significant differences in the bacterial communities of feces were detected between host-phenotype groups. Relative to controls, abundances of Proteobacteria were increased for aged animals and Bacteroidetes, Firmicutes, and Actinobacteria were increased for obese animals. Over 500 bacterial operational taxonomic units (OTUs) differed significantly between host-phenotype groups. No consistent pattern of changes in discriminant OTUs between groups were maintained across groups and between years. The core bacterial populations contained 21 OTUs, 6.7% of recovered sequences. Distance-based Redundancy Analyses separated fecal bacterial communities with respect to markers of obesity and insulin dysregulation, as opposed to age. Host-phenotype had no impact on the apparent digestibility of dietary GE or DM, fecal volatile fatty acid concentrations or the fecal metabolome (FT-IR). The current study demonstrates that host-phenotype has major effects on equine fecal microbial population structure. Changes were predominantly associated with the obese state, confirming an obesity-associated impact in the absence of nutritional differences. Clear biomarkers of animal-phenotype were not identified within either the fecal microbiome or metabolome, suggesting functional redundancy within the gut microbiome and/or metabolome.

Genetic and non-genetic determinants of clinical phenotypes in cardiomyopathy

Cardiomyopathy, a leading cause of death worldwide, is etiologically and phenotypically heterogeneous and is caused by a combination of genetic and non-genetic factors. Major genomic determinants of dilated cardiomyopathy (DCM) are titin truncating mutations and lamin A/C mutations. Patients with these two genotypes show critically different phenotypes, including penetrance, coexistence with a conduction system abnormality, cardiac prognosis, and treatment response. The transcriptomic and epigenomic characteristics of DCM include activation of the DNA damage response, metabolic reprogramming, and dedifferentiation. The proteomic and metabolomic signatures of the DCM heart include a rigorous dependency for free fatty acids, activation of the stress response, and metabolic reprogramming. Proteomic and metabolomic analyses of blood show a distinct immune response and an unexpected link with pathology-specific microbiota in DCM. The direct integration of multi-omics data will not only elucidate inter-omics associations but also enable omics-based patient stratification, which will lead to a deeper understanding of cardiomyopathy and the development of precision medicine in cardiology.

Insights into microbiome research 3: Who's there versus what are they doing?

The main two questions that large microbiome studies typically address are "who's there?" and "what are they doing?" The first question aims at screening what kind of organisms are present, and it provides a low-resolution, relative composition of the microbiome. The second question focuses on precisely characterizing microbial communities by sequencing their entire genome on and providing insights into their metabolic capabilities. While DNA sequencing has become relatively affordable, differences in cost still exist between targeted and shotgun approaches, thus making these strategies quite complementary and commonly used.

Dietary Protein and Muscle in Aging People: The Potential Role of the Gut Microbiome

Muscle mass, strength, and physical function are known to decline with age. This is associated with the development of geriatric syndromes including sarcopenia and frailty. Dietary protein is essential for skeletal muscle function. Resistance exercise appears to be the most beneficial form of physical activity for preserving skeletal muscle and a synergistic effect has been noted when this is combined with dietary protein. However, older adults have shown evidence of anabolic resistance, where greater amounts of protein are required to stimulate muscle protein synthesis, and response is variable. Thus, the recommended daily amount of protein is greater for older people. The aetiologies and mechanisms responsible for anabolic resistance are not fully understood. The gut microbiota is implicated in many of the postulated mechanisms for anabolic resistance, either directly or indirectly. The gut microbiota change with age, and are influenced by dietary protein. Research also implies a role for the gut microbiome in skeletal muscle function. This leads to the hypothesis that the gut microbiome might modulate individual response to protein in the diet. We summarise the existing evidence for the role of the gut microbiota in anabolic resistance and skeletal muscle in aging people, and introduce the metabolome as a tool to probe this relationship in the future.