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Tilocca B, Soggiu A, Iavarone F, Greco V, Putignani L, Ristori MV, Macari G, Spina AA, Morittu VM, Ceniti C, Piras C, Bonizzi L, Britti D, Urbani A, Figeys D, Roncada P. The Functional Characteristics of Goat Cheese Microbiota from a One-Health Perspective. Int J Mol Sci 2022; 23:ijms232214131. [PMID: 36430609 PMCID: PMC9698706 DOI: 10.3390/ijms232214131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Goat cheese is an important element of the Mediterranean diet, appreciated for its health-promoting features and unique taste. A pivotal role in the development of these characteristics is attributed to the microbiota and its continuous remodeling over space and time. Nevertheless, no thorough study of the cheese-associated microbiota using two metaomics approaches has previously been conducted. Here, we employed 16S rRNA gene sequencing and metaproteomics to explore the microbiota of a typical raw goat milk cheese at various ripening timepoints and depths of the cheese wheel. The 16S rRNA gene-sequencing and metaproteomics results described a stable microbiota ecology across the selected ripening timepoints, providing evidence for the microbiologically driven fermentation of goat milk products. The important features of the microbiota harbored on the surface and in the core of the cheese mass were highlighted in both compositional and functional terms. We observed the rind microbiota struggling to maintain the biosafety of the cheese through competition mechanisms and/or by preventing the colonization of the cheese by pathobionts of animal or environmental origin. The core microbiota was focused on other biochemical processes, supporting its role in the development of both the health benefits and the pleasant gustatory nuances of goat cheese.
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Affiliation(s)
- Bruno Tilocca
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Alessio Soggiu
- One Health Unit, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via della Commenda 10, 20133 Milano, Italy
| | - Federica Iavarone
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Viviana Greco
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Lorenza Putignani
- Unit of Parasitology, Unit of Human Microbiome, Bambino Gesù Children’s Hospital IRCCS, Piazza Sant’Onofrio, 4, 00165 Rome, Italy
| | - Maria Vittoria Ristori
- Unit of Parasitology, Unit of Human Microbiome, Bambino Gesù Children’s Hospital IRCCS, Piazza Sant’Onofrio, 4, 00165 Rome, Italy
| | | | - Anna Antonella Spina
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Valeria Maria Morittu
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Carlotta Ceniti
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Cristian Piras
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Luigi Bonizzi
- One Health Unit, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Via della Commenda 10, 20133 Milano, Italy
| | - Domenico Britti
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Andrea Urbani
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Largo Vito, 00168 Rome, Italy
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Paola Roncada
- Department of Health Sciences, University ‘Magna Græcia’ of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Correspondence: ; Tel.: +39-096-1369-4284
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Gu J, Cui S, Tang X, Liu Z, Zhao J, Zhang H, Mao B, Chen W. Fructooligosaccharides (FOS) significantly increased the relative abundance of intestinal B. pseudolongum in mice with different genotypes. Curr Res Food Sci 2022; 5:2178-2189. [PMID: 36387600 PMCID: PMC9661384 DOI: 10.1016/j.crfs.2022.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/22/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Fructooligosaccharides (FOS) promote the proliferation of Bifidobacterium, especially Bifidobacterium pseudolongum in C57BL/6J mice. However, the response of intestinal microbes to FOS is influenced by host genotypes. Therefore, we compared the intestinal microbiota of four commonly used mice before and after FOS intervention, including C57BL/6J, BALB/c, Institute Cancer Research (ICR), and Kunming (KM) mice. The intestinal microbiota of the four genotypes exhibited similarities in composition but differences in relative abundance. Bifidobacterium was significantly increased to different degrees in the four genotypes of mice after FOS intervention, and Akkermansia and Bacteroides were also significantly increased in BALB/c and KM mice. Lactobacillus and Alistipes levels were unchanged or decreased. Within the genus Bifidobacterium, B. pseudolongum was the dominant species in the four genotypes of mice and proliferated significantly after FOS intervention, with dramatic proliferation in C57BL/6J mice (9.49%). Furthermore, eight strains of B. pseudolongum were screened from the feces of mice with four genotypes, and there was a great difference in the ability and manner of utilizing FOS among the strains. The strains from C57BL/6J mice exhibited the strongest utilization of 1-kestose (GF2), whereas other strains could utilize both GF2 and nistose (GF3) weakly. The gut microbial analysis of mice with different genotypes complemented our previous studies. The results provided the background strains of the different mouse genotypes and suggested a correlation between the utilization ability and the response of the strains to FOS. Further studies on the utilization ability of strains and competition in the intestine will contribute to the understanding of the mechanisms of the intestinal microbial response to diet. The intestinal microbiota is similar in composition for mice of different genotypes. B. pseudolongum predominates in bifidobacteria in mice of different genotypes. The relative abundance of B. pseudolongum increases after FOS intake. B. pseudolongum strains show different abilities in utilizing FOS.
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A pilot study characterizing longitudinal changes in fecal microbiota of patients with Hirschsprung-associated enterocolitis. Pediatr Surg Int 2022; 38:1541-1553. [PMID: 35951092 DOI: 10.1007/s00383-022-05191-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/13/2022] [Indexed: 10/15/2022]
Abstract
PURPOSE Hirschsprung disease is a neurointestinal disease that occurs due to failure of enteric neural crest-derived cells to complete their rostrocaudal migration along the gut mesenchyme, resulting in aganglionosis along variable lengths of the distal bowel. Despite the effective surgery that removes the aganglionic segment, children with Hirschsprung disease remain at high risk for developing a potentially life-threatening enterocolitis (Hirschsprung-associated enterocolitis). Although the etiology of this enterocolitis remains poorly understood, several recent studies in both mouse models and in human subjects suggest potential involvement of gastrointestinal microbiota in the underlying pathogenesis of Hirschsprung-associated enterocolitis. METHODS We present the first study to exploit the Illumina MiSeq next-generation sequencing platform within a longitudinal framework focused on microbiomes of Hirschsprung-associated enterocolitis in five patients. We analyzed bacterial communities from fecal samples collected at different timepoints starting from active enterocolitis and progressing into remission. RESULTS We observed compositional differences between patients largely attributable to variability in age at the time of sample collection. Remission samples across patients exhibited compositional similarity, including enrichment of Blautia, while active enterocolitis samples showed substantial variability in composition. CONCLUSIONS Overall, our findings provide continued support for the role of GI microbiota in the pathogenesis of Hirschsprung-associated enterocolitis.
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Dey P, Malik A, Singh DK, Haange SB, von Bergen M, Jehmlich N. Insight Into the Molecular Mechanisms Underpinning the Mycoremediation of Multiple Metals by Proteomic Technique. Front Microbiol 2022; 13:872576. [PMID: 35756008 PMCID: PMC9221998 DOI: 10.3389/fmicb.2022.872576] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
We investigated the fungus Aspergillus fumigatus PD-18 responses when subjected to the multimetal combination (Total Cr, Cd2+, Cu2+, Ni2+, Pb2+, and Zn2+) in synthetic composite media. To understand how multimetal stress impacts fungal cells at the molecular level, the cellular response of A. fumigatus PD-18 to 30 mg/L multimetal stress (5 mg/L of each heavy metal) was determined by proteomics. The comparative fungal proteomics displayed the remarkable inherent intracellular and extracellular mechanism of metal resistance and tolerance potential of A. fumigatus PD-18. This study reported 2,238 proteins of which 434 proteins were exclusively expressed in multimetal extracts. The most predominant functional class expressed was for cellular processing and signaling. The type of proteins and the number of proteins that were upregulated due to various stress tolerance mechanisms were post-translational modification, protein turnover, and chaperones (42); translation, ribosomal structure, and biogenesis (60); and intracellular trafficking, secretion, and vesicular transport (18). In addition, free radical scavenging antioxidant proteins, such as superoxide dismutase, were upregulated upto 3.45-fold and transporter systems, such as protein transport (SEC31), upto 3.31-fold to combat the oxidative stress caused by the multiple metals. Also, protein–protein interaction network analysis revealed that cytochrome c oxidase and 60S ribosomal protein played key roles to detoxify the multimetal. To the best of our knowledge, this study of A. fumigatus PD-18 provides valuable insights toward the growing research in comprehending the metal microbe interactions in the presence of multimetal. This will facilitate in development of novel molecular markers for contaminant bioremediation.
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Affiliation(s)
- Priyadarshini Dey
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- Department of Biotechnology, MS Ramaiah Institute of Technology, Bengaluru, India
| | - Anushree Malik
- Applied Microbiology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Dileep Kumar Singh
- Department of Zoology, Faculty of Science, University of Delhi, New Delhi, India
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity, Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Helmholtz Association of German Research Centres (HZ), Leipzig, Germany
- *Correspondence: Nico Jehmlich,
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Pettersen VK, Antunes LCM, Dufour A, Arrieta MC. Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics. Comput Struct Biotechnol J 2021; 20:274-286. [PMID: 35024099 PMCID: PMC8718658 DOI: 10.1016/j.csbj.2021.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022] Open
Abstract
Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography-mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.
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Affiliation(s)
- Veronika Kuchařová Pettersen
- Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Pediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Centre for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Luis Caetano Martha Antunes
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
- National Institute of Science and Technology of Innovation on Diseases of Neglected Populations, Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - Marie-Claire Arrieta
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
- International Microbiome Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Kurz A, Seifert J. Factors Influencing Proteolysis and Protein Utilization in the Intestine of Pigs: A Review. Animals (Basel) 2021; 11:3551. [PMID: 34944326 PMCID: PMC8698117 DOI: 10.3390/ani11123551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/03/2021] [Accepted: 12/11/2021] [Indexed: 11/16/2022] Open
Abstract
Pigs are among the most important farm animals for meat production worldwide. In order to meet the amino acid requirements of the animals, pigs rely on the regular intake of proteins and amino acids with their feed. Unfortunately, pigs excrete about two thirds of the used protein, and production of pork is currently associated with a high emission of nitrogen compounds resulting in negative impacts on the environment. Thus, improving protein efficiency in pigs is a central aim to decrease the usage of protein carriers in feed and to lower nitrogen emissions. This is necessary as the supply of plant protein sources is limited by the yield and the cultivable acreage for protein plants. Strategies to increase protein efficiency that go beyond the known feeding options have to be investigated considering the characteristics of the individual animals. This requires a deep understanding of the intestinal processes including enzymatic activities, capacities of amino acid transporters and the microbiome. This review provides an overview of these physiological factors and the respective analyses methods.
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Affiliation(s)
- Alina Kurz
- HoLMIR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, 70599 Stuttgart, Germany;
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 8, 70599 Stuttgart, Germany
| | - Jana Seifert
- HoLMIR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, 70599 Stuttgart, Germany;
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 8, 70599 Stuttgart, Germany
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Fritz-Wallace K, Engelmann B, Krause JL, Schäpe SS, Pöppe J, Herberth G, Rösler U, Jehmlich N, von Bergen M, Rolle-Kampczyk U. Quantification of glyphosate and aminomethylphosphonic acid from microbiome reactor fluids. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8668. [PMID: 31961458 DOI: 10.1002/rcm.8668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Glyphosate is one of the most widely used herbicides and it is suspected to affect the intestinal microbiota through inhibition of aromatic amino acid synthesis via the shikimate pathway. In vitro microbiome bioreactors are increasingly used as model systems to investigate effects on intestinal microbiota and consequently methods for the quantitation of glyphosate and its degradation product aminomethylphosphonic acid (AMPA) in microbiome model systems are required. METHODS An optimized protocol enables the analysis of both glyphosate and AMPA by simple extraction with methanol:acetonitrile:water (2:3:1) without further enrichment steps. Glyphosate and AMPA are separated by liquid chromatography on an amide column and identified and quantified with a targeted tandem mass spectrometry method using a QTRAP 5500 system (AB Sciex). RESULTS Our method has a limit of detection (LOD) in extracted water samples of <2 ng/mL for both glyphosate and AMPA. In complex intestinal medium, the LOD is 2 and 5 ng/mL for glyphosate and AMPA, respectively. These LODs allow for measurement at exposure-relevant concentrations. Glyphosate levels in a bioreactor model of porcine colon were determined and consequently it was verified whether AMPA was produced by porcine gut microbiota. CONCLUSIONS The method presented here allows quantitation of glyphosate and AMPA in complex bioreactor fluids and thus enables studies of the impact of glyphosate and its metabolism on intestinal microbiota. In addition, the extraction protocol is compatible with an untargeted metabolomics analysis, thus allowing one to look for other perturbations caused by glyphosate in the same sample.
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Affiliation(s)
- Katarina Fritz-Wallace
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Beatrice Engelmann
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jannike L Krause
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Stephanie S Schäpe
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Judith Pöppe
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Uwe Rösler
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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Lohmann P, Schäpe SS, Haange SB, Oliphant K, Allen-Vercoe E, Jehmlich N, Von Bergen M. Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics. Expert Rev Proteomics 2020; 17:163-173. [PMID: 32174200 DOI: 10.1080/14789450.2020.1738931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Introduction: Metaproteomics is an established method to obtain a comprehensive taxonomic and functional view of microbial communities. After more than a decade, we are now able to describe the promise, reality, and perspectives of metaproteomics and provide useful information about the choice of method, applications, and potential improvement strategies.Areas covered: In this article, we will discuss current challenges of species and proteome coverage, and also highlight functional aspects of metaproteomics analysis of microbial communities with different levels of complexity. To do this, we re-analyzed data from microbial communities with low to high complexity (8, 72, 200 and >300 species). High species diversity leads to a reduced number of protein group identifications in a complex community, and thus the number of species resolved is underestimated. Ultimately, low abundance species remain undiscovered in complex communities. However, we observed that the main functional categories were better represented within complex microbiomes when compared to species coverage.Expert opinion: Our findings showed that even with low species coverage, metaproteomics has the potential to reveal habitat-specific functional features. Finally, we exploit this information to highlight future research avenues that are urgently needed to enhance our understanding of taxonomic composition and functions of complex microbiomes.
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Affiliation(s)
- Patrick Lohmann
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephanie Serena Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin Von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Biochemistry, University of Leipzig, Leipzig, Germany
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Haange SB, Jehmlich N, Krügel U, Hintschich C, Wehrmann D, Hankir M, Seyfried F, Froment J, Hübschmann T, Müller S, Wissenbach DK, Kang K, Buettner C, Panagiotou G, Noll M, Rolle-Kampczyk U, Fenske W, von Bergen M. Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss. MICROBIOME 2020; 8:13. [PMID: 32033593 PMCID: PMC7007695 DOI: 10.1186/s40168-020-0788-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 01/13/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND Roux-en-Y gastric bypass (RYGB) surgery is a last-resort treatment to induce substantial and sustained weight loss in cases of severe obesity. This anatomical rearrangement affects the intestinal microbiota, but so far, little information is available on how it interferes with microbial functionality and microbial-host interactions independently of weight loss. METHODS A rat model was employed where the RYGB-surgery cohort is compared to sham-operated controls which were kept at a matched body weight by food restriction. We investigated the microbial taxonomy and functional activity using 16S rRNA amplicon gene sequencing, metaproteomics, and metabolomics on samples collected from theileum, the cecum, and the colon, and separately analysed the lumen and mucus-associated microbiota. RESULTS Altered gut architecture in RYGB increased the relative occurrence of Actinobacteria, especially Bifidobacteriaceae and Proteobacteria, while in general, Firmicutes were decreased although Streptococcaceae and Clostridium perfringens were observed at relative higher abundances independent of weight loss. A decrease of conjugated and secondary bile acids was observed in the RYGB-gut lumen. The arginine biosynthesis pathway in the microbiota was altered, as indicated by the changes in the abundance of upstream metabolites and enzymes, resulting in lower levels of arginine and higher levels of aspartate in the colon after RYGB. CONCLUSION The anatomical rearrangement in RYGB affects microbiota composition and functionality as well as changes in amino acid and bile acid metabolism independently of weight loss. The shift in the taxonomic structure of the microbiota after RYGB may be mediated by the resulting change in the composition of the bile acid pool in the gut and by changes in the composition of nutrients in the gut. Video abstract.
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Affiliation(s)
- Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Ute Krügel
- Rudolf Boehm Institute of Pharmacology and Toxicology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Constantin Hintschich
- Neuroendocrine Regulation of Energy Homeostasis Group, IFB Adiposity Diseases, Leipzig, Germany
| | - Dorothee Wehrmann
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Mohammed Hankir
- Neuroendocrine Regulation of Energy Homeostasis Group, IFB Adiposity Diseases, Leipzig, Germany
- Current address: Department of Experimental Surgery, Wuerzburg University Hospital, Wuerzburg, Germany
| | - Florian Seyfried
- Department of General, Visceral, Vascular and Pediatric Surgery, Wuerzburg University Hospital, Wuerzburg, Germany
| | - Jean Froment
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Thomas Hübschmann
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Dirk K. Wissenbach
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Current address: Institute of Forensic Medicine, Jena University Hospital, Jena, Germany
| | - Kang Kang
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoll Institute, Jena, Germany
| | - Christian Buettner
- Institute for Bioanalysis, Faculty of Applied Sciences, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Group, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Matthias Noll
- Institute for Bioanalysis, Faculty of Applied Sciences, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Wiebke Fenske
- Neuroendocrine Regulation of Energy Homeostasis Group, IFB Adiposity Diseases, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
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Yin F, Wang X, Hu Y, Xie H, Liu X, Qin L, Zhang J, Zhou D, Shahidi F. Evaluation of Absorption and Plasma Pharmacokinetics of Tyrosol Acyl Esters in Rats. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1248-1256. [PMID: 31927921 DOI: 10.1021/acs.jafc.9b05112] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lipophenols are regarded as an emerging source of functional food ingredients. However, little is known about their in vivo digestion, absorption, and metabolism. Thus, the pharmacokinetic characteristics in rat and the gut microbial degradation of tyrosol acyl esters (TYr-Es) with fatty acids of C12:0, C18:0, and C18:2 were investigated for the first time. Major metabolites including tyrosol sulfate and tyrosol glucuronide, rather than the parent compounds, were detected in rat plasma after oral administration of TYr-Es. The increased plasma half-life (T1/2) and mean residence time demonstrated that TYr-Es display a longer duration of action in vivo than TYr, potentially leading to higher oral bioavailability. TYr-Es could be hydrolyzed by the gut microbiota to free TYr, which may result in the appearance of the second absorption peak in pharmacokinetic profiles. Therefore, TYr-Es exhibit improved bioavailability compared to that of TYr because of their prolonged duration of action.
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Affiliation(s)
- Fawen Yin
- School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
- National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
| | - Xinmiao Wang
- School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
| | - Yuanyuan Hu
- School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
| | - Hongkai Xie
- Beijing Advanced Innovation Center for Food Nutrition and Human Health , Beijing 100083 , People's Republic of China
| | - Xiaoyang Liu
- School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
- National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
| | - Lei Qin
- School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
- National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
| | - Jianghua Zhang
- School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
| | - Dayong Zhou
- School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
- National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian 116034 , People's Republic of China
| | - Fereidoon Shahidi
- Department of Biochemistry , Memorial University of Newfoundland , St. John's , Newfoundland A1B 3X9 , Canada
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Ziganshin AM, Wintsche B, Seifert J, Carstensen M, Born J, Kleinsteuber S. Spatial separation of metabolic stages in a tube anaerobic baffled reactor: reactor performance and microbial community dynamics. Appl Microbiol Biotechnol 2019; 103:3915-3929. [DOI: 10.1007/s00253-019-09767-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 12/14/2022]
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Haange SB, Jehmlich N, Hoffmann M, Weber K, Lehmann J, von Bergen M, Slanina U. Disease Development Is Accompanied by Changes in Bacterial Protein Abundance and Functions in a Refined Model of Dextran Sulfate Sodium (DSS)-Induced Colitis. J Proteome Res 2019; 18:1774-1786. [PMID: 30767541 DOI: 10.1021/acs.jproteome.8b00974] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Using the acute dextran sulfate sodium (DSS)-induced colitis model, studies have demonstrated that intestinal inflammation is accompanied by major changes in the composition of the intestinal microbiota. Only little is known about the microbial changes and more importantly their functional impact in the chronic DSS colitis model. We used a refined model of chronic DSS-induced colitis that reflects typical symptoms of the human disease without detrimental weight loss usually observed in DSS models. We sampled cecum and colon content as well as colon mucus from healthy and diseased mouse cohorts ( n = 12) and applied 16S rRNA gene sequencing and metaproteomics. An increase of Prevotella sp. in both colon content and mucus was observed. Functional differences were observed between sample types demonstrating the importance of separately sampling lumen content and mucus. The abundance of Desulfovibrio, a sulfate-reducing bacterium, was positively associated with the carbon metabolism. Lachnoclostridium was positively correlated to both vitamin B6 and tryptophan metabolism. In summary, functional changes in the distal colon caused by DSS treatment were more pronounced in the mucus-associated microbiota than in the microbiota present in the distal colon content.
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Affiliation(s)
- Sven-Bastiaan Haange
- Department of Molecular Systems Biology , Helmholtz-Centre for Environmental Research - UFZ , Leipzig 04318 , Germany.,Faculty of Life Sciences, Institute of Biochemistry , University of Leipzig , Leipzig 04103 , Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology , Helmholtz-Centre for Environmental Research - UFZ , Leipzig 04318 , Germany
| | - Maximilian Hoffmann
- Department of Therapy Validation , Fraunhofer Institute for Cell Therapy and Immunology , Leipzig 04103 , Germany
| | | | - Jörg Lehmann
- Department of Therapy Validation , Fraunhofer Institute for Cell Therapy and Immunology , Leipzig 04103 , Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology , Helmholtz-Centre for Environmental Research - UFZ , Leipzig 04318 , Germany.,Faculty of Life Sciences, Institute of Biochemistry , University of Leipzig , Leipzig 04103 , Germany
| | - Ulla Slanina
- Department of Therapy Validation , Fraunhofer Institute for Cell Therapy and Immunology , Leipzig 04103 , Germany
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McKeen S, Young W, Mullaney J, Fraser K, McNabb WC, Roy NC. Infant Complementary Feeding of Prebiotics for theMicrobiome and Immunity. Nutrients 2019; 11:nu11020364. [PMID: 30744134 PMCID: PMC6412789 DOI: 10.3390/nu11020364] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/01/2019] [Accepted: 02/06/2019] [Indexed: 02/06/2023] Open
Abstract
Complementary feeding transitions infants from a milk-based diet to solid foods, providing essential nutrients to the infant and the developing gut microbiome while influencing immune development. Some of the earliest microbial colonisers readily ferment select oligosaccharides, influencing the ongoing establishment of the microbiome. Non-digestible oligosaccharides in prebiotic-supplemented formula and human milk oligosaccharides promote commensal immune-modulating bacteria such as Bifidobacterium, which decrease in abundance during weaning. Incorporating complex, bifidogenic, non-digestible carbohydrates during the transition to solid foods may present an opportunity to feed commensal bacteria and promote balanced concentrations of beneficial short chain fatty acid concentrations and vitamins that support gut barrier maturation and immunity throughout the complementary feeding window.
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Affiliation(s)
- Starin McKeen
- AgResearch, Food Nutrition & Health, Grasslands Research Centre, Private Bag 11008, Palmerston north4442, New Zealand.
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.
| | - Wayne Young
- AgResearch, Food Nutrition & Health, Grasslands Research Centre, Private Bag 11008, Palmerston north4442, New Zealand.
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.
| | - Jane Mullaney
- AgResearch, Food Nutrition & Health, Grasslands Research Centre, Private Bag 11008, Palmerston north4442, New Zealand.
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.
| | - Karl Fraser
- AgResearch, Food Nutrition & Health, Grasslands Research Centre, Private Bag 11008, Palmerston north4442, New Zealand.
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.
| | - Warren C McNabb
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.
| | - Nicole C Roy
- AgResearch, Food Nutrition & Health, Grasslands Research Centre, Private Bag 11008, Palmerston north4442, New Zealand.
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.
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Kispal ZF, Vajda P, Kardos D, Klymiuk I, Moissl-Eichinger C, Castellani C, Singer G, Till H. The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota. J Pediatr Urol 2019; 15:30.e1-30.e7. [PMID: 30206025 DOI: 10.1016/j.jpurol.2018.07.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/26/2018] [Indexed: 01/26/2023]
Abstract
INTRODUCTION Next-generation sequencing (NGS) techniques have provided novel insights into the microbiome of the urinary bladder (UB). In children after bladder augmentation using either ileum (ileocystoplasty, ICP) or colon (colocystoplasty, CCP), the fate of the mucosal microbiome introduced into the urinary tract remains unknown. OBJECTIVE The aim was to compare the mucosal microbiome of the native UB vs the augmented intestinal segment (IS) using NGS. STUDY DESIGN Twelve children after bladder augmentation (ICP n = 6, CCP n = 6) were included. Biopsies were taken during routine postoperative cystoscopy from the native UB and the IS. Specimens underwent whole-genome DNA extraction, 16S rRNA gene amplification, NGS, and Quantitative Insights Into Microbial Ecology (QIIME) data analysis. Downstream statistical data analyses were performed in Calypso. RESULTS Patients' median age at the time of surgery was 11 years (6-17 years), and the median interval between augmentation and sampling was 7 years (4-13 years). α-Diversity (Shannon diversity index) was not significantly different between IS vs UB, ICP vs CCP, and male vs female. No general differences in the overall bacterial pattern (β-diversity) were found between IS, UB, ICP, and CCP groups. The groups overlapped in principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) analysis (Figure). Age at sampling had a statistically significant influence on β-diversity at the genus level. Corynebacterium, Pseudoxanthomonas, Lactobacillus, Flavobacterium, and Micrococcus were the most dominating taxa detected over all samples. There was an obvious dominance of the genus Corynebacterium in the samples taken from the UB and IS in both ICP and CCP patients. Limitations of this study include the relatively small number of patients. CONCLUSION After bladder augmentation, the native UB and augmented ISs (ICP and CCP) host similar microbiota despite their distinct differences of originating mucosal anatomy.
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Affiliation(s)
- Z F Kispal
- Department of Pediatric and Adolescent Surgery, Medical University of Graz, Auenbruggerplatz 34, 8036 Graz, Austria
| | - P Vajda
- Department of Pediatrics, Surgical Division, University of Pecs, József A Str 7, 7623 Pecs, Hungary
| | - D Kardos
- Department of Pediatrics, Surgical Division, University of Pecs, József A Str 7, 7623 Pecs, Hungary
| | - I Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Stiftingtalstraße 24, 8036 Graz, Austria
| | - C Moissl-Eichinger
- Department of Internal Medicine, Joint Facilities, Medical University of Graz, Stiftingtalstraße 24, 8036 Graz, Austria; BioTechMed, Mozartgasse 12/II, 8010 Graz, Austria
| | - C Castellani
- Department of Pediatric and Adolescent Surgery, Medical University of Graz, Auenbruggerplatz 34, 8036 Graz, Austria
| | - G Singer
- Department of Pediatric and Adolescent Surgery, Medical University of Graz, Auenbruggerplatz 34, 8036 Graz, Austria.
| | - H Till
- Department of Pediatric and Adolescent Surgery, Medical University of Graz, Auenbruggerplatz 34, 8036 Graz, Austria
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Analysis of the Bacterial and Host Proteins along and across the Porcine Gastrointestinal Tract. Proteomes 2019; 7:proteomes7010004. [PMID: 30634649 PMCID: PMC6473940 DOI: 10.3390/proteomes7010004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/19/2018] [Accepted: 01/04/2019] [Indexed: 12/26/2022] Open
Abstract
Pigs are among the most important farm animals worldwide and research to optimize their feed efficiency and improve their welfare is still in progress. The porcine intestinal microbiome is so far mainly known from sequencing-based studies. Digesta and mucosa samples from five different porcine gastrointestinal tract sections were analyzed by metaproteomics to obtain a deeper insight into the functions of bacterial groups with concomitant analyses of host proteins. Firmicutes (Prevotellaceae) dominated mucosa and digesta samples, followed by Bacteroidetes. Actinobacteria and Proteobacteria were much higher in abundance in mucosa compared to digesta samples. Functional profiling reveals the presence of core functions shared between digesta and mucosa samples. Protein abundances of energy production and conversion were higher in mucosa samples, whereas in digesta samples more proteins were involved in lipid transport and metabolism; short-chain fatty acids production were detected. Differences were also highlighted between sections, with the small intestine appearing more involved in carbohydrate transport and metabolism than the large intestine. Thus, this study produced the first functional analyses of the porcine GIT biology, discussing the findings in relation to expected bacterial and host functions.
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Mihăşan M, Babii C, Aslebagh R, Channaveerappa D, Dupree EJ, Darie CC. Exploration of Nicotine Metabolism in Paenarthrobacter nicotinovorans pAO1 by Microbial Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:515-529. [DOI: 10.1007/978-3-030-15950-4_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Wu H, Xing Y, Sun H, Mao X. Gut microbial diversity in two insectivorous bats: Insights into the effect of different sampling sources. Microbiologyopen 2018; 8:e00670. [PMID: 29971963 PMCID: PMC6530527 DOI: 10.1002/mbo3.670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/03/2018] [Accepted: 05/17/2018] [Indexed: 11/30/2022] Open
Abstract
The gut microbiota is now known as a key factor in mammalian physiology and health. Our understanding of the gut microbial communities and their effects on ecology and evolution of their hosts is extremely limited in bats which represent the second largest mammalian order. In the current study, gut microbiota of three sampling sources (small intestine, large intestine, and feces) were characterized in two sympatric and insectivorous bats (Rhinolophus sinicus and Myotis altarium) by high‐throughput sequencing of the V3‐V4 region of the 16S rRNA gene. Combining with published studies, this work reveals that Gammaproteobacteria may be a dominant class in the whole Chiroptera and Fusobacteria is less observed in bats although it has been proven to be dominant in other mammals. Our results reveal that the sampling source influences alpha diversity of the microbial community in both studied species although no significant variations of beta diversity were observed, which support that fecal samples cannot be used as a proxy of the microbiota in other gut regions in wild animals.
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Affiliation(s)
- Haonan Wu
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Yutong Xing
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Haijian Sun
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Xiuguang Mao
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, China
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18
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Polysaccharide of Hericium erinaceus attenuates colitis in C57BL/6 mice via regulation of oxidative stress, inflammation-related signaling pathways and modulating the composition of the gut microbiota. J Nutr Biochem 2018; 57:67-76. [DOI: 10.1016/j.jnutbio.2018.03.005] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/25/2018] [Accepted: 03/06/2018] [Indexed: 12/13/2022]
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Blank C, Easterly C, Gruening B, Johnson J, Kolmeder CA, Kumar P, May D, Mehta S, Mesuere B, Brown Z, Elias JE, Hervey WJ, McGowan T, Muth T, Nunn B, Rudney J, Tanca A, Griffin TJ, Jagtap PD. Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. Proteomes 2018; 6:proteomes6010007. [PMID: 29385081 PMCID: PMC5874766 DOI: 10.3390/proteomes6010007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 01/12/2023] Open
Abstract
The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics "Contribution Fest" undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.
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Affiliation(s)
- Clemens Blank
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Germany.
| | - Caleb Easterly
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Bjoern Gruening
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg im Breisgau, Germany.
| | - James Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Carolin A Kolmeder
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Damon May
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Bart Mesuere
- Computational Biology Group, Ghent University, Krijgslaan 281, B-9000 Ghent, Belgium.
| | - Zachary Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Joshua E Elias
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, USA.
| | - W Judson Hervey
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA.
| | - Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Thilo Muth
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany.
| | - Brook Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Joel Rudney
- Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Alessandro Tanca
- Porto Conte Ricerche Science and Technology Park of Sardinia, 07041 Alghero, Italy.
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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Tilocca B, Burbach K, Heyer CME, Hoelzle LE, Mosenthin R, Stefanski V, Camarinha-Silva A, Seifert J. Dietary changes in nutritional studies shape the structural and functional composition of the pigs' fecal microbiome-from days to weeks. MICROBIOME 2017; 5:144. [PMID: 29078812 PMCID: PMC5659009 DOI: 10.1186/s40168-017-0362-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 10/17/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND The possible impact of changes in diet composition on the intestinal microbiome is mostly studied after some days of adaptation to the diet of interest. The question arises if a few days are enough to reflect the microbial response to the diet by changing the community composition and function. The present study investigated the fecal microbiome of pigs during a time span of 4 weeks after a dietary change to obtain insights regarding the time required for adaptation. Four different diets were used differing in either protein source (field peas meal vs. soybean meal) or the concentration of calcium and phosphorus (CaP). RESULTS Twelve pigs were sampled at seven time points within 4 weeks after the dietary change. Fecal samples were used to sequence the 16S rRNA gene amplicons to analyse microbial proteins via LC-MS/MS and to determine the SCFA production. The analysis of OTU abundances and quantification values of proteins showed a significant separation of three periods of time (p = 0.001). Samples from the first day are used to define the 'zero period'; samples of weeks 1 and 2 are combined as 'metabolic period' and an 'equilibrium period was defined based on samples from weeks 3 and 4. Only in this last period, a separation according to the supplementation of CaP was significantly detectable (p = 0.001). No changes were found based on the corn-soybean meal or corn-field peas administration. The analysis of possible factors causing this significant separation showed only an overall change of bacterial members and functional properties. The metaproteomic approach yielded a total of about 9700 proteins, which were used to deduce possible metabolic functions of the bacterial community. CONCLUSIONS A gradual taxonomic and functional rearrangement of the bacterial community has been depicted after a change of diet composition. The adaptation lasts several weeks despite the usually assumed time span of several days. The obtained knowledge is of a great importance for the design of future nutritional studies. Moreover, considering the high similarities between the porcine and human gastrointestinal tract anatomy and physiology, the findings of the current study might imply in the design of human-related nutritional studies.
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Affiliation(s)
- Bruno Tilocca
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Katharina Burbach
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Charlotte M. E. Heyer
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Ludwig E. Hoelzle
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Rainer Mosenthin
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Volker Stefanski
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
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Castellani C, Singer G, Kashofer K, Huber-Zeyringer A, Flucher C, Kaiser M, Till H. The Influence of Proton Pump Inhibitors on the Fecal Microbiome of Infants with Gastroesophageal Reflux-A Prospective Longitudinal Interventional Study. Front Cell Infect Microbiol 2017; 7:444. [PMID: 29075620 PMCID: PMC5641566 DOI: 10.3389/fcimb.2017.00444] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/29/2017] [Indexed: 12/13/2022] Open
Abstract
Proton pump inhibitors (PPIs) are the standard therapy for gastroesophageal reflux disease. In adults, PPI treatment is associated with Clostridium difficile infections (CDI). In contrast to adults the microbiome of infants develops from sterility at birth toward an adult-like profile in the first years of life. The effect of PPIs on this developing microbiome has never been studied. The aim of the present study was to determine the effect of oral PPIs on the fecal microbiome in infants with gastroesophageal reflux disease (GERD). In this prospective longitudinal study 12 infants with proven GERD received oral PPIs for a mean period of 18 weeks (range 8–44). Stool samples were collected before (“before PPI”) and 4 weeks after initiation of PPI therapy (“on PPI”). A third sample was obtained 4 weeks after PPI discontinuation (“after PPI”). The fecal microbiome was determined by NGS based 16S rDNA sequencing. This trial was registered with clinicaltrials.gov (NCT02359604). In a comparison of “before PPI” and “on PPI” neither α- nor β-diversity changed significantly. On the genus level, however, the relative abundances showed a decrease of Lactobacillus and Stenotrophomonas and an increase of Haemophilus. After PPI therapy there was a significant increase of α- and β-diversity. Additionally, the relative abundances of the phyla Firmicutes, Bacteroidetes, and Proteobacteria were significantly changed and correlated to patients' age and the introduction of solid foods. PPI treatment has only minor effects on the fecal microbiome. After discontinuation of PPI treatment the fecal microbiome correlated to patients' age and nutrition.
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Affiliation(s)
- Christoph Castellani
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Georg Singer
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Andrea Huber-Zeyringer
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Christina Flucher
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Margarita Kaiser
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
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Lee PY, Chin SF, Neoh HM, Jamal R. Metaproteomic analysis of human gut microbiota: where are we heading? J Biomed Sci 2017; 24:36. [PMID: 28606141 PMCID: PMC5469034 DOI: 10.1186/s12929-017-0342-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/01/2017] [Indexed: 02/08/2023] Open
Abstract
The human gut is home to complex microbial populations that change dynamically in response to various internal and external stimuli. The gut microbiota provides numerous functional benefits that are crucial for human health but in the setting of a disturbed equilibrium, the microbial community can cause deleterious outcomes such as diseases and cancers. Characterization of the functional activities of human gut microbiota is fundamental to understand their roles in human health and disease. Metaproteomics, which refers to the study of the entire protein collection of the microbial community in a given sample is an emerging area of research that provides informative details concerning functional aspects of the microbiota. In this mini review, we present a summary of the progress of metaproteomic analysis for studying the functional role of gut microbiota. This is followed by an overview of the experimental approaches focusing on fecal specimen for metaproteomics and is concluded by a discussion on the challenges and future directions of metaproteomic research.
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Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia.
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
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Short Term High Fat Diet Induces Obesity-Enhancing Changes in Mouse Gut Microbiota That are Partially Reversed by Cessation of the High Fat Diet. Lipids 2017; 52:499-511. [DOI: 10.1007/s11745-017-4253-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/07/2017] [Indexed: 12/28/2022]
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Oberbach A, Haange SB, Schlichting N, Heinrich M, Lehmann S, Till H, Hugenholtz F, Kullnick Y, Smidt H, Frank K, Seifert J, Jehmlich N, von Bergen M. Metabolic in Vivo Labeling Highlights Differences of Metabolically Active Microbes from the Mucosal Gastrointestinal Microbiome between High-Fat and Normal Chow Diet. J Proteome Res 2017; 16:1593-1604. [PMID: 28252966 DOI: 10.1021/acs.jproteome.6b00973] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The gastrointestinal microbiota in the gut interacts metabolically and immunologically with the host tissue in the contact zone of the mucus layer. For understanding the details of these interactions and especially their dynamics it is crucial to identify the metabolically active subset of the microbiome. This became possible by the development of stable isotope probing techniques, which have only sparsely been applied to microbiome research. We applied the in vivo stable isotope approach using 15N-labeled diet with subsequent identification of metabolically active bacterial species. Four-week old male Sprague-Dawley rats were randomly assigned to chow diet (CD, n =15) and high-fat diet (HFD, n =15). After 11 weeks, three animals from each group were sacrificed for baseline characterization of anthropometric and metabolic obesity. The remaining animals were exposed to either a 15N-labeled (n =9) or a 14N-unlabeled experimental diet (n =3). Three rats from each cohort (HFD and CD) were sacrificed at 12, 24, and 72 h. The remaining three animals from each cohort, which received the 14N-unlabeled diet, were sacrificed after 72 h. The colon was harvested and divided into three equal sections (proximal, medial, and distal), and the mucus layer of each specimen was sampled by scraping. We identified the active subset in an HFD model of obesity in comparison with lean controls rats using metaproteomics. In addition, all samples were investigated by 16S rRNA amplicon gene sequencing. The active microbiome of the HFD group showed an increase in bacterial taxa for Verrucomicrobia and Desulfovibrionaceae. In contrast with no significant changes in alpha diversity, time- and localization-dependent effects in beta-diversity were clearly observed. In terms of enzymatic functions the HFD group showed strong affected metabolic pathways such as energy production and carbohydrate metabolism. In vivo isotope labeling combined with metaproteomics provides a valuable method to distinguish the active from the non-active bacterial phylogenetic groups that are relevant for microbiota-host interaction. For morbid obesity such analysis may provide potentially new strategies for targeted pre- or probiotic treatments.
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Affiliation(s)
- Andreas Oberbach
- Department of Cardiac Surgery, University of Leipzig, Heart Center , 04289 Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, UFZ-Helmholtz Centre for Environmental Research , 04318 Leipzig, Germany
| | - Nadine Schlichting
- Department of Cardiac Surgery, University of Leipzig, Heart Center , 04289 Leipzig, Germany.,Department of Pediatric Surgery, University of Leipzig , 04103 Leipzig, Germany
| | - Marco Heinrich
- Department of Cardiac Surgery, University of Leipzig, Heart Center , 04289 Leipzig, Germany.,Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig , 04103 Leipzig, Germany
| | - Stefanie Lehmann
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig , 04103 Leipzig, Germany
| | - Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University of Graz , 8036 Graz, Austria
| | - Floor Hugenholtz
- Laboratory of Microbiology, Wageningen University , 6708 PB Wageningen, The Netherlands
| | - Yvonne Kullnick
- Department of Cardiac Surgery, University of Leipzig, Heart Center , 04289 Leipzig, Germany.,Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig , 04103 Leipzig, Germany
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University , 6708 PB Wageningen, The Netherlands
| | - Karin Frank
- Department of Ecological Modelling, UFZ-Helmholtz Centre for Environmental Research , 04318 Leipzig, Germany
| | - Jana Seifert
- Department of Molecular Systems Biology, UFZ-Helmholtz Centre for Environmental Research , 04318 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, UFZ-Helmholtz Centre for Environmental Research , 04318 Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, UFZ-Helmholtz Centre for Environmental Research , 04318 Leipzig, Germany.,Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig , 04103 Leipzig, Germany.,Department of Life Sciences and Chemistry, Centre for Microbial Communities, University of Aalborg , 9220 Aalborg, Denmark
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26
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Tanca A, Manghina V, Fraumene C, Palomba A, Abbondio M, Deligios M, Silverman M, Uzzau S. Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse. Front Microbiol 2017; 8:391. [PMID: 28352255 PMCID: PMC5348496 DOI: 10.3389/fmicb.2017.00391] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/24/2017] [Indexed: 02/01/2023] Open
Abstract
Previous studies on mouse models report that cecal and fecal microbial communities may differ in the taxonomic structure, but little is known about their respective functional activities. Here, we employed a metaproteogenomic approach, including 16S rRNA gene sequencing, shotgun metagenomics and shotgun metaproteomics, to analyze the microbiota of paired mouse cecal contents (CCs) and feces, with the aim of identifying changes in taxon-specific functions. As a result, Gram-positive anaerobes were observed as considerably higher in CCs, while several key enzymes, involved in oxalate degradation, glutamate/glutamine metabolism, and redox homeostasis, and most actively expressed by Bacteroidetes, were clearly more represented in feces. On the whole, taxon and function abundance appeared to vary consistently with environmental changes expected to occur throughout the transit from the cecum to outside the intestine, especially when considering metaproteomic data. The results of this study indicate that functional and metabolic differences exist between CC and stool samples, paving the way to further metaproteogenomic investigations aimed at elucidating the functional dynamics of the intestinal microbiota.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia Alghero, Italy
| | - Valeria Manghina
- Porto Conte Ricerche, Science and Technology Park of SardiniaAlghero, Italy; Department of Biomedical Sciences, University of SassariSassari, Italy
| | - Cristina Fraumene
- Porto Conte Ricerche, Science and Technology Park of Sardinia Alghero, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia Alghero, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari Sassari, Italy
| | - Massimo Deligios
- Department of Biomedical Sciences, University of Sassari Sassari, Italy
| | - Michael Silverman
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical SchoolBoston, MA, USA; Division of Infectious Diseases, Department of Pediatrics, Boston Children's HospitalBoston, MA, USA
| | - Sergio Uzzau
- Porto Conte Ricerche, Science and Technology Park of SardiniaAlghero, Italy; Department of Biomedical Sciences, University of SassariSassari, Italy
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Venters M, Carlson RP, Gedeon T, Heys JJ. Effects of Spatial Localization on Microbial Consortia Growth. PLoS One 2017; 12:e0168592. [PMID: 28045924 PMCID: PMC5207726 DOI: 10.1371/journal.pone.0168592] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/02/2016] [Indexed: 11/19/2022] Open
Abstract
Microbial consortia are commonly observed in natural and synthetic systems, and these consortia frequently result in higher biomass production relative to monocultures. The focus here is on the impact of initial spatial localization and substrate diffusivity on the growth of a model microbial consortium consisting of a producer strain that consumes glucose and produces acetate and a scavenger strain that consumes the acetate. The mathematical model is based on an individual cell model where growth is described by Monod kinetics, and substrate transport is described by a continuum-based, non-equilibrium reaction-diffusion model where convective transport is negligible (e.g., in a biofilm). The first set of results focus on a single producer cell at the center of the domain and surrounded by an initial population of scavenger cells. The impact of the initial population density and substrate diffusivity is examined. A transition is observed from the highest initial density resulting in the greatest cell growth to cell growth being independent of initial density. A high initial density minimizes diffusive transport time and is typically expected to result in the highest growth, but this expected behavior is not predicted in environments with lower diffusivity or larger length scales. When the producer cells are placed on the bottom of the domain with the scavenger cells above in a layered biofilm arrangement, a similar critical transition is observed. For the highest diffusivity values examined, a thin, dense initial scavenger layer is optimal for cell growth. However, for smaller diffusivity values, a thicker, less dense initial scavenger layer provides maximal growth. The overall conclusion is that high density clustering of members of a food chain is optimal under most common transport conditions, but under some slow transport conditions, high density clustering may not be optimal for microbial growth.
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Affiliation(s)
- Michael Venters
- Chemical and Biological Engineering Department, Montana State University, Bozeman, Montana, United States of America
| | - Ross P. Carlson
- Chemical and Biological Engineering Department, Montana State University, Bozeman, Montana, United States of America
| | - Tomas Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Jeffrey J. Heys
- Chemical and Biological Engineering Department, Montana State University, Bozeman, Montana, United States of America
- * E-mail:
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28
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Fetissov SO. Role of the gut microbiota in host appetite control: bacterial growth to animal feeding behaviour. Nat Rev Endocrinol 2017; 13:11-25. [PMID: 27616451 DOI: 10.1038/nrendo.2016.150] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The life of all animals is dominated by alternating feelings of hunger and satiety - the main involuntary motivations for feeding-related behaviour. Gut bacteria depend fully on their host for providing the nutrients necessary for their growth. The intrinsic ability of bacteria to regulate their growth and to maintain their population within the gut suggests that gut bacteria can interfere with molecular pathways controlling energy balance in the host. The current model of appetite control is based mainly on gut-brain signalling and the animal's own needs to maintain energy homeostasis; an alternative model might also involve bacteria-host communications. Several bacterial components and metabolites have been shown to stimulate intestinal satiety pathways; at the same time, their production depends on bacterial growth cycles. This short-term bacterial growth-linked modulation of intestinal satiety can be coupled with long-term regulation of appetite, controlled by the neuropeptidergic circuitry in the hypothalamus. Indeed, several bacterial products are detected in the systemic circulation, which might act directly on hypothalamic neurons. This Review analyses the data relevant to possible involvement of the gut bacteria in the regulation of host appetite and proposes an integrative homeostatic model of appetite control that includes energy needs of both the host and its gut bacteria.
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Affiliation(s)
- Sergueï O Fetissov
- Nutrition, Gut &Brain Laboratory, Inserm UMR 1073, University of Rouen Normandy, 22 Boulevard Gambetta, 76183 Rouen, France
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29
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Borda-Molina D, Vital M, Sommerfeld V, Rodehutscord M, Camarinha-Silva A. Insights into Broilers' Gut Microbiota Fed with Phosphorus, Calcium, and Phytase Supplemented Diets. Front Microbiol 2016; 7:2033. [PMID: 28066358 PMCID: PMC5165256 DOI: 10.3389/fmicb.2016.02033] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/02/2016] [Indexed: 11/13/2022] Open
Abstract
Phytase supplementation in broiler diets is a common practice to improve phosphorus (P) availability and to reduce P loss by excretion. An enhanced P availability, and its concomitant supplementation with calcium (Ca), can affect the structure of the microbial community in the digestive tract of broiler chickens. Here, we aim to distinguish the effects of mineral P, Ca, and phytase on the composition of microbial communities present in the content and the mucosa layer of the gastrointestinal tract (GIT) of broiler chickens. Significant differences were observed between digesta and mucosa samples for the GIT sections studied (p = 0.001). The analyses of 56 individual birds showed a high microbial composition variability within the replicates of the same diet. The average similarity within replicates of digesta and mucosa samples across all diets ranged from 29 to 82% in crop, 19-49% in ileum, and 17-39% in caeca. Broilers fed with a diet only supplemented with Ca had the lowest body weight gain and feed conversion values while diets supplemented with P showed the best performance results. An effect of each diet on crop mucosa samples was observed, however, similar results were not obtained from digesta samples. Microbial communities colonizing the ileum mucosa samples were affected by P supplementation. Caeca-derived samples showed the highest microbial diversity when compared to the other GIT sections and the most prominent phylotypes were related to genus Faecalibacterium and Pseudoflavonifractor, known for their influence on gut health and as butyrate producers. Lower microbial diversity in crop digesta was linked to lower growth performance of birds fed with a diet only supplemented with Ca. Each diet affected microbial communities within individual sections, however, no diet showed a comprehensive effect across all GIT sections, which can primarily be attributed to the great variability among replicates. The substantial community differences between digesta and mucosa derived samples indicate that both habitats have to be considered when the influence of diet on the gut microbiota, broiler growth performance, and animal health is investigated.
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Affiliation(s)
- Daniel Borda-Molina
- Animal Nutrition Department, Institute of Animal Science, University of Hohenheim Stuttgart, Germany
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research Braunschweig, Germany
| | - Vera Sommerfeld
- Animal Nutrition Department, Institute of Animal Science, University of Hohenheim Stuttgart, Germany
| | - Markus Rodehutscord
- Animal Nutrition Department, Institute of Animal Science, University of Hohenheim Stuttgart, Germany
| | - Amélia Camarinha-Silva
- Animal Nutrition Department, Institute of Animal Science, University of Hohenheim Stuttgart, Germany
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30
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Tilocca B, Witzig M, Rodehutscord M, Seifert J. Variations of Phosphorous Accessibility Causing Changes in Microbiome Functions in the Gastrointestinal Tract of Chickens. PLoS One 2016; 11:e0164735. [PMID: 27760159 PMCID: PMC5070839 DOI: 10.1371/journal.pone.0164735] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/29/2016] [Indexed: 12/11/2022] Open
Abstract
The chicken gastrointestinal tract (GIT) harbours a complex microbial community, involved in several physiological processes such as host immunomodulation and feed digestion. For the first time, the present study analysed dietary effects on the protein inventory of the microbiome in crop and ceca of broilers. We performed quantitative label-free metaproteomics by using 1-D-gel electrophoresis coupled with LC-MS/MS to identify the structural and functional changes triggered by diets supplied with varying amount of mineral phosphorous (P) and microbial phytase (MP). Phylogenetic assessment based on label-free quantification (LFQ) values of the proteins identified Lactobacillaceae as the major family in the crop section regardless of the diet, whereas proteins belonging to the family Veillonellaceae increased with the P supplementation. Within the ceca section, proteins of Bacteroidaceae were more abundant in the P-supplied diets, whereas proteins of Eubacteriaceae decreased with the P-addition. Proteins of the Ruminococcaceae increased with the amount of MP while proteins of Lactobacillaceae were more abundant in the MP-lacking diets. Classification of the identified proteins indicated a thriving microbial community in the case of P and MP supplementation, and stressed microbial community when no P and MP were supplied. Data are available via ProteomeXchange with identifier PXD003805.
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Affiliation(s)
- Bruno Tilocca
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Maren Witzig
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | | | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- * E-mail:
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31
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Levi Mortera S, Del Chierico F, Vernocchi P, Rosado MM, Cavola A, Chierici M, Pieroni L, Urbani A, Carsetti R, Lante I, Dallapiccola B, Putignani L. Monitoring Perinatal Gut Microbiota in Mouse Models by Mass Spectrometry Approaches: Parental Genetic Background and Breastfeeding Effects. Front Microbiol 2016; 7:1523. [PMID: 27725814 PMCID: PMC5036385 DOI: 10.3389/fmicb.2016.01523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/12/2016] [Indexed: 01/22/2023] Open
Abstract
At birth, contact with external stimuli, such as nutrients derived from food, is necessary to modulate the symbiotic balance between commensal and pathogenic bacteria, protect against bacterial dysbiosis, and initiate the development of the mucosal immune response. Among a variety of different feeding patterns, breastfeeding represents the best modality. In fact, the capacity of breast milk to modulate the composition of infants’ gut microbiota leads to beneficial effects on their health. In this study, we used newborn mice as a model to evaluate the effect of parental genetic background (i.e., IgA-producing mice and IgA-deficient mice) and feeding modulation (i.e., maternal feeding and cross-feeding) on the onset and shaping of gut microbiota after birth. To investigate these topics, we used either a culturomic approach that employed Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MS), or bottom–up Liquid Chromatography, with subsequent MSMS shotgun metaproteomic analysis that compared and assembled results of the two techniques. We found that the microbial community was enriched by lactic acid bacteria when pups were breastfed by wild-type (WT) mothers, while IgA-deficient milk led to an increase in the opportunistic bacterial pathogen (OBP) population. Cross-feeding results suggested that IgA supplementation promoted the exclusion of some OBPs and the temporary appearance of beneficial species in pups fed by WT foster mothers. Our results show that both techniques yield a picture of microbiota from different angles and with varying depths. In particular, our metaproteomic pipeline was found to be a reliable tool in the description of microbiota. Data from these studies are available via ProteomeXchange, with identifier PXD004033.
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Affiliation(s)
- Stefano Levi Mortera
- Human Microbiome Unit, Area of Genetic and Rare Diseases, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Federica Del Chierico
- Human Microbiome Unit, Area of Genetic and Rare Diseases, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Pamela Vernocchi
- Human Microbiome Unit, Area of Genetic and Rare Diseases, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Maria M Rosado
- Immunology Research Area, B-cell Physiopathology Unit and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Agnese Cavola
- Department of Experimental Medicine, University of Rome Tor Vergata Rome, Italy
| | | | | | - Andrea Urbani
- IRCCS-Santa Lucia FoundationRome, Italy; Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro CuoreRome, Italy
| | - Rita Carsetti
- Immunology Research Area, B-cell Physiopathology Unit and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Isabella Lante
- Laboratory Medicine Department, San Camillo Hospital Treviso, Italy
| | | | - Lorenza Putignani
- Human Microbiome Unit, Area of Genetic and Rare Diseases, Bambino Gesù Children's Hospital, IRCCSRome, Italy; Unit of Parasitology, Department of Laboratory, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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32
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Wieck MM, Debelius JW, Spurrier RG, Trecartin A, Knight R, Grikscheit TC. The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic disease. Surgery 2016; 160:350-8. [PMID: 27302104 DOI: 10.1016/j.surg.2016.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/15/2016] [Accepted: 05/05/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND The pediatric intestinal microbiome is impacted by many factors, including age, diet, antibiotics, and environment. We hypothesized that in operative patients, alterations to antibiotics and mechanoluminal stimulation would demonstrate measurable changes in the intestinal microbiome and that microbial diversity would be reduced without normal mechanoluminal stimulation and with prolonged antibiotic treatment. METHODS Bacterial 16s rRNA was extracted from swabbed samples of 43 intestines from 29 patients, aged 5 days to 13 years old. Swabs were obtained during initial resection or later stoma closure. Samples were compared using phylogenetic diversity whole tree alpha diversity and unweighted UniFrac distance beta diversity and by comparing significantly different taxonomic groups. RESULTS Microbial community structure varied significantly between obstructive and inflammatory diseases (P = .001), with an effect size of 0.99 (0.97, 1.00). This difference persisted even 6 weeks after return to health. Family Enterobacter and Clostridiaceae predominated in patients with necrotizing enterocolitis or focal intestinal perforation; patients with an obstructive pathology had an abundance of Bacteroides. Comparison of UniFrac distance between paired proximal and distal intestines demonstrated that paired samples were significantly closer than any other comparison. CONCLUSION In infants, inflammatory and ischemic intestinal pathologies treated with prolonged courses of antibiotics durably alter the intestinal mucosal microbiome. Diversion of mechanoluminal stimulation, however, does not.
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Affiliation(s)
- Minna M Wieck
- Division of Pediatric Surgery, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA
| | | | - Ryan G Spurrier
- Division of Pediatric Surgery, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA
| | - Andrew Trecartin
- Division of Pediatric Surgery, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, CA; Department of Computer Science & Engineering, University of California, San Diego, CA
| | - Tracy C Grikscheit
- Division of Pediatric Surgery, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA.
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33
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Haange SB, Jehmlich N. Proteomic interrogation of the gut microbiota: potential clinical impact. Expert Rev Proteomics 2016; 13:535-7. [PMID: 27187145 DOI: 10.1080/14789450.2016.1190652] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sven-Bastiaan Haange
- a Department of Molecular Systems Biology , Helmholtz-Centre for Environmental Research - UFZ , Leipzig , Germany
| | - Nico Jehmlich
- a Department of Molecular Systems Biology , Helmholtz-Centre for Environmental Research - UFZ , Leipzig , Germany
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34
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Heinritz SN, Weiss E, Eklund M, Aumiller T, Louis S, Rings A, Messner S, Camarinha-Silva A, Seifert J, Bischoff SC, Mosenthin R. Intestinal Microbiota and Microbial Metabolites Are Changed in a Pig Model Fed a High-Fat/Low-Fiber or a Low-Fat/High-Fiber Diet. PLoS One 2016; 11:e0154329. [PMID: 27100182 PMCID: PMC4839692 DOI: 10.1371/journal.pone.0154329] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/12/2016] [Indexed: 12/11/2022] Open
Abstract
The intestinal microbiota and its metabolites appear to be an important factor for gastrointestinal function and health. However, research is still needed to further elaborate potential relationships between nutrition, gut microbiota and host’s health by means of a suitable animal model. The present study examined the effect of two different diets on microbial composition and activity by using the pig as a model for humans. Eight pigs were equally allotted to two treatments, either fed a low-fat/high-fiber (LF), or a high-fat/low-fiber (HF) diet for 7 weeks. Feces were sampled at day 7 of every experimental week. Diet effects on fecal microbiota were assessed using quantitative real-time PCR, DNA fingerprinting and metaproteomics. Furthermore, fecal short-chain fatty acid (SCFA) profiles and ammonia concentrations were determined. Gene copy numbers of lactobacilli, bifidobacteria (P<0.001) and Faecalibacterium prausnitzii (P<0.05) were higher in the LF pigs, while Enterobacteriaceae were more abundant in the HF pigs (P<0.001). Higher numbers of proteins affiliated to Enterobacteriaceae were also present in the HF samples. Proteins for polysaccharide breakdown did almost exclusively originate from Prevotellaceae. Total and individual fecal SCFA concentrations were higher for pigs of the LF treatment (P<0.05), whereas fecal ammonia concentrations did not differ between treatments (P>0.05). Results provide evidence that beginning from the start of the experiment, the LF diet stimulated beneficial bacteria and SCFA production, especially butyrate (P<0.05), while the HF diet fostered those bacterial groups which have been associated with a negative impact on health conditions. These findings correspond to results in humans and might strengthen the hypothesis that the response of the porcine gut microbiota to a specific dietary modulation is in support of using the pig as suitable animal model for humans to assess diet-gut-microbiota interactions. Data are available via ProteomeXchange with identifier PXD003447.
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Affiliation(s)
- Sonja N. Heinritz
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Eva Weiss
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Meike Eklund
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Tobias Aumiller
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Sandrine Louis
- Department of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Andreas Rings
- Department of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Sabine Messner
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | | | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Stephan C. Bischoff
- Department of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Rainer Mosenthin
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- * E-mail:
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35
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Wissenbach DK, Oliphant K, Rolle-Kampczyk U, Yen S, Höke H, Baumann S, Haange SB, Verdu EF, Allen-Vercoe E, von Bergen M. Optimization of metabolomics of defined in vitro gut microbial ecosystems. Int J Med Microbiol 2016; 306:280-289. [PMID: 27020116 DOI: 10.1016/j.ijmm.2016.03.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 01/05/2023] Open
Abstract
The metabolic functionality of a microbial community is a key to the understanding of its inherent ecological processes and the interaction with the host. However, the study of the human gut microbiota is hindered by the complexity of this ecosystem. One way to resolve this issue is to derive defined communities that may be cultured ex vivo in bioreactor systems and used to approximate the native ecosystem. Doing so has the advantage of experimental reproducibility and ease of sampling, and furthermore, in-depth analysis of metabolic processes becomes highly accessible. Here, we review the use of bioreactor systems for ex vivo modelling of the human gut microbiota with respect to analysis of the metabolic output of the microbial ecosystem, and discuss the possibility of mechanistic insights using these combined techniques. We summarize the different platforms currently used for metabolomics and suitable for analysis of gut microbiota samples from a bioreactor system. With the help of representative datasets obtained from a series of bioreactor runs, we compare the outputs of both NMR and mass spectrometry based approaches in terms of their coverage, sensitivity and quantification. We also discuss the use of untargeted and targeted analyses in mass spectroscopy and how these techniques can be combined for optimal biological interpretation. Potential solutions for linking metabolomic and phylogenetic datasets with regards to active, key species within the ecosystem will be presented.
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Affiliation(s)
- Dirk K Wissenbach
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
| | - Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
| | - Sandi Yen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Henrike Höke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany; Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Leipzig, Leipzig, Germany
| | - Sven Baumann
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
| | - Sven B Haange
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
| | - Elena F Verdu
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Germany; Aalborg University, Department of Chemistry and Biosciences, Aalborg University, 9000 Aalborg, Denmark.
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Breton J, Tennoune N, Lucas N, Francois M, Legrand R, Jacquemot J, Goichon A, Guérin C, Peltier J, Pestel-Caron M, Chan P, Vaudry D, do Rego JC, Liénard F, Pénicaud L, Fioramonti X, Ebenezer IS, Hökfelt T, Déchelotte P, Fetissov SO. Gut Commensal E. coli Proteins Activate Host Satiety Pathways following Nutrient-Induced Bacterial Growth. Cell Metab 2016; 23:324-34. [PMID: 26621107 DOI: 10.1016/j.cmet.2015.10.017] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/01/2015] [Accepted: 10/27/2015] [Indexed: 01/07/2023]
Abstract
The composition of gut microbiota has been associated with host metabolic phenotypes, but it is not known if gut bacteria may influence host appetite. Here we show that regular nutrient provision stabilizes exponential growth of E. coli, with the stationary phase occurring 20 min after nutrient supply accompanied by bacterial proteome changes, suggesting involvement of bacterial proteins in host satiety. Indeed, intestinal infusions of E. coli stationary phase proteins increased plasma PYY and their intraperitoneal injections suppressed acutely food intake and activated c-Fos in hypothalamic POMC neurons, while their repeated administrations reduced meal size. ClpB, a bacterial protein mimetic of α-MSH, was upregulated in the E. coli stationary phase, was detected in plasma proportional to ClpB DNA in feces, and stimulated firing rate of hypothalamic POMC neurons. Thus, these data show that bacterial proteins produced after nutrient-induced E. coli growth may signal meal termination. Furthermore, continuous exposure to E. coli proteins may influence long-term meal pattern.
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Affiliation(s)
- Jonathan Breton
- Inserm UMR1073, Nutrition, Gut and Brain Laboratory, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Naouel Tennoune
- Inserm UMR1073, Nutrition, Gut and Brain Laboratory, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Nicolas Lucas
- Inserm UMR1073, Nutrition, Gut and Brain Laboratory, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Marie Francois
- Inserm UMR1073, Nutrition, Gut and Brain Laboratory, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Romain Legrand
- Inserm UMR1073, Nutrition, Gut and Brain Laboratory, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Justine Jacquemot
- Inserm UMR1073, Nutrition, Gut and Brain Laboratory, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Alexis Goichon
- Inserm UMR1073, Nutrition, Gut and Brain Laboratory, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Charlène Guérin
- Inserm UMR1073, Nutrition, Gut and Brain Laboratory, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Johann Peltier
- Microbiology Laboratory GRAM, EA2656, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Martine Pestel-Caron
- Microbiology Laboratory GRAM, EA2656, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France; Rouen University Hospital, CHU Charles Nicolle, Rouen 76183, France
| | - Philippe Chan
- PISSARO Proteomic Platform, Mont-Saint-Aignan 76821, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - David Vaudry
- PISSARO Proteomic Platform, Mont-Saint-Aignan 76821, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Jean-Claude do Rego
- Animal Behavior Platform (SCAC), Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France
| | - Fabienne Liénard
- Centre for Taste and Feeding Behaviour, UMR 6265-CNRS, 1324-INRA, Bourgogne Franche Comté University, Dijon F 21000, France
| | - Luc Pénicaud
- Centre for Taste and Feeding Behaviour, UMR 6265-CNRS, 1324-INRA, Bourgogne Franche Comté University, Dijon F 21000, France
| | - Xavier Fioramonti
- Centre for Taste and Feeding Behaviour, UMR 6265-CNRS, 1324-INRA, Bourgogne Franche Comté University, Dijon F 21000, France
| | - Ivor S Ebenezer
- Neuropharmacology Research Group, School of Pharmacy and Biomedical Sciences University of Portsmouth, Portsmouth PO 1 2DT, UK
| | - Tomas Hökfelt
- Department of Neuroscience, Karolinska Institutet, Stockholm 17176, Sweden
| | - Pierre Déchelotte
- Inserm UMR1073, Nutrition, Gut and Brain Laboratory, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France; Rouen University Hospital, CHU Charles Nicolle, Rouen 76183, France
| | - Sergueï O Fetissov
- Inserm UMR1073, Nutrition, Gut and Brain Laboratory, Rouen 76183, France; Institute for Research and Innovation in Biomedicine (IRIB), Rouen University, Normandy University, Rouen 76000, France.
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Herbst FA, Lünsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Nielsen JL, Hettich RL, Seifert J, Nielsen PH. Enhancing metaproteomics--The value of models and defined environmental microbial systems. Proteomics 2016; 16:783-98. [PMID: 26621789 DOI: 10.1002/pmic.201500305] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/03/2015] [Accepted: 11/26/2015] [Indexed: 12/24/2022]
Abstract
Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.
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Affiliation(s)
- Florian-Alexander Herbst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Vanessa Lünsmann
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Henrik Kjeldal
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Nico Jehmlich
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martin von Bergen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.,Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN, USA
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Per Halkjaer Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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Till H, Castellani C, Moissl-Eichinger C, Gorkiewicz G, Singer G. Disruptions of the intestinal microbiome in necrotizing enterocolitis, short bowel syndrome, and Hirschsprung's associated enterocolitis. Front Microbiol 2015; 6:1154. [PMID: 26528281 PMCID: PMC4607865 DOI: 10.3389/fmicb.2015.01154] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 10/05/2015] [Indexed: 12/22/2022] Open
Abstract
Next generation sequencing techniques are currently revealing novel insight into the microbiome of the human gut. This new area of research seems especially relevant for neonatal diseases, because the development of the intestinal microbiome already starts in the perinatal period and preterm infants with a still immature gut associated immune system may be harmed by a dysproportional microbial colonization. For most gastrointestinal diseases requiring pediatric surgery there is very limited information about the role of the intestinal microbiome. This review aims to summarize the current knowledge and outline future perspectives for important pathologies like necrotizing enterocolitis (NEC) of the newborn, short bowel syndrome (SBS), and Hirschsprung’s disease associated enterocolitis (HAEC). Only studies applying next generation sequencing techniques to analyze the diversity of the intestinal microbiome were included. In NEC patients intestinal dysbiosis could already be detected prior to any clinical evidence of the disease resulting in a reduction of the bacterial diversity. In SBS patients the diversity seems to be reduced compared to controls. In children with Hirschsprung’s disease the intestinal microbiome differs between those with and without episodes of enterocolitis. One common finding for all three diseases seems to be an overabundance of Proteobacteria. However, most human studies are based on fecal samples and experimental data question whether fecal samples actually represent the microbiome at the site of the diseased bowel and whether the luminal (transient) microbiome compares to the mucosal (resident) microbiome. In conclusion current studies already allow a preliminary understanding of the potential role of the intestinal microbiome in pediatric surgical diseases. Future investigations could clarify the interface between the intestinal epithelium, its immunological competence and mucosal microbiome. Advances in this field may have an impact on the understanding and non-operative treatment of such diseases in infancy.
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Affiliation(s)
- Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University of Graz Graz, Austria
| | - Christoph Castellani
- Department of Paediatric and Adolescent Surgery, Medical University of Graz Graz, Austria
| | | | | | - Georg Singer
- Department of Paediatric and Adolescent Surgery, Medical University of Graz Graz, Austria
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Jagtap PD, Blakely A, Murray K, Stewart S, Kooren J, Johnson JE, Rhodus NL, Rudney J, Griffin TJ. Metaproteomic analysis using the Galaxy framework. Proteomics 2015; 15:3553-65. [DOI: 10.1002/pmic.201500074] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/25/2015] [Accepted: 06/04/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Pratik D. Jagtap
- Center for Mass Spectrometry and Proteomics; University of Minnesota; Minneapolis MN USA
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
| | | | - Kevin Murray
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
| | | | - Joel Kooren
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
| | | | - Nelson L. Rhodus
- School of Dentistry; University of Minnesota; Minneapolis MN USA
| | - Joel Rudney
- School of Dentistry; University of Minnesota; Minneapolis MN USA
| | - Timothy J. Griffin
- Center for Mass Spectrometry and Proteomics; University of Minnesota; Minneapolis MN USA
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
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40
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Mika A, Van Treuren W, González A, Herrera JJ, Knight R, Fleshner M. Exercise is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats. PLoS One 2015; 10:e0125889. [PMID: 26016739 PMCID: PMC4446322 DOI: 10.1371/journal.pone.0125889] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/23/2015] [Indexed: 02/07/2023] Open
Abstract
The mammalian intestine harbors a complex microbial ecosystem that influences many aspects of host physiology. Exposure to specific microbes early in development affects host metabolism, immune function, and behavior across the lifespan. Just as the physiology of the developing organism undergoes a period of plasticity, the developing microbial ecosystem is characterized by instability and may also be more sensitive to change. Early life thus presents a window of opportunity for manipulations that produce adaptive changes in microbial composition. Recent insights have revealed that increasing physical activity can increase the abundance of beneficial microbial species. We therefore investigated whether six weeks of wheel running initiated in the juvenile period (postnatal day 24) would produce more robust and stable changes in microbial communities versus exercise initiated in adulthood (postnatal day 70) in male F344 rats. 16S rRNA gene sequencing was used to characterize the microbial composition of juvenile versus adult runners and their sedentary counterparts across multiple time points during exercise and following exercise cessation. Alpha diversity measures revealed that the microbial communities of young runners were less even and diverse, a community structure that reflects volatility and malleability. Juvenile onset exercise altered several phyla and, notably, increased Bacteroidetes and decreased Firmicutes, a configuration associated with leanness. At the genus level of taxonomy, exercise altered more genera in juveniles than in the adults and produced patterns associated with adaptive metabolic consequences. Given the potential of these changes to contribute to a lean phenotype, we examined body composition in juvenile versus adult runners. Interestingly, exercise produced persistent increases in lean body mass in juvenile but not adult runners. Taken together, these results indicate that the impact of exercise on gut microbiota composition as well as body composition may depend on the developmental stage during which exercise is initiated.
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Affiliation(s)
- Agnieszka Mika
- Department of Integrative Physiology and the Center for Neuroscience, University of Colorado, Boulder, Colorado, 80301, United States of America
| | - Will Van Treuren
- Department of Microbiology and Immunology, Stanford University, Stanford, California, 94305, United States of America
| | - Antonio González
- Departments of Pediatrics, University of California San Diego, La Jolla, California, 29093, United States of America
| | - Jonathan J. Herrera
- Department of Integrative Physiology and the Center for Neuroscience, University of Colorado, Boulder, Colorado, 80301, United States of America
| | - Rob Knight
- Departments of Pediatrics, University of California San Diego, La Jolla, California, 29093, United States of America
- Computer Science & Engineering, University of California San Diego, La Jolla, California, 29093, United States of America
| | - Monika Fleshner
- Department of Integrative Physiology and the Center for Neuroscience, University of Colorado, Boulder, Colorado, 80301, United States of America
- * E-mail:
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41
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Deusch S, Seifert J. Catching the tip of the iceberg - Evaluation of sample preparation protocols for metaproteomic studies of the rumen microbiota. Proteomics 2015; 15:3590-5. [DOI: 10.1002/pmic.201400556] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/29/2015] [Accepted: 03/10/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Simon Deusch
- Institute of Animal Science; University of Hohenheim; Stuttgart Germany
| | - Jana Seifert
- Institute of Animal Science; University of Hohenheim; Stuttgart Germany
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Tanca A, Palomba A, Pisanu S, Addis MF, Uzzau S. Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota. Proteomics 2015; 15:3474-85. [PMID: 25677681 DOI: 10.1002/pmic.201400573] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/15/2015] [Accepted: 02/05/2015] [Indexed: 02/03/2023]
Abstract
To date, most metaproteomic studies of the gut microbiota employ stool sample pretreatment methods to enrich for microbial components. However, a specific investigation aimed at assessing if, how, and to what extent this may impact on the final taxonomic and functional results is still lacking. Here, stool replicates were either pretreated by differential centrifugation (DC) or not centrifuged. Protein extracts were then processed by filter-aided sample preparation, single-run LC, and high-resolution MS, and the metaproteomic data were compared by spectral counting. DC led to a higher number of identifications, a significantly richer microbial diversity, as well as to reduced information on the nonmicrobial components (host and food) when compared to not centrifuged. Nevertheless, dramatic differences in the relative abundance of several gut microbial taxa were also observed, including a significant change in the Firmicutes/Bacteroidetes ratio. Furthermore, some important microbial functional categories, including cell surface enzymes, membrane-associated proteins, extracellular proteins, and flagella, were significantly reduced after DC. In conclusion, this work underlines that a critical evaluation is needed when selecting the appropriate stool sample processing protocol in the context of a metaproteomic study, depending on the specific target to which the research is aimed. All MS data have been deposited in the ProteomeXchange with identifier PXD001573 (http://proteomecentral.proteomexchange.org/dataset/PXD001573).
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Affiliation(s)
| | | | | | | | - Sergio Uzzau
- Porto Conte Ricerche, Tramariglio, Alghero, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
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43
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Sauer S, Luge T. Nutriproteomics: Facts, concepts, and perspectives. Proteomics 2015; 15:997-1013. [DOI: 10.1002/pmic.201400383] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/03/2014] [Accepted: 11/27/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Sascha Sauer
- Otto Warburg Laboratory; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Toni Luge
- Otto Warburg Laboratory; Max Planck Institute for Molecular Genetics; Berlin Germany
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Tanca A, Palomba A, Pisanu S, Deligios M, Fraumene C, Manghina V, Pagnozzi D, Addis MF, Uzzau S. A straightforward and efficient analytical pipeline for metaproteome characterization. MICROBIOME 2014; 2:49. [PMID: 25516796 PMCID: PMC4266899 DOI: 10.1186/s40168-014-0049-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/11/2014] [Indexed: 05/27/2023]
Abstract
BACKGROUND The massive characterization of host-associated and environmental microbial communities has represented a real breakthrough in the life sciences in the last years. In this context, metaproteomics specifically enables the transition from assessing the genomic potential to actually measuring the functional expression of a microbiome. However, significant research efforts are still required to develop analysis pipelines optimized for metaproteome characterization. RESULTS This work presents an efficient analytical pipeline for shotgun metaproteomic analysis, combining bead-beating/freeze-thawing for protein extraction, filter-aided sample preparation for cleanup and digestion, and single-run liquid chromatography-tandem mass spectrometry for peptide separation and identification. The overall procedure is more time-effective and less labor-intensive when compared to state-of-the-art metaproteomic techniques. The pipeline was first evaluated using mock microbial mixtures containing different types of bacteria and yeasts, enabling the identification of up to over 15,000 non-redundant peptide sequences per run with a linear dynamic range from 10(4) to 10(8) colony-forming units. The pipeline was then applied to the mouse fecal metaproteome, leading to the overall identification of over 13,000 non-redundant microbial peptides with a false discovery rate of <1%, belonging to over 600 different microbial species and 250 functionally relevant protein families. An extensive mapping of the main microbial metabolic pathways actively functioning in the gut microbiome was also achieved. CONCLUSIONS The analytical pipeline presented here may be successfully used for the in-depth and time-effective characterization of complex microbial communities, such as the gut microbiome, and represents a useful tool for the microbiome research community.
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Affiliation(s)
- Alessandro Tanca
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Antonio Palomba
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Salvatore Pisanu
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Massimo Deligios
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Cristina Fraumene
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Valeria Manghina
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Daniela Pagnozzi
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Maria Filippa Addis
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Sergio Uzzau
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
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Evans CC, LePard KJ, Kwak JW, Stancukas MC, Laskowski S, Dougherty J, Moulton L, Glawe A, Wang Y, Leone V, Antonopoulos DA, Smith D, Chang EB, Ciancio MJ. Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity. PLoS One 2014; 9:e92193. [PMID: 24670791 PMCID: PMC3966766 DOI: 10.1371/journal.pone.0092193] [Citation(s) in RCA: 394] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 02/20/2014] [Indexed: 12/18/2022] Open
Abstract
Background Diet-induced obesity (DIO) is a significant health concern which has been linked to structural and functional changes in the gut microbiota. Exercise (Ex) is effective in preventing obesity, but whether Ex alters the gut microbiota during development with high fat (HF) feeding is unknown. Objective Determine the effects of voluntary Ex on the gastrointestinal microbiota in LF-fed mice and in HF-DIO. Methods Male C57BL/6 littermates (5 weeks) were distributed equally into 4 groups: low fat (LF) sedentary (Sed) LF/Sed, LF/Ex, HF/Sed and HF/Ex. Mice were individually housed and LF/Ex and HF/Ex cages were equipped with a wheel and odometer to record Ex. Fecal samples were collected at baseline, 6 weeks and 12 weeks and used for bacterial DNA isolation. DNA was subjected both to quantitative PCR using primers specific to the 16S rRNA encoding genes for Bacteroidetes and Firmicutes and to sequencing for lower taxonomic identification using the Illumina MiSeq platform. Data were analyzed using a one or two-way ANOVA or Pearson correlation. Results HF diet resulted in significantly greater body weight and adiposity as well as decreased glucose tolerance that were prevented by voluntary Ex (p<0.05). Visualization of Unifrac distance data with principal coordinates analysis indicated clustering by both diet and Ex at week 12. Sequencing demonstrated Ex-induced changes in the percentage of major bacterial phyla at 12 weeks. A correlation between total Ex distance and the ΔCt Bacteroidetes: ΔCt Firmicutes ratio from qPCR demonstrated a significant inverse correlation (r2 = 0.35, p = 0.043). Conclusion Ex induces a unique shift in the gut microbiota that is different from dietary effects. Microbiota changes may play a role in Ex prevention of HF-DIO.
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Affiliation(s)
- Christian C. Evans
- Department of Physical Therapy, College of Health Sciences, Midwestern University, Downers Grove, Illinois, United States of America
- * E-mail:
| | - Kathy J. LePard
- Department of Physiology, College of Osteopathic Medicine, Midwestern University, Downers Grove, Illinois, United States of America
| | - Jeff W. Kwak
- Department of Biomedical Sciences, College of Health Sciences, Midwestern University, Downers Grove, Illinois, United States of America
| | - Mary C. Stancukas
- Department of Biomedical Sciences, College of Health Sciences, Midwestern University, Downers Grove, Illinois, United States of America
| | - Samantha Laskowski
- College of Osteopathic Medicine, Midwestern University, Downers Grove, Illinois, United States of America
| | - Joseph Dougherty
- Department of Biomedical Sciences, College of Health Sciences, Midwestern University, Downers Grove, Illinois, United States of America
- Department of Dental Medicine, College of Dental Medicine, Midwestern University, Downers Grove, Illinois, United States of America
| | - Laura Moulton
- Department of Biomedical Sciences, College of Health Sciences, Midwestern University, Downers Grove, Illinois, United States of America
| | - Adam Glawe
- Department of Biomedical Sciences, College of Health Sciences, Midwestern University, Downers Grove, Illinois, United States of America
| | - Yunwei Wang
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Vanessa Leone
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Dionysios A. Antonopoulos
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Dan Smith
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Eugene B. Chang
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Mae J. Ciancio
- Department of Biomedical Sciences, College of Health Sciences, Midwestern University, Downers Grove, Illinois, United States of America
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Di Girolamo F, Lante I, Muraca M, Putignani L. The Role of Mass Spectrometry in the "Omics" Era. CURR ORG CHEM 2013; 17:2891-2905. [PMID: 24376367 PMCID: PMC3873040 DOI: 10.2174/1385272817888131118162725] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/06/2013] [Accepted: 09/06/2013] [Indexed: 11/15/2022]
Abstract
Mass spectrometry (MS) is one of the key analytical technology on which the emerging ''-omics'' approaches are based. It may provide detection and quantization of thousands of proteins and biologically active metabolites from a tissue, body fluid or cell culture working in a ''global'' or ''targeted'' manner, down to ultra-trace levels. It can be expected that the high performance of MS technology, coupled to routine data handling, will soon bring fruit in the request for a better understanding of human diseases, leading to new molecular biomarkers, hence affecting drug targets and therapies. In this review, we focus on the main advances in the MS technologies, influencing genomics, transcriptomics, proteomics, lipidomics and metabolomics fields, up to the most recent MS applications to meta-omic studies.
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Affiliation(s)
- Francesco Di Girolamo
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Isabella Lante
- Laboratory Medicine, San Camillo Hospital, Viale Vittorio Veneto 18, 31100, Treviso, Italy
| | - Maurizio Muraca
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Lorenza Putignani
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
- Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
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Del Chierico F, Petrucca A, Mortera SL, Vernocchi P, Rosado MM, Pieroni L, Carsetti R, Urbani A, Putignani L. A metaproteomic pipeline to identify newborn mouse gut phylotypes. J Proteomics 2013; 97:17-26. [PMID: 24176786 DOI: 10.1016/j.jprot.2013.10.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 09/20/2013] [Accepted: 10/18/2013] [Indexed: 12/12/2022]
Abstract
UNLABELLED In order to characterize newborn mouse gut microbiota phylotypes in very early-life stages, an original metaproteomic pipeline, based on LC-MS(2)-spectra and Mascot driven NCBI non-redundant repository database interrogation was developed. An original computational analysis assisted in the generation of a taxonomic gut architecture from protein hits to operational taxonomic units (OTUs) and related functional categories. Regardless of the mouse's genetic background, a prevalence of Firmicutes (Lactobacillaceae) and Proteobacteria (Enterobacteriaceae) was observed among the entire Eubacteria taxonomic node. However, a higher abundance of Firmicutes was retrieved for Balb/c gut microbiota compared to Rag2(ko) mice, the latter was mainly characterized by a Proteobacteria enriched microbiota. The metaproteomic-obtained OTUs were supported, for the identification (ID) of the cultivable bacteria fraction, corroborated by axenic culture-based MALDI-TOF MS IDs. Particularly, functional analysis of Rag2(ko) mice gut microbiota proteins revealed the presence of abundant glutathione, riboflavin metabolism and pentose phosphate pathway components, possibly related to genetic background. The metaproteomic pipeline herein presented may represent a useful tool to investigate the highly debated onset of the human gut microbiota in the first days of life, when the bacterial composition, despite its very low diversity (complexity), is still very far from an exhaustive description and other complex microbial consortia. BIOLOGICAL SIGNIFICANCE The manuscript deals with a "frontier" topic regarding the study of the gut microbiota and the application of a metaproteomic pipeline to unveil the complexity of this fascinating ecosystem at the very early stages of life. Indeed during these phases, its diversity is very low but the bacterial content is highly "instable", and the relative balance between mucosal and fecal bacteria starts its dynamics of "fight" to get homeostasis. However, in the neonatal period, especially immediately after birth, a comprehensive description of this microbial eco-organ is still lacking, while it should be mandatory to highlight its first mechanisms of homeostasis and perturbation, while it co-develops with and within the host species. In order to unravel its low but almost unknown microbial community multiplicity, the newborn mouse gut, characterized by a "very" low complexity, was herein selected as model to design a LC-MS(2)-based shotgun metaproteomic approach, potentially suitable to study onset and shaping in human newborns. A microbiological semi-automatic computational analysis was performed to infer gut phylotypes; such as proof of evidence, related OTUs were compared to axenic-culture-based MALDI-TOF MS IDs showing consistency at family and phyla levels for the bacterial cultivable fraction. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Federica Del Chierico
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Petrucca
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Diagnostic Science, Sant'Andrea Hospital, Rome, Italy
| | - Stefano Levi Mortera
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy
| | - Pamela Vernocchi
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Interdipartimental Centre for Industrial Research, Alma Mater Studiorum, University of Bologna, Italy
| | - Maria M Rosado
- B-cell development Unit and Immunological Diagnosis Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Luisa Pieroni
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy
| | - Rita Carsetti
- B-cell development Unit and Immunological Diagnosis Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Urbani
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy.
| | - Lorenza Putignani
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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48
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Del Chierico F, Petrucca A, Vernocchi P, Bracaglia G, Fiscarelli E, Bernaschi P, Muraca M, Urbani A, Putignani L. Proteomics boosts translational and clinical microbiology. J Proteomics 2013; 97:69-87. [PMID: 24145144 DOI: 10.1016/j.jprot.2013.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 07/28/2013] [Accepted: 10/09/2013] [Indexed: 01/17/2023]
Abstract
The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- F Del Chierico
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - A Petrucca
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Department of Diagnostic Science, Sant'Andrea Hospital, Via di Grottarossa 1035, 00185 Rome, Italy
| | - P Vernocchi
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - G Bracaglia
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - E Fiscarelli
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - P Bernaschi
- Unit of Microbiology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - M Muraca
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - A Urbani
- Department of Experimental Medicine and Surgery, University "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy
| | - L Putignani
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
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High-fat diet alters gut microbiota physiology in mice. ISME JOURNAL 2013; 8:295-308. [PMID: 24030595 DOI: 10.1038/ismej.2013.155] [Citation(s) in RCA: 487] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 08/04/2013] [Indexed: 12/13/2022]
Abstract
The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by high-calorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by Fourier-transform infrared- (FT-IR) and Raman micro-spectroscopy and (iii) metaproteome and metabolome via high-resolution mass spectrometry. High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the impact of the diet on cecal chemical fingerprints is greater than the impact of microbiota composition. Diet-driven changes in biochemical fingerprints of members of the Bacteroidales and Lachnospiraceae were also observed at the level of single cells, indicating that there were distinct differences in cellular composition of dominant phylotypes under different diets. Metaproteome and metabolome analyses based on the occurrence of 1760 bacterial proteins and 86 annotated metabolites revealed distinct HF diet-specific profiles. Alteration of hormonal and anti-microbial networks, bile acid and bilirubin metabolism and shifts towards amino acid and simple sugars metabolism were observed. We conclude that a HF diet markedly affects the gut bacterial ecosystem at the functional level.
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Seifert J, Herbst FA, Halkjaer Nielsen P, Planes FJ, Jehmlich N, Ferrer M, von Bergen M. Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities. Proteomics 2013; 13:2786-804. [PMID: 23625762 DOI: 10.1002/pmic.201200566] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/07/2013] [Accepted: 03/28/2013] [Indexed: 11/06/2022]
Abstract
Metaproteomics of microbial communities promises to add functional information to the blueprint of genes derived from metagenomics. Right from its beginning, the achievements and developments in metaproteomics were closely interlinked with metagenomics. In addition, the evaluation, visualization, and interpretation of metaproteome data demanded for the developments in bioinformatics. This review will give an overview about recent strategies to use genomic data either from public databases or organismal specific genomes/metagenomes to increase the number of identified proteins obtained by mass spectrometric measurements. We will review different published metaproteogenomic approaches in respect to the used MS pipeline and to the used protein identification workflow. Furthermore, different approaches of data visualization and strategies for phylogenetic interpretation of metaproteome data are discussed as well as approaches for functional mapping of the results to the investigated biological systems. This information will in the end allow a comprehensive analysis of interactions and interdependencies within microbial communities.
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Affiliation(s)
- Jana Seifert
- Department of Proteomics, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany; Institute of Animal Nutrition, University of Hohenheim, Stuttgart, Germany
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