The first 1000 cultured species of the human gastrointestinal microbiota

Rajilić‐Stojanović, Mirjana; Vos, Willem M. de

doi:10.1111/1574-6976.12075

Cited by 897 publications

(664 citation statements)

References 366 publications

Supporting

Mentioning

616

Contrasting

Unclassified

Order By: Relevance

“…The fecal microbiota of PNA animals contained higher abundance of bacteria commonly associated with steroid hormone synthesis, including bacteria from the families Nocardiaceae 120 and Clostridiaceae . 121 , 122 In addition, PNA animals have significantly increased abundance of fecal bacteria associated with cardiovascular function including cardiac muscle contraction, proximal tubule bicarbonate reclamation, and the renin-angiotensin (RAS) system. In previous studies of the fecal microbiota of hypertensive rats, Allobaculum, Aggregatibacter , and Sutturela were enriched however, we found that only Aggregatibacter was enriched and Allobaculum and Sutturela were significantly decreased in relative abundance within the fecal microbiota of the PNA animals; these bacteria are associated with glucose metabolism and the specific role is unknown.…”

Section: Discussionmentioning

confidence: 99%

Prenatal androgen exposure causes hypertension and gut microbiota dysbiosis

et al. 2018

View full text Add to dashboard Cite

Background: Conditions of excess androgen in women, such as polycystic ovary syndrome (PCOS), often exhibit intergenerational transmission. One way in which the risk for PCOS may be increased in daughters of affected women is through exposure to elevated androgens in utero. Hyperandrogenemic conditions have serious health consequences, including increased risk for hypertension and cardiovascular disease. Recently, gut dysbiosis has been found to induce hypertension in rats, such that blood pressure can be normalized through fecal microbial transplant. Therefore, we hypothesized that the hypertension seen in PCOS has early origins in gut dysbiosis caused by in utero exposure to excess androgen. We investigated this hypothesis with a model of prenatal androgen (PNA) exposure and maternal hyperandrogenemia by single-injection of testosterone cypionate or sesame oil vehicle (VEH) to pregnant dams in late gestation. We then completed a gut microbiota and cardiometabolic profile of the adult female offspring. Results: The metabolic assessment revealed that adult PNA rats had increased body weight and increased mRNA expression of adipokines: adipocyte binding protein 2, adiponectin, and leptin in inguinal white adipose tissue. Radiotelemetry analysis revealed hypertension with decreased heart rate in PNA animals. The fecal microbiota profile of PNA animals contained higher relative abundance of bacteria associated with steroid hormone synthesis, Nocardiaceae and Clostridiaceae, and lower abundance of Akkermansia, Bacteroides, Lactobacillus, Clostridium. The PNA animals also had an increased relative abundance of bacteria associated with biosynthesis and elongation of unsaturated short chain fatty acids (SCFAs). Conclusions: We found that prenatal exposure to excess androgen negatively impacted cardiovascular function by increasing systolic and diastolic blood pressure and decreasing heart rate. Prenatal androgen was also associated with gut microbial dysbiosis and altered abundance of bacteria involved in metabolite production of short chain fatty acids. These results suggest that early-life exposure to hyperandrogenemia in daughters of women with PCOS may lead to long-term alterations in gut microbiota and cardiometabolic function.

show abstract

Section: Discussionmentioning

confidence: 99%

Prenatal androgen exposure causes hypertension and gut microbiota dysbiosis

et al. 2018

View full text Add to dashboard Cite

show abstract

“…In a previous study 50 , we retrieved 301 draft reconstructions from Model SEED 14 . Based on lists of human gut microbes reported by Qin et al (2010) 30 and by Rajilić-Stojanović and de Vos (2014) 51 , we obtained 472 additional draft reconstructions from Model SEED and KBase (Department of Energy Systems Biology Knowledgebase, http://kbase.us), both of which use the RAST annotation server 52 to annotate the genomes and build the draft metabolic networks 14 . All reconstructions were downloaded in SBML format and imported into Matlab (Mathworks, Inc., Natick, MA, USA) using the COBRA Toolbox 8 .…”

Section: Methodsmentioning

confidence: 99%

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

et al. 2016

View full text Add to dashboard Cite

1 r e s o u r c eChanges in the composition of the human gut microbiota have been associated with the development of chronic diseases including type 2 diabetes, obesity, and colorectal cancer 1 . Gut bacterial functions, such as synthesis of amino acids and vitamins 2 , breakdown of indigestible plant polysaccharides 3 , and production of metabolites involved in energy metabolism 4 , have been linked to human health. The use of 'omics approaches to study human microbiome communities has led to the generation of enormous data sets whose interpretations require systems biology tools to shed light on the functional capacity of gut microbiomes and their interactions with the human host 5 .In order to infer the metabolic repertoire of a gut metagenome data set, researchers usually map sequenced genes or organisms onto metabolic networks derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) 6 , and functional annotations from KEGG ontologies 7 . However, this approach cannot identify the contribution of each bacterial species to the metabolic repertoire of the whole gut microbiome, nor can it infer the effects of different gut microbial communities on host metabolism.A technique that can bridge this gap is constraint-based reconstruction and analysis (COBRA) 8 using genome-scale metabolic reconstructions (GENREs) of individual human gut microbes. GENREs are assembled using the genome sequence and experimental information 9 . These reconstructions form the basis for the development of condition-specific metabolic models whose functions are simulated and validated by comparison with experimental results. The models can be used to investigate genotype-phenotype relationships 10 , microbe-microbe interactions 11 , and host-microbe interactions 11 . Numerous tools can be used to automatically generate draft GENREs but such models contain errors 12 and are incomplete.Manual curation of draft reconstructions is time consuming because it involves an extensive literature review and experimental validation of metabolic functions 9 .To provide an extensive resource of GENREs for human gut microbes, we developed a comparative metabolic reconstruction method that enables any refinement to one metabolic reconstruction to be propagated to others. This accelerates reconstruction and improves model quality. We generated AGORA, which includes 773 gut microbes, comprising 205 genera and 605 species. All reconstructions were based on literature-derived experimental data and comparative genomics. The metabolic predictions of two AGORA reconstructions and their derived metabolic models were validated against experimental data. RESULTS Metabolic reconstruction pipelineWe devised a comparative metabolic reconstruction method (Fig. 1a,c), which is analogous to the comparative microbial genome annotation approach 13 that has enabled accelerated annotation by propagation of refinements to one genome to others. First, we downloaded draft GENREs using Model SEED 14 and KBase (US Department of Energy Systems Biology Knowledgebase, http:/...

show abstract

“…During childhood, gut microbiota assumes the composition of adulthood, comprising 5 phyla and 160 species in the large intestine [24], weighing up to 2 kg [25]. In the microbial community of the human intestine, the dominant bacterial phyla are the Firmicutes (~ 60%) and Bacteriodetes (~ 20%) whereas Actinobacteria, Proteobacteria and Verrucomicrobia are in relatively low abundance [26].…”

Section: Gut Microbiota: the Overcalled Cardmentioning

confidence: 99%

Exercise has the guts: How physical activity may positively modulate gut microbiota in chronic and immune-based diseases

Codella

Luzi

Terruzzi³

2018

Digestive and Liver Disease

124

View full text Add to dashboard Cite

Please cite this article as: Codella Roberto, Luzi Livio, Terruzzi Ileana.Exercise has the guts: how physical activity may positively modulate gut microbiota in chronic and immune-based diseases.Digestive and Liver Disease https://doi.org/10.1016/j.dld. 2017.11.016 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. AbstractLimited animal and human research findings implied that exercise might have a

show abstract

The first 1000 cultured species of the human gastrointestinal microbiota

Cited by 897 publications

References 366 publications

Prenatal androgen exposure causes hypertension and gut microbiota dysbiosis

Prenatal androgen exposure causes hypertension and gut microbiota dysbiosis

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Exercise has the guts: How physical activity may positively modulate gut microbiota in chronic and immune-based diseases

Contact Info

Product

Resources

About