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1.
Julia B. Honneffer Jörg M. Steiner Jonathan A. Lidbury Jan S. Suchodolski 《Metabolomics : Official journal of the Metabolomic Society》2017,13(3):26
Introduction
The fecal microbiota are relevant to the health and disease of many species. The importance of the fecal metabolome has more recently been appreciated, but our knowledge of the microbiota and metabolome at other sites along the gastrointestinal tract remains deficient.Objective
To analyze the gastrointestinal microbiota and metabolome of healthy domestic dogs at four anatomical sites.Methods
Samples of the duodenal, ileal, colonic, and rectal contents were collected from six adult dogs after humane euthanasia for an unrelated study. The microbiota were characterized using Illumina sequencing of 16S rRNA genes. The metabolome was characterized by mass spectrometry-based methods.Results
Prevalent phyla throughout the samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes, consistent with previous findings in dogs and other species. A total of 530 unique metabolites were detected; 199 of these were identified as previously named compounds, but 141 of them had at least one significantly different site-pair comparison. Noteworthy examples include relative concentrations of amino acids, which decreased from the small to large intestine; pyruvate, which peaked in the ileum; and several phenol-containing carboxylic acid compounds that increased in the large intestine.Conclusion
The microbiota and metabolome vary significantly at different sites along the canine gastrointestinal tract.2.
Eriko Tomitsuka Katsura Igai Kiyoshi Tadokoro Ayako Morita Jun Baba Wataru Suda Andrew R. Greenhill Paul F. Horwood Kevin W. Soli Peter M. Siba Shingo Odani Kazumi Natsuhara Hidetoshi Morita Masahiro Umezaki 《Metabolomics : Official journal of the Metabolomic Society》2017,13(9):105
Introduction
Adequate amount of proteins from foods are normally needed to maintain muscle mass of the human body. Although protein intakes of Papua New Guinea (PNG) highlanders are less than biologically adequate, protein deficiency related disorders have rarely been reported. It has been postulated that gut microbiota play a role in such low-protein-adaptation.Objective
To explore underlying biological mechanisms of low-protein adaptation among PNG highlanders by investigating metabolomic profiles of faecal water and urine.Methods
We performed metabolome analysis using faecal water extracted from faecal samples of PNG highlanders, PNG non-highlanders and Japanese subjects. We paid special attention to amino acids and other metabolites produced by gut microbiota, as well as to metabolites involved in nitrogen recycling in the human gut.Results
Our results indicated that amino acid levels were higher in faecal water from PNG highlanders than PNG non-highlanders, but amino acid levels did not differ between PNG highlanders and Japanese subjects. Among PNG highlander samples, amino acid levels tended to be higher in those who consumed less protein.Conclusion
We speculated that a greater proportion of urea was excreted to the intestine among the PNG highlanders than other groups, and that the urea was used for nitrogen salvage. Intestinal bacteria are essential for producing ammonia from urea and also for producing amino acids from ammonia, which is a key process in low-protein adaptation. Profiling the gut microbiota of PNG highlanders is an important avenue for further research into the mechanisms of low-protein adaptation.3.
Background
Pandemic is a typical spreading phenomenon that can be observed in the human society and is dependent on the structure of the social network. The Susceptible-Infective-Recovered (SIR) model describes spreading phenomena using two spreading factors; contagiousness (β) and recovery rate (γ). Some network models are trying to reflect the social network, but the real structure is difficult to uncover.Methods
We have developed a spreading phenomenon simulator that can input the epidemic parameters and network parameters and performed the experiment of disease propagation. The simulation result was analyzed to construct a new marker VRTP distribution. We also induced the VRTP formula for three of the network mathematical models.Results
We suggest new marker VRTP (value of recovered on turning point) to describe the coupling between the SIR spreading and the Scale-free (SF) network and observe the aspects of the coupling effects with the various of spreading and network parameters. We also derive the analytic formulation of VRTP in the fully mixed model, the configuration model, and the degree-based model respectively in the mathematical function form for the insights on the relationship between experimental simulation and theoretical consideration.Conclusions
We discover the coupling effect between SIR spreading and SF network through devising novel marker VRTP which reflects the shifting effect and relates to entropy.4.
Madhusmita Dehingia Supriyo Sen Bhuwan Bhaskar Tulsi K. Joishy Manab Deka Narayan C. Talukdar Mojibur R. Khan 《Metabolomics : Official journal of the Metabolomic Society》2017,13(6):69
Introduction
The human gut microbes and their metabolites are involved in multiple host metabolic pathways. Dysbiosis in the gut microbiota and altered metabolite profiles were reported in diseased state. In a region like Assam, where 12.4% of the populations are tribal population, evaluating the influence of ethnicity on gut microbiota and metabolites has become important to further differentiate it from the diseased state.Objective
To study the influence of ethnicity on fecal metabolite profile and their association with the gut microbiota composition.Methods
In this study, we determined the untargeted fecal metabolites from five ethnic groups of Assam (Tai-Aiton, Bodo, Karbi, Tea-tribe and Tai-Phake) using GC–MS and compared them among the tribes for common and unique metabolites. Metabolites of microbial origin were related with the available metagenomic data on gut bacterial profiles of the same ethnic groups and functional analysis were carried out based on HMDB.Results
The core fecal metabolite profile of the Tea-tribe contained aniline, benzoate and acetaldehyde. PLS-DA based on the metabolites suggested that the individuals grouped based on their ethnicity. PCA plot of the data on bacterial abundance at the level of genus indicated clustering of individuals based on ethnicity. Positive correlations were observed between propionic acid and the genus Clostridium (R?=?0.43 and p?=?0.03), butyric acid and the genus Lactobacillus (R?=?0.45 and p?=?0.024), acetic acid and the genus Bacteroides (R?=?0.63 and p?=?0.001) and methane and the genus Escherichia (R?=?0.58 and p?=?0.002).Conclusion
Results of this study indicated that ethnicity influences both gut bacterial profile and their metabolites.5.
Rachel A. Spicer Christoph Steinbeck 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):16
Introduction
Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.Objectives
(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.Methods
A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.Results
Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.Conclusion
Further efforts are required to improve data sharing in metabolomics.6.
7.
BACKGROUND
Microbes affect the growth of plants. In this study, the diversity and plant growth-supporting activities of wheat rhizospheric bacteria were examined.METHODS
Sampling was performed thrice at different phases of plant growth. Microbes associated with the rhizoplane of three wheat varieties (Seher, Lasani, and Faisalabad) were cultured and assessed for their plant growth-promoting abilities based on auxin production, hydrogen cyanide production, phosphate solubilization, and nitrogen fixation.RESULTS
Bacterial load (CFU/mL) declined, and the succession of bacterial diversity occurred as the plants aged. Most auxin-producing bacteria and the highest concentrations of auxin (77 μg/mL) were observed during the second sampling point at the tillering stage. The Seher variety harbored the most auxin-producing as well as phosphate-solubilizing bacteria. Most of the bacteria belonged to Bacillus and Pseudomonas. Planomicrobium, Serratia, Rhizobium, Brevundimonas, Stenotrophomonas, and Exiguobacterium sp. were also found.CONCLUSION
These results suggest that the rhizoplane microbiota associated with higher-yield plant varieties have better plant growth-promoting abilities as compared to the microbiota associated with lower-yield plant varieties.8.
9.
Objective
To determine if there is any non-linearity in the biomagnetic recordings of uterine myomas and to find any differences that may be present in the mechanisms underlying their signal dynamics.Methods
Twenty-four women were included in the study. Sixteen of them were characterised with large myomas and 8 with small ones. Uterine artery waveform measurements were evaluated by use of Pulsatility Index (PI) (normal value PI<1.45).Results
Applying nonlinear analysis to the biomagnetic signals of the uterine myomas, we observed a clear saturation value for the group of large ones (mean = 11.35 ± 1.49) and no saturation for the small ones.Conclusion
The comparison of the saturation values in the biomagnetic recordings of large and small myomas may be a valuable tool in the evaluation of functional changes in their dynamic behavior.10.
Effect of gut microbiota on host whole metabolome 总被引:1,自引:0,他引:1
Takeo Moriya Yoshinori Satomi Shumpei Murata Hiroshi Sawada Hiroyuki Kobayashi 《Metabolomics : Official journal of the Metabolomic Society》2017,13(9):101
Introduction
Recent advances in microbiome research have revealed the diverse participation of gut microbiota in a number of diseases. Bacteria-specific endogenous small molecules are produced in the gut, are transported throughout the whole body by circulation, and play key roles in disease establishment. However, the factors and mechanisms underlying these microbial influences largely remain unknown.Objectives
The purpose of this study was to use metabolomics to better understand the influence of microbiota on host physiology.Methods
Germ-free mice (GF) were orally administered with the feces of specific pathogen-free (SPF) mice and were maintained in a vinyl isolator for 4 weeks for establishing the so-called ExGF mice. Comparative metabolomics was performed on luminal contents, feces, urine, plasma, and tissues of GF and ExGF mice.Results
The metabolomics profile of 1716 compounds showed marked difference between GF and ExGF for each matrix. Intestinal differences clearly showed the contribution of microbiota to host digestive activities. In addition, colonic metabolomics revealed the efficient conversion of primary to secondary metabolites by microbiota. Furthermore, metabolomics of tissues and excrements demonstrated the effect of microbiota on the accumulation of metabolites in tissues and during excretion. These effects included known bacterial effects (such as bile acids and amino acids) as well as novel ones, including a drastic decrease of sphingolipids in the host.Conclusion
The diverse effects of microbiota on different sites of the host metabolome were revealed and novel influences on host physiology were demonstrated. These findings should contribute to a deeper understanding of the influence of gut microbiota on disease states and aid in the development of effective intervention strategies.11.
Nadine Strehmel David Strunk Veronika Strehmel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):135
Introduction
Aqueous–methanol mixtures have successfully been applied to extract a broad range of metabolites from plant tissue. However, a certain amount of material remains insoluble.Objectives
To enlarge the metabolic compendium, two ionic liquids were selected to extract the methanol insoluble part of trunk from Betula pendula.Methods
The extracted compounds were analyzed by LC/MS and GC/MS.Results
The results show that 1-butyl-3-methylimidazolium acetate (IL-Ac) predominantly resulted in fatty acids, whereas 1-ethyl-3-methylimidazolium tosylate (IL-Tos) mostly yielded phenolic structures. Interestingly, bark yielded more ionic liquid soluble metabolites compared to interior wood.Conclusion
From this one can conclude that the application of ionic liquids may expand the metabolic snapshot.12.
Martin Steen Mortensen Betina Hebbelstrup Jensen Jeanne Williams Asker Daniel Brejnrod Lee O’Brien Andersen Dennis Röser Bente Utoft Andreassen Andreas Munk Petersen Christen Rune Stensvold Søren Johannes Sørensen Karen Angeliki Krogfelt 《BMC microbiology》2018,18(1):223
Background
We performed a 12-month cohort study of the stability and resilience of the intestinal microbiota of healthy children in daycare in Denmark in relation to diarrheal events and exposure to known risk factors for gastrointestinal health such as travelling and antibiotic use. In addition, we analyzed how gut microbiota recover from such exposures.Results
We monitored 32 children in daycare aged 1–6?years. Fecal samples were submitted every second month during a one-year observational period. Information regarding exposures and diarrheal episodes was obtained through questionnaires. Bacterial communities were identified using 16S rRNA gene sequencing. The core microbiota (mean abundance >?95%) dominated the intestinal microbiota, and none of the tested exposures (diarrheal events, travel, antibiotic use) were associated with decreases in the relative abundance of the core microbiota. Samples exhibited lower intra-individual variation than inter-individual variation. Half of all the variation between samples was explained by which child a sample originated from. Age explained 7.6–9.6% of the variation, while traveling, diarrheal events, and antibiotic use explained minor parts of the beta diversity. We found an age-dependent increase of alpha diversity in children aged 1–3?years, and while diarrheal events caused a decrease in alpha diversity, a recovery time of 40–45?days was observed.Among children having had a diarrheal event, we observed a 10x higher relative abundance of Prevotella. After travelling, a higher abundance of two Bacteroides species and 40% less Lachnospiraceae were seen. Antibiotic use did not correlate with changes in the abundance of any bacteria.Conclusion
We present data showing that Danish children in daycare have stable intestinal microbiota, resilient to the exposures investigated. An early age-dependent increase in the diversity was demonstrated. Diarrheal episodes decreased alpha diversity with an estimated recovery time of 40–45?days.13.
Nazila Ariaee Shima Zarei Mojgan Mohamadi Farahzad Jabbari 《Clinical and molecular allergy : CMA》2017,15(1):22
Background
Spontaneous urticaria is a common allergic skin condition affecting 0.5–1% of individuals and may burden on health care expenditure or may be associated with remarkable morbidity.Aim
In this study, we measured the effect of vitamin D supplementation in patients with a diagnosis of CSU. Furthermore, quality of life and cytokine changes were evaluated.Methods
The clinical trial was conducted on 20 patients with idiopathic chronic urticaria. Vitamin D was administered orally for 8 weeks and disease activity was measured pre- and post-treatment using USS and DLQI. On the other hand expressions of IL-17, IL-10, Foxp3, and TGF-β by Real-time RT-PCR were assessed.Results
USS questionnaire showed that severity of idiopathic urticaria after the intervention, which compared with the first day reached a significant 55% reduction. The DLQI quality of life questionnaire 2 months after treatment showed 55% improvement. Along with the significant improvement of clinical symptoms, use of vitamin D increase FOXP3 gene expression and downregulation of IL-10, TGF-B, and FOXP3, IL-17, but these changes were not statistically significant.Limitation
These might happen due to lack of enrolled population in the investigation.Conclusion
Vitamin D can be used along with standard medical care and it’s a safe and cost-effective method for the treatment of chronic urticaria with deficiency of vitamin D.14.
Nwora Lance Okeke Damian M. Craig Michael J. Muehlbauer Olga Ilkayeva Meredith E. Clement Susanna Naggie Svati H. Shah 《Metabolomics : Official journal of the Metabolomic Society》2018,14(3):23
Introduction
Persons living with HIV (PLWH) are at higher risk for cardiovascular disease (CVD) events than uninfected persons. Current risk-stratification methods to define PLWH at highest risk for CVD events are lacking.Methods
Using tandem flow injection mass spectrometry, we quantified plasma levels of 60 metabolites in 24 matched pairs of PLWH [1:1 with and without known coronary artery disease (CAD)]. Metabolite levels were reduced to interpretable factors using principal components analysis.Results
Factors derived from short-chain dicarboxylacylcarnitines (SCDA) (p?=?0.08) and glutamine/valine (p?=?0.003) were elevated in CAD cases compared to controls.Conclusion
SCDAs and glutamine/valine may be valuable markers of cardiovascular risk among persons living with HIV in the future, pending validation in larger cohorts.15.
Background
Fatigue can be triggered by previous perceived stress which may lead to impairment of performance and function. The purpose of the study was to investigate the relationship between fatigue and perceived stress.Method
Health determinants including sociodemographic factors for associations between fatigue and perceived stress in the general population (N = 2,483) are outlined. Fatigue and stress were assessed with the Chalder Fatigue Scale (CFS) and the Perceived Stress Questionnaire (PSQ).Results
Within the general population, 25.9% of male and 34.5% of female respondents reported moderate fatigue during the last six months; 9.7% of subjects reported substantial fatigue lasting six months or longer. An adjusted regression analysis (R2corr = .28, p < .001) showed that fatigue is highest associated with perceived stress and self-perceived health status. The following factors were correlated with increased rates of fatigue and perceived stress: female gender, divorce/separation, low social class and poor health status.Conclusion
We conclude that the two conditions overlap most in terms of socio-economic status and self-perceived health status.16.
Tobias Engl Veronika Michalkova Brian L. Weiss Güler D. Uzel Peter Takac Wolfgang J. Miller Adly M. M. Abd-Alla Serap Aksoy Martin Kaltenpoth 《BMC microbiology》2018,18(1):145
Background
Symbiotic microbes represent a driving force of evolutionary innovation by conferring novel ecological traits to their hosts. Many insects are associated with microbial symbionts that contribute to their host’s nutrition, digestion, detoxification, reproduction, immune homeostasis, and defense. In addition, recent studies suggest a microbial involvement in chemical communication and mating behavior, which can ultimately impact reproductive isolation and, hence, speciation. Here we investigated whether a disruption of the microbiota through antibiotic treatment or irradiation affects cuticular hydrocarbon profiles, and possibly mate choice behavior in the tsetse fly, Glossina morsitans morsitans. Four independent experiments that differentially knock down the multiple bacterial symbionts of tsetse flies were conducted by subjecting tsetse flies to ampicillin, tetracycline, or gamma-irradiation and analyzing their cuticular hydrocarbon profiles in comparison to untreated controls by gas chromatography – mass spectrometry. In two of the antibiotic experiments, flies were mass-reared, while individual rearing was done for the third experiment to avoid possible chemical cross-contamination between individual flies.Results
All three antibiotic experiments yielded significant effects of antibiotic treatment (particularly tetracycline) on cuticular hydrocarbon profiles in both female and male G. m. morsitans, while irradiation itself had no effect on the CHC profiles. Importantly, tetracycline treatment reduced relative amounts of 15,19,23-trimethyl-heptatriacontane, a known compound of the female contact sex pheromone, in two of the three experiments, suggesting a possible implication of microbiota disturbance on mate choice decisions. Concordantly, both female and male flies preferred non-treated over tetracycline-treated flies in direct choice assays.Conclusions
While we cannot exclude the possibility that antibiotic treatment had a directly detrimental effect on fly vigor as we are unable to recolonize antibiotic treated flies with individual symbiont taxa, our results are consistent with an effect of the microbiota, particularly the obligate nutritional endosymbiont Wigglesworthia, on CHC profiles and mate choice behavior. These findings highlight the importance of considering host-microbiota interactions when studying chemical communication and mate choice in insects.17.
Background
Microbial communities are influenced by environmental factors including host genetics. We investigated the relationship between host bitter taste receptor genotype hTAS2R38 and oral microbiota, together with the influence of geographical location.Methods
hTAS2R38 polymorphisms and 16S bacterial gene sequencing from oral samples were analyzed from a total of 45 healthy volunteers from different geographical locations.Results
Genetic variation in the bitter taste receptor TAS2R38 reflected in the microbial composition of oral mucosa in Finnish and Spanish subjects. Multivariate analysis showed significant differences in the microbial composition between country and also dependent on taste genotype. Oral microbiota was shown to be more stable to the geographical location impact among AVI-homozygotes than PAV-homozygotes or heterozygotes (PAV/AVI).Conclusion
Geographical location and genetic variation in the hTAS2R38 taste receptor impact oral mucosa microbial composition. These findings provide an advance in the knowledge regarding the interactions between taste receptor genes and oral microbiota. This study suggests the role of host-microbiota interactions on the food taste perception in food choices, nutrition, and eating behavior.18.
Samir Rezki Claire Campion Philippe Simoneau Marie-Agnès Jacques Ashley Shade Matthieu Barret 《Plant and Soil》2018,422(1-2):67-79
Background and aims
Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.Methods
Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model.Results
Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota.Conclusions
These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.19.
Nguyen Si-Tuan Hua My Ngoc Pham Thi Thu Hang Cuong Nguyen Pham Hung Van Nguyen Thuy Huong 《Annals of clinical microbiology and antimicrobials》2017,16(1):74
Background
Acinetobacter baumannii is an important nosocomial pathogen that can develop multidrug resistance. In this study, we characterized the genome of the A. baumannii strain DMS06669 (isolated from the sputum of a male patient with hospital-acquired pneumonia) and focused on identification of genes relevant to antibiotic resistance.Methods
Whole genome analysis of A. baumannii DMS06669 from hospital-acquired pneumonia patients included de novo assembly; gene prediction; functional annotation to public databases; phylogenetics tree construction and antibiotics genes identification.Results
After sequencing the A. baumannii DMS06669 genome and performing quality control, de novo genome assembly was carried out, producing 24 scaffolds. Public databases were used for gene prediction and functional annotation to construct a phylogenetic tree of the DMS06669 strain with 21 other A. baumannii strains. A total of 18 possible antibiotic resistance genes, conferring resistance to eight distinct classes of antibiotics, were identified. Eight of these genes have not previously been reported to occur in A. baumannii.Conclusions
Our results provide important information regarding mechanisms that may contribute to antibiotic resistance in the DMS06669 strain, and have implications for treatment of patients infected with A. baumannii.20.