Effects of prolonged confined space operations on human gut microbiota and serum metabolome

As an important part of ecosystem, microbes are widely distributed in various habitats. In recent years, more and more attention has been paid to the study on gut microbiota. The gut microbiota and their metabolites influence human and animal nutrition processing, metabolic balance, immune function, gastrointestinal development and other physiological activities. With the deepening of studies on human and animal gut microbiota, it has been found that some factors, such as diet, age, gender, and living environment, impacting on the composition of gut microbiota, while the differences among animal species have more significant influence on the gut microbiota composition. In relatively primitive grassland ecosystems, soil microbes interact with human and animal activities. On the one hand, microbes in the soil environment are the driving forces for the transformation and circulation of organic matter and nutrients. The improvement of soil microbial community diversity is beneficial for the soil fertility. On the other hand, human and animal activities will affect the diversity of soil microbial community. Although there are a lot of researches on soil microbiota, animal and human gut microbiota, their differences in diversity and composition within the same environment have not been studied. The advent of sequencing technology provides an effective mean for the accurate and comprehensive understanding of microbes, especially for the study of uncultivable microorganisms. The PacBio single-molecule real-time (SMRT) technology is advantageous in producing long sequence reads with high accuracy. Based on sequencing the full length 16S rRNA genes, the microbiota composition can be identified to the species level. Therefore, it is an effective approach for studying microbial diversity. We collected 56 stool and soil samples from Xilinguole, including 6, 10, 11, 9, and 10 stool samples from human, goat, cattle, horse, and sheep, respectively, as well as 10 soil samples. Genomic DNA was extracted from the samples. After DNA extraction and quality check, the 16S rRNA genes of all samples were amplified from the genomic DNA. The PCR products were sequenced using the PacBio RS II instrument. The QIIME software (V1.7) was used to analyze the sequencing data, and the R software (version 3.5.0) was used to further analyze and visualize the results. Firstly, it was found that the gut microbiota diversity of human was significantly lower than other samples ( P 0.01). The overall composition of the human and animal gut microbiota were dominated by the Firmicutes and Bacteroidetes phyla. However, the soil microbiota was dominated by Proteobacteria and Acidobacteria. At the genus level, the sheep, goat and cattle gut microbiota were dominated by Clostridium , Bacteroides , and Oscillibacter , while the horse gut microbiota was mainly composed of Clostridium , Eubacterium , and Treponema . The soil microbiota was composed mainly of Blastocatella and Bacillus . The human gut microbiota comprised much of Veillonella , Clostridium , Escherichia/Shigella . At the species level, the human gut microbiota mainly contained Escherichia/Shigella , dysenteriae , Streptococcus salivarius . The sheep, goat, cattle, and horse gut microbiota were dominated by Oscillibacter valericigenes and Eubacterium coprostanoligenes . The major species in soil were Blastocatella fastidiosa and Bacillus longiquaesitum . Moreover, principal coordinate analysis (PCoA) and hierarchical clustering analysis showed some differences in the microbiota structure among human gut, animal gut and soil samples. The gut microbiota structure was similar among cattle, goats and sheep. They were more different from the samples collected from human, horse and soil. We classified all samples into four clusters. Cluster 1 only included human samples; cluster 2 comprised the horse samples; cluster 3 was consisted of the sheep, goat, and cattle samples; while cluster 4 contained only the soil samples. Lastly, we identified the discriminatory OTUs and assigned them taxonomically to the species level. In conclusion, there were significant differences between animal gut microbiota and soil microbiota. The soil microbiota was more complex. As an omnivore, human gut microbiota diversity was significantly lower than other herbivorous animal (namely cattle, goat, horse and sheep). Although cattle, sheep, goat and horses are all herbivorous animals, the distinct features of the digestive systems could contribute to the difference in gut microbiota composition of horse from those of sheep, goat and cattle. This study revealed the differences of gut microbiota diversity between human and other animals, as well as from the soil microbial community. This work has laid a theoretical foundation for further studies on microbial diversity in different habitats.

(1) Background: Dyslipidemia represents a major risk factor for atherosclerosis-driven cardiovascular disease. Emerging evidence suggests a close relationship between cholesterol metabolism and gut microbiota. Recently, we demonstrated that the short-chain fatty acid (SCFA) propionate (PA) reduces serum cholesterol levels through an immunomodulatory mechanism. Here, we investigated the effects of oral PA supplementation on the human serum metabolome and analyzed changes in the serum metabolome in relation to the cholesterol-lowering properties of PA. (2) Methods: The serum metabolome of patients supplemented with either placebo or propionate orally for 8 weeks was assessed using a combination of flow injection analysis-tandem (FIA-MS/MS) as well as liquid chromatography (LC-MS/MS) and mass spectrometry using a targeted metabolomics kit (MxP®Quant 500 kit: BIOCRATES Life Sciences AG, Innsbruck, Austria). A total of 431 metabolites were employed for further investigation in this study. (3) Results: We observed a significant increase in distinct bile acids (GCDCA: fold change = 1.41, DCA: fold change = 1.39, GUDCA: fold change = 1.51) following PA supplementation over the study period, with the secondary bile acid DCA displaying a significant negative correlation with the serum cholesterol levels. (4) Conclusions: Oral supplementation with PA modulates the serum metabolome with a particular impact on the circulatory bile acid profile. Since cholesterol and bile acid metabolism are interconnected, the elevation of the secondary bile acid DCA may contribute to the cholesterol-lowering effect of PA.

Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have undertaken the task of characterizing the human serum metabolome. In doing so, we have combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome. Our use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these platforms or technologies. Tables containing the complete set of 4229 confirmed and highly probable human serum compounds, their concentrations, related literature references and links to their known disease associations are freely available at http://www.serummetabolome.ca.

While the gut microbiome has been reported to play a role in bone metabolism, the individual species and underlying functional mechanisms have not yet been characterized. We conducted a systematic multi-omics analysis using paired metagenomic and untargeted serum metabolomic profiles from a large sample of 499 peri- and early post-menopausal women to identify the potential crosstalk between these biological factors which may be involved in the regulation of bone mineral density (BMD). Single omics association analyses identified 22 bacteria species and 17 serum metabolites for putative association with BMD. Among the identified bacteria, Bacteroidetes and Fusobacteria were negatively associated, while Firmicutes were positively associated. Several of the identified serum metabolites including 3-phenylpropanoic acid, mainly derived from dietary polyphenols, and glycolithocholic acid, a secondary bile acid, are metabolic byproducts of the microbiota. We further conducted a supervised integrative feature selection with respect to BMD and constructed the inter-omics partial correlation network. Although still requiring replication and validation in future studies, the findings from this exploratory analysis provide novel insights into the interrelationships between the gut microbiome and serum metabolome that may potentially play a role in skeletal remodeling processes.

This study investigated the chronic effect of inspiratory muscle training (IMT) on the human serum metabolome in healthy male recreational cyclists. Using a randomized, parallel group design, twenty-eight participants were randomized to three IMT groups: low intensity (LI, n = 7); moderate intensity (MI, n = 10); and high intensity (HI, n = 11). The IMT was performed for 11 weeks. Another group of participants under the same conditions, who did not perform the IMT but participated in all procedures, was included as controls (CG, n = 6). Blood samples were collected one week before and after 11 weeks of IMT and analyzed for metabolite shifts using 1H NMR. Statistical analysis included a 4 (group) × 2 (time) repeated measures ANOVA using the general linear model (GLM), and multivariate principal component analysis (PCA). Untargeted metabolomics analysis of serum samples identified 22 metabolites, including amino acids, lipids, and tricarboxylic acid cycle intermediates. Metabolites shifts did not differ between groups, indicating that IMT at three intensity levels did not alter the serum metabolome relative to the control group. These results reveal novel insights into the metabolic effects of the IMT and are consistent with the results from other studies showing negligible chronic alterations in the serum metabolome in response to physical training.

Influence of the co-exposure of microplastics and tetrabromobisphenol A on human gut: Simulation in vitro with human cell Caco-2 and gut microbiota

Metabolic Footprinting of Fermented Milk Consumption in Serum of Healthy Men

Phenotyping of 1,200 ‘healthy’ adults from the UK has been performed through the investigation of diverse classes of hydrophilic and lipophilic metabolites present in serum by applying a series of chromatography–mass spectrometry platforms. These data were made robust to instrumental drift by numerical correction; this was prerequisite to allow detection of subtle metabolic differences. The variation in observed metabolite relative concentrations between the 1,200 subjects ranged from less than 5 % to more than 200 %. Variations in metabolites could be related to differences in gender, age, BMI, blood pressure, and smoking. Investigations suggest that a sample size of 600 subjects is both necessary and sufficient for robust analysis of these data. Overall, this is a large scale and non-targeted chromatographic MS-based metabolomics study, using samples from over 1,000 individuals, to provide a comprehensive measurement of their serum metabolomes. This work provides an important baseline or reference dataset for understanding the ‘normal’ relative concentrations and variation in the human serum metabolome. These may be related to our increasing knowledge of the human metabolic network map. Information on the Husermet study is available at http://www.husermet.org/. Importantly, all of the data are made freely available at MetaboLights (http://www.ebi.ac.uk/metabolights/).Electronic supplementary materialThe online version of this article (doi:10.1007/s11306-014-0707-1) contains supplementary material, which is available to authorized users.

To explore the effect of ultra-strong static magnetic field on gut microbiota, 16 T static magnetic field was used to study the changes in the structure and composition of human and mouse gut microbiota in this environment. In the mouse gut microbiota, at the genus level, the magnetic field significantly decreased the relative abundances of Escherichia-Shigella, Lactobacillus, Enterococcus, Burkholderia-Caballeronia-Paraburkholderia, Parasutterella, and Ralstonia and significantly increased those of Parabacteroides, Alloprevotella, Alistipes, Odoribacter, Bacteroides, Mucispirillum, Sutterella, and Prevotellaceae_UCG-001. Similarly, at the genus level, the relative abundances of Bacteroides, Parabacteroides, Romboutsia, and Streptococcus significantly decreased in the human gut microbiota. Contrary to the changing trend of the abundance in the mouse gut, the abundances of Bacteroides and Parabacteroides in the human gut were significantly reduced under magnetic field. The BugBase phenotypic prediction analysis showed that the relative abundances of five phenotypes, including anaerobism, mobile elements, potential pathogenicity, stress-tolerant, and biofilm formation, changed significantly in the mouse gut microbiota, while the relative abundances of two phenotypes, including Gram-positive and Gram-negative phenotypes, changed significantly in the human gut microbiota. The 16 T magnetic field could differently affect the composition, structure, and phenotypes of gut microbiota in human and mice, suggesting the importance of model selection in studying the biological effects of magnetic field.

Human gut microbiota is the complex community of microorganisms that live in the digestive tracts, including bacteria, archaea, virus, fungi and protists. These microorganisms coevolved together with human body for a long history, forming a balanced micro-ecosystem. Recent researches discovered the close association between gut microbiota and human health. The gut microbiota was thought to be the biggest endocrine organ, which keeps and restores human health by regulating the its composition and structure. Dysregulation in the composition and diversity of microbiota (dysbiosis) is closely associated with diverse metabolism and immune disorders, such as diabetes, allergy, autoimmunity, and gastrointestinal inflammatory disorders. Thus, a balanced network between gut microbiota and human body will be of great help for diagnosis, treatment and prognosis in the field of precision medicine. Gut microbiota also interacts with diet to degrade nutrients and provide additional nutrients. Meanwhile, faecal bacteria can exert a fundamental role in modulating energy metabolism. Studies have shown that in obesity individuals, the gut microbiota composition can be significantly different from that of lean individuals, and that modifications of gut microbiota composition can be associated with increases or reductions of body weight and body mass index. On the other hand, gut bacterial was related with nutrients absorption. Such as, decreased abundance of Lactobacillus maybe relate with iron (Fe) deficiency, which indicated the intimate connection between gut microbiota and nutrients. Development of nutriology has contributed greatly to human health. A well-balanced diet is the basis for a healthy life. Both the western diet and special diets can have a relevant impact on the microbiome and promote the development of various diseases. An increasing in food-related disorders in recent years, largely associated with dramatic changes in food consumption trends and main nutrients. Nutrition has a very special influence on the microbiome as it is an important factor throughout age. Gut bacteria are specialized in the fermentation of various substrates, thus, complex diets can lead to a number of metabolic products, especially vitamins and SCFAs, which are important to human health. Dietary-associated changes in compositional and functional microbiota traits should be correlated with the health status for the future development of dietary recommendations and potential clinical interventions. We have realized the close relationship between human body, gut microbiota, nutrients and immunity, which will bring an unprecedented opportunity for developing precision nutrition. This review will focus on the gut microbiota, nutrition and health. Due to rapid advances in this inter-discipline, we here only choose several facets to discuss.

The Human Serum Metabolome of Vitamin B-12 Deficiency and Repletion, and Associations with Neurological Function in Elderly Adults

The gut microbiota has been identified as a leading cause of irreproducibility in mouse models, but current resources are insufficient to address this core challenge in immunology research. Furthermore, although mouse models are central tools for biomedical science, it is not known how the bacteria in the mouse gut – important determinants of immunological phenotypes – affect their ability to recapitulate human disease. To better characterise the mouse gut microbiota and facilitate its functional and taxonomic comparison to the human microbiota, we developed the Mouse Microbial Genome Collection (MMGC), the most comprehensive representation of the global laboratory mouse microbiome to date. The MMGC is a repository of 276 genomes from cultured isolates and 18,075 non-redundant, near-complete metagenome-assembled genomes (MAGs) reassembled from 1,960 mouse metagenomes. Using the MMGC, we define species-level signatures of inter-institutional variation in the mouse gut microbiota and provide a roadmap to achieve more relevant and reproducible mouse models. In addition, we confirm that while only 2.65% of bacterial species are common to human and mouse gut microbiotas, over 80% of annotatable functions are shared between hosts. The MMGC further enables the identification of functionally equivalent taxa in the mouse and human gut microbiotas, which we illustrate by comparing the pathways for butyrate synthesis and drug metabolism as proof-of-concept examples. In conclusion, the MMGC facilitates unprecedented insights into the mouse gut microbiota and enhances the use of mouse models in immunology research by providing access to the conservation status and taxonomic locations of microbial functions of interest.

Application of Ion Chromatography Coupled with Mass Spectrometry for Human Serum and Urine Metabolomics

One of the major threats to human health in the 21st century is the emergence of pathogenic bacteria that are resistant to multiple antibiotics, thereby limiting treatment options. An important route through which pathogens become resistant is via acquisition of resistance genes from environmental and human-associated bacteria. Yet, it is poorly understood to what extent and by what mechanisms these so-called reservoirs contribute to emerging resistance. Therefore, the work described in this thesis focussed on generating novel insights into different niches as sources of resistance, with a particular focus on the human gut microbiota as well as on microbial communities associated with marine sponges, especially because the latter have been described as one of the richest sources of bioactive secondary metabolites, including a broad range of antimicrobials. Cultivation-based methods were complemented with culture-independent approaches in order to study bacterial taxa that are not readily cultivated. Using metatranscriptomics it was found that clinically relevant antibiotic resistance genes are expressed in a broad range of environmental niches including human, mouse and pig gut microbiota, sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment. The diversity of resistance gene transcripts differed greatly per niche indicating that the environment contains a rich reservoir of functional resistance that could be accessible by pathogens. Even though resistance gene expression might be linked to the presence of natural antibiotics, we did not detect expression of the corresponding secondary metabolite biosynthesis clusters. Thirty-one antibiotic-resistant bacteria, amongst which three belonging to potentially novel Flavobacteriaceae spp., were isolated from the Mediterranean sponges Aplysina aerophoba, Corticium candelabrum and Petrosia ficiformis. Isolates were identified in a high throughput manner by double-barcoded 16S rRNA gene amplicon sequencing. Furthermore, analysis of sponge tissue-derived bacterial biomass growing on agar media showed that many novel bacterial taxa can still be isolated by conventional cultivation methods. Genomic DNA from the 31 antibiotic resistant bacteria was interrogated with respect to the presence of active resistance genes by functional metagenomics. In addition, we also screened metagenomic libraries prepared from DNA directly isolated from sponge tissue in order to circumvent the need for cultivation. In total, 37 unique resistance genes were identified, and the predicted gene products of 15 of these shared <90% amino acid identity with known gene products. One resistance gene (blaPSV-1), which was classified into a new β-lactamase family, was found to be exclusive to the marine specific genus Pseudovibrio. These findings raised questions as to the functional roles of these genes in sponges, but more importantly, the functionality of these genes in E. coli shows that they can potentially be harnessed by phylogenetically distinct bacteria in other environments, including human pathogens. As such, it is a wake-up call as to the significance of marine resistance reservoirs. Pseudovibrio, a genus of α-Proteobacteria, was studied in more detail by comparative genomics as it comprises bacteria that potentially play a role as sponge symbionts and marine hubs of antibiotics resistance. Based on gene content, members of the genus Pseudovibrio were found to cluster by sponge sampling location indicating geographic speciation. Furthermore, Pseudovibrio spp. isolated from sponges near the Spanish coast clustered by sponge, suggesting host-specific colonization or adaptation. Strong support for Pseudovibrio spp. forming symbiotic relations with sponges came from the presence of a plethora of (predicted) conserved symbiosis-related functions in their genomes. A final study aimed to isolate novel antibiotic resistant reservoir species from the human gut microbiota using a targeted approach. Faecal samples from hospitalized patients that received Selective Digestive Decontamination (SDD), a prophylactic treatment with a cocktail of different antibiotics (tobramycin, polymyxin E, amphotericin B and cefotaxime), were inoculated anaerobically on agar media, after which bacterial biomass was analysed by 16S rRNA gene amplicon sequencing. Six novel taxa were identified that, based on their growth on media supplemented with the SDD antibiotics, could serve as clinically relevant reservoirs of antibiotic resistance. For one of these six taxa a member was obtained in pure culture by targeted isolation. The abundance of antibiotic resistant uncultivated taxa in the human gut microbiota warrants further research as to their potential roles in resistance dissemination. In conclusion, this thesis provides deeper insights into different environmental niches as reservoirs of antibiotic resistance. The results can serve to prime and inspire future research.

The gut microbiota plays a key role in the maintenance of healthy gut function as well as many other aspects of health. High-throughput sequence analyses have revealed the composition of the gut microbiota, showing that there is a core signature to the human gut microbiota, as well as variation in its composition between people. The gut microbiota of animals is also being investigated. We are interested in the relationship between bacterial taxa of the human gut microbiota and those in the gut microbiota of domestic and semi-wild animals. While it is clear that some human gut bacterial pathogens come from animals (showing that human – animal transmission occurs), the extent to which the usually non-pathogenic commensal taxa are shared between humans and animals has not been explored. To investigate this we compared the distal gut microbiota of humans, cattle and semi-captive chimpanzees in communities that are geographically sympatric in Uganda. The gut microbiotas of these three host species could be distinguished by the different proportions of bacterial taxa present. We defined multiple operational taxonomic units (OTUs) by sequence similarity and found evidence that some OTUs were common between human, cattle and chimpanzees, with the largest number of shared OTUs occurring between chimpanzees and humans, as might be expected with their close physiological similarity. These results show the potential for the sharing of usually commensal bacterial taxa between humans and other animals. This suggests that further investigation of this phenomenon is needed to fully understand how it drives the composition of human and animal gut microbiotas.