Proteomic interrogation of the gut microbiota: potential clinical impact

Haange, Sven-Bastiaan; Jehmlich, Nico

doi:10.1080/14789450.2016.1190652

Cited by 17 publications

(13 citation statements)

References 20 publications

(21 reference statements)

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“…Compared with metaproteomics, which measures proteins - the direct effectors of biological processes, provides an opportunity to characterize gut microbial functions and activities at a deeper level. The clinical importance of interrogating gut microbiota using metaproteomics has been highlighted recently [74]. To our knowledge, this is the first study that illustrates the effects of synbiotics on the gut microbiota in the context of metabolic disorders using metaproteomics.…”

Section: Discussionmentioning

confidence: 88%

Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice

Walker

Haange

et al. 2019

Molecular Metabolism

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112

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Objective The gut microbiota is an important influencing factor of metabolic health. Although dietary interventions with probiotics, prebiotics, and synbiotics can be effective means to regulate obesity and associated comorbidities, the underlying shifts in gut microbial communities, especially at the functional level, have not been characterized in great details. In this study, we sought to investigate the effects of synbiotics on the regulation of gut microbiota and the alleviation of high-fat diet (HFD)-induced metabolic disorders in mice. Methods Specific pathogen-free (SPF) male C57BL/6J mice were fed diets with either 10% (normal diet, ND) or 60% (high-fat diet, HFD) of total calories from fat (lard). Dietary interventions in the HFD-fed mice included (i) probiotic ( Bifidobacterium animalis subsp. lactis and Lactobacillus paracasei subsp. paracasei DSM 46331), (ii) prebiotic (oat β-glucan), and (iii) synbiotic (a mixture of i and ii) treatments for 12 weeks. Besides detailed characterization of host metabolic parameters, a multi-omics approach was used to systematically profile the microbial signatures at both the phylogenetic and functional levels using 16S rRNA gene sequencing, metaproteomics and targeted metabolomics analysis. Results The synbiotic intervention significantly reduced body weight gain and alleviated features of metabolic complications. At the phylogenetic level, the synbiotic treatment significantly reversed HFD-induced changes in microbial populations, both in terms of richness and the relative abundance of specific taxa. Potentially important species such as Faecalibaculum rodentium and Alistipes putredinis that might mediate the beneficial effects of the synbiotic were identified. At the functional level, short-chain fatty acid and bile acid profiles revealed that all dietary interventions significantly restored cecal levels of acetate, propionate, and butyrate, while the synbiotic treatment reduced the bile acid pools most efficiently. Metaproteomics revealed that the effects of the synbiotic intervention might be mediated through metabolic pathways involved in carbohydrate, amino acid, and energy metabolisms. Conclusions Our results suggested that dietary intervention using the novel synbiotic can alleviate HFD-induced weight gain and restore gut microbial ecosystem homeostasis phylogenetically and functionally.

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Section: Discussionmentioning

confidence: 88%

Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice

Walker

Haange

et al. 2019

Molecular Metabolism

Self Cite

112

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“…This has led to concern that disruption of gut microbiota could improve conditions such as inflammatory bowel disease, obesity, diabetes, metabolic syndrome, cancer, autoimmune disorders [23]. The human gut microbiome maintains a high intra- and inter-subject variability with four dominant phyla of Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria [24]. Up to 90% of the gut microbiota belongs to Firmicutes, Bacteroidetes, and Actinobacteria phyla [25, 26].…”

Section: Discussionmentioning

confidence: 99%

Deciphering bacterial community changes in zucker diabetic fatty rats based on 16S rRNA gene sequences analysis

Yang

Xiang

et al. 2016

Oncotarget

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The aim of the present pilot study was deciphering bacterial community changes in Zucker diabetic fatty rats (ZDF rats), a model of type 2 diabetes. Recent studies unmasked that the status of gastrointestinal tract microbiota has a marked impact on nutrition-related syndromes such as obesity and type-2 diabetes (T2D). In this study, samples taken from the gastrointestinal tracts (GI tracts) of ZDF and their lean littermates (ZL rats) were subjected to 16S rRNA gene sequence-based analysis to examine the characteristic bacterial communities, including those located in the stomach, duodenum, jejunum, ileum, cecum and feces. Results revealed that the Firmicutes/Bacteroidetes ratio was increased and greater numbers of Lactobacillus were detected along GI tracts in ZDF rats compared to ZL rats. In conclusion, this work is the first study to systematically characterize bacterial communities along ZDF rat GI tract and provides substantial evidence supporting a prospective strategy to alter the GI microbial communities improving obesity and T2D.

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“…Furthermore, mapping peptides to proteins and taxa is not trivial due to the many (usually tryptic) peptides that are shared by homologous proteins [21]. In addition, metaproteomic analysis is further challenged by high levels of proteomic sample complexity, dynamic range of the species present and their protein expression levels and, importantly, by large inter- and intra-patient variability [22].…”

Section: Introductionmentioning

confidence: 99%

Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae

et al. 2019

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The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts.

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Proteomic interrogation of the gut microbiota: potential clinical impact

Cited by 17 publications

References 20 publications

Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice

Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice

Deciphering bacterial community changes in zucker diabetic fatty rats based on 16S rRNA gene sequences analysis

Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae

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