101
|
Sommer F, Anderson JM, Bharti R, Raes J, Rosenstiel P. The resilience of the intestinal microbiota influences health and disease. Nat Rev Microbiol 2017. [DOI: 10.1038/nrmicro.2017.58] [Citation(s) in RCA: 460] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
102
|
Bendtsen KM, Hansen CHF, Krych Ł, Skovgaard K, Kot W, Vogensen FK, Hansen AK. Immunological effects of reduced mucosal integrity in the early life of BALB/c mice. PLoS One 2017; 12:e0176662. [PMID: 28459871 PMCID: PMC5411035 DOI: 10.1371/journal.pone.0176662] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 04/14/2017] [Indexed: 02/07/2023] Open
Abstract
Certain stimuli at the gut barrier may be necessary in early life to establish a proper balance of immune tolerance. We evaluated a compromised barrier in juvenile mice in relation to microbiota and local and systemic immunity. BALB/c mice were treated with a low dose of dextran sulfate sodium (DSS) with or without ampicillin and lipopolysaccharide (LPS) to clarify the importance of microbial antigens and interaction between microbial-associated patterns and toll-like receptors. The barrier breach resulted in increased plasma LPS, which was highest in mice treated simultaneously with ampicillin. Adding LPS in the food reduced its levels in plasma. Regulatory T cells were acutely increased in mesenteric lymph nodes (MLN) and spleen during DSS treatment regardless of simultaneous ampicillin treatment. In contrast, NK T and NK cells decreased in MLN and in spleen. This acute DSS effect was reflected in fold changes of haptoglobin and Il1a in colon, and this was also more pronounced in mice simultaneously treated with ampicillin. On day 1 post-treatment, major upregulations of Ifng, Foxp3, Il1b, Il2, and Il6 genes in colon were only observed in the mice simultaneously treated with ampicillin. A two-fold upregulation of colonic Foxp3 and Il1a was evident 25 days post-treatment. DSS skewed the microbiota in favor of Gram negative phyla. Therefore, increased permeability induced tolerogenic immunity independent of microbiota, and this was enhanced by LPS stimulation.
Collapse
Affiliation(s)
- Katja Maria Bendtsen
- Section of Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Camilla Hartmann Friis Hansen
- Section of Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Łukasz Krych
- Department of Food Science, Faculty of Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kerstin Skovgaard
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Finn Kvist Vogensen
- Department of Food Science, Faculty of Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Axel Kornerup Hansen
- Section of Experimental Animal Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
103
|
Engineered Resistant-Starch (ERS) Diet Shapes Colon Microbiota Profile in Parallel with the Retardation of Tumor Growth in In Vitro and In Vivo Pancreatic Cancer Models. Nutrients 2017; 9:nu9040331. [PMID: 28346394 PMCID: PMC5409670 DOI: 10.3390/nu9040331] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022] Open
Abstract
Background/aims: Pancreatic cancer (PC) is ranked as the fourth leading cause of cancer-related deaths worldwide. Despite recent advances in treatment options, a modest impact on the outcome of the disease is observed so far. We have previously demonstrated that short-term fasting cycles have the potential to improve the efficacy of chemotherapy against PC. The aim of this study was to assess the effect of an engineered resistant-starch (ERS) mimicking diet on the growth of cancer cell lines in vitro, on the composition of fecal microbiota, and on tumor growth in an in vivo pancreatic cancer mouse xenograft model. Materials and Methods: BxPC-3, MIA PaCa-2 and PANC-1 cells were cultured in the control, and in the ERS-mimicking diet culturing condition, to evaluate tumor growth and proliferation pathways. Pancreatic cancer xenograft mice were subjected to an ERS diet to assess tumor volume and weight as compared to mice fed with a control diet. The composition and activity of fecal microbiota were further analyzed in growth experiments by isothermal microcalorimetry. Results: Pancreatic cancer cells cultured in an ERS diet-mimicking medium showed decreased levels of phospho-ERK1/2 (extracellular signal-regulated kinase proteins) and phospho-mTOR (mammalian target of rapamycin) levels, as compared to those cultured in standard medium. Consistently, xenograft pancreatic cancer mice subjected to an ERS diet displayed significant retardation in tumor growth. In in vitro growth experiments, the fecal microbial cultures from mice fed with an ERS diet showed enhanced growth on residual substrates, higher production of formate and lactate, and decreased amounts of propionate, compared to fecal microbiota from mice fed with the control diet. Conclusion: A positive effect of the ERS diet on composition and metabolism of mouse fecal microbiota shown in vitro is associated with the decrease of tumor progression in the in vivo PC xenograft mouse model. These results suggest that engineered dietary interventions could be supportive as a synergistic approach to enhance the efficacy of existing cancer treatments in pancreatic cancer patients.
Collapse
|
104
|
Ursodeoxycholic Acid and Its Taurine- or Glycine-Conjugated Species Reduce Colitogenic Dysbiosis and Equally Suppress Experimental Colitis in Mice. Appl Environ Microbiol 2017; 83:AEM.02766-16. [PMID: 28115375 DOI: 10.1128/aem.02766-16] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/10/2017] [Indexed: 02/06/2023] Open
Abstract
The promising results seen in studies of secondary bile acids in experimental colitis suggest that they may represent an attractive and safe class of drugs for the treatment of inflammatory bowel diseases (IBD). However, the exact mechanism by which bile acid therapy confers protection from colitogenesis is currently unknown. Since the gut microbiota plays a crucial role in the pathogenesis of IBD, and exogenous bile acid administration may affect the community structure of the microbiota, we examined the impact of the secondary bile acid ursodeoxycholic acid (UDCA) and its taurine or glycine conjugates on the fecal microbial community structure during experimental colitis. Daily oral administration of UDCA, tauroursodeoxycholic acid (TUDCA), or glycoursodeoxycholic acid (GUDCA) equally lowered the severity of dextran sodium sulfate-induced colitis in mice, as evidenced by reduced body weight loss, colonic shortening, and expression of inflammatory cytokines. Illumina sequencing demonstrated that bile acid therapy during colitis did not restore fecal bacterial richness and diversity. However, bile acid therapy normalized the colitis-associated increased ratio of Firmicutes to Bacteroidetes Interestingly, administration of bile acids prevented the loss of Clostridium cluster XIVa and increased the abundance of Akkermansia muciniphila, bacterial species known to be particularly decreased in IBD patients. We conclude that UDCA, which is an FDA-approved drug for cholestatic liver disorders, could be an attractive treatment option to reduce dysbiosis and ameliorate inflammation in human IBD.IMPORTANCE Secondary bile acids are emerging as attractive candidates for the treatment of inflammatory bowel disease. Although bile acids may affect the intestinal microbial community structure, which significantly contributes to the course of these inflammatory disorders, the impact of bile acid therapy on the fecal microbiota during colitis has not yet been considered. Here, we studied the alterations in the fecal microbial abundance in colitic mice following the administration of secondary bile acids. Our results show that secondary bile acids reduce the severity of colitis and ameliorate colitis-associated fecal dysbiosis at the phylum level. This study indicates that secondary bile acids might act as a safe and effective drug for inflammatory bowel disease.
Collapse
|
105
|
Cooper DN, Kable ME, Marco ML, De Leon A, Rust B, Baker JE, Horn W, Burnett D, Keim NL. The Effects of Moderate Whole Grain Consumption on Fasting Glucose and Lipids, Gastrointestinal Symptoms, and Microbiota. Nutrients 2017; 9:nu9020173. [PMID: 28230784 PMCID: PMC5331604 DOI: 10.3390/nu9020173] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/01/2017] [Accepted: 02/16/2017] [Indexed: 01/18/2023] Open
Abstract
This study was designed to determine if providing wheat, corn, and rice as whole (WG) or refined grains (RG) under free-living conditions will change parameters of health over a six-week intervention in healthy, habitual non-WG consumers. Measurements of body composition, fecal microbiota, fasting blood glucose, total cholesterol, high density lipoprotein (HDL), low density lipoprotein (LDL), and triglycerides were made at baseline and post intervention. Subjects were given adequate servings of either WG or RG products based on their caloric need and asked to keep records of grain consumption, bowel movements, and GI symptoms weekly. After six weeks, subjects repeated baseline testing. Significant decreases in total, LDL, and non-HDL cholesterol were seen after the WG treatments but were not observed in the RG treatment. During Week 6, bowel movement frequency increased with increased WG consumption. No significant differences in microbiota were seen between baseline and post intervention, although, abundance of order Erysipelotrichales increased in RG subjects who ate more than 50% of the RG market basket products. Increasing consumption of WGs can alter parameters of health, but more research is needed to better elucidate the relationship between the amount consumed and the health-related outcome.
Collapse
Affiliation(s)
- Danielle N Cooper
- Department of Nutrition, University of California at Davis, 1 Shields Ave, Davis, CA 95616, USA.
| | - Mary E Kable
- Western Human Nutrition Research Center, USDA-ARS, 430 West Health Sciences Drive, Davis, CA 95616, USA.
| | - Maria L Marco
- Food Science and Technology, University of California at Davis, 1 Shields Ave, Davis, CA 95616, USA.
| | - Angela De Leon
- Department of Nutrition, University of California at Davis, 1 Shields Ave, Davis, CA 95616, USA.
| | - Bret Rust
- Department of Nutrition, University of California at Davis, 1 Shields Ave, Davis, CA 95616, USA.
- Western Human Nutrition Research Center, USDA-ARS, 430 West Health Sciences Drive, Davis, CA 95616, USA.
| | - Julita E Baker
- Department of Nutrition, University of California at Davis, 1 Shields Ave, Davis, CA 95616, USA.
| | - William Horn
- Western Human Nutrition Research Center, USDA-ARS, 430 West Health Sciences Drive, Davis, CA 95616, USA.
| | - Dustin Burnett
- Western Human Nutrition Research Center, USDA-ARS, 430 West Health Sciences Drive, Davis, CA 95616, USA.
| | - Nancy L Keim
- Department of Nutrition, University of California at Davis, 1 Shields Ave, Davis, CA 95616, USA.
- Western Human Nutrition Research Center, USDA-ARS, 430 West Health Sciences Drive, Davis, CA 95616, USA.
| |
Collapse
|
106
|
Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota. mSystems 2017; 2:mSystems00171-16. [PMID: 28168224 PMCID: PMC5285517 DOI: 10.1128/msystems.00171-16] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 01/04/2017] [Indexed: 01/01/2023] Open
Abstract
Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease. Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.
Collapse
|
107
|
Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis: Relevance to Human Inflammatory Bowel Disease. Inflamm Bowel Dis 2016; 22:2767-2787. [PMID: 27824648 DOI: 10.1097/mib.0000000000000970] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Dysbiosis of the gut microbiota may be involved in the pathogenesis of inflammatory bowel disease (IBD). However, the mechanisms underlying the role of the intestinal microbiome and metabolome in IBD onset and its alteration during active treatment and recovery remain unknown. Animal models of chronic intestinal inflammation with similar microbial and metabolomic profiles would enable investigation of these mechanisms and development of more effective treatments. Recently, the Winnie mouse model of colitis closely representing the clinical symptoms and characteristics of human IBD has been developed. In this study, we have analyzed fecal microbial and metabolomic profiles in Winnie mice and discussed their relevance to human IBD. METHODS The 16S rRNA gene was sequenced from fecal DNA of Winnie and C57BL/6 mice to define operational taxonomic units at ≥97% similarity threshold. Metabolomic profiling of the same fecal samples was performed by gas chromatography-mass spectrometry. RESULTS Composition of the dominant microbiota was disturbed, and prominent differences were evident at all levels of the intestinal microbiome in fecal samples from Winnie mice, similar to observations in patients with IBD. Metabolomic profiling revealed that chronic colitis in Winnie mice upregulated production of metabolites and altered several metabolic pathways, mostly affecting amino acid synthesis and breakdown of monosaccharides to short chain fatty acids. CONCLUSIONS Significant dysbiosis in the Winnie mouse gut replicates many changes observed in patients with IBD. These results provide justification for the suitability of this model to investigate mechanisms underlying the role of intestinal microbiota and metabolome in the pathophysiology of IBD.
Collapse
|
108
|
Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe. Proc Natl Acad Sci U S A 2016; 113:14127-14132. [PMID: 27911803 DOI: 10.1073/pnas.1612753113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A major roadblock to understanding how microbes in the gastrointestinal tract colonize and influence the physiology of their hosts is our inability to genetically manipulate new bacterial species and experimentally assess the function of their genes. We describe the application of population-based genomic sequencing after chemical mutagenesis to map bacterial genes responsible for motility in Exiguobacterium acetylicum, a representative intestinal Firmicutes bacterium that is intractable to molecular genetic manipulation. We derived strong associations between mutations in 57 E. acetylicum genes and impaired motility. Surprisingly, less than half of these genes were annotated as motility-related based on sequence homologies. We confirmed the genetic link between individual mutations and loss of motility for several of these genes by performing a large-scale analysis of spontaneous suppressor mutations. In the process, we reannotated genes belonging to a broad family of diguanylate cyclases and phosphodiesterases to highlight their specific role in motility and assigned functions to uncharacterized genes. Furthermore, we generated isogenic strains that allowed us to establish that Exiguobacterium motility is important for the colonization of its vertebrate host. These results indicate that genetic dissection of a complex trait, functional annotation of new genes, and the generation of mutant strains to define the role of genes in complex environments can be accomplished in bacteria without the development of species-specific molecular genetic tools.
Collapse
|
109
|
Power KA, Lu JT, Monk JM, Lepp D, Wu W, Zhang C, Liu R, Tsao R, Robinson LE, Wood GA, Wolyn DJ. Purified rutin and rutin-rich asparagus attenuates disease severity and tissue damage following dextran sodium sulfate-induced colitis. Mol Nutr Food Res 2016; 60:2396-2412. [PMID: 27349947 DOI: 10.1002/mnfr.201500890] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 06/07/2016] [Accepted: 06/15/2016] [Indexed: 12/25/2022]
Abstract
SCOPE This study investigated the effects of cooked whole asparagus (ASP) versus its equivalent level of purified flavonoid glycoside, rutin (RUT), on dextran sodium sulfate (DSS)-induced colitis and subsequent colitis recovery in mice. METHODS AND RESULTS C57BL/6 male mice were fed an AIN-93G basal diet (BD), or BD supplemented with 2% cooked ASP or 0.025% RUT for 2 wks prior to and during colitis induction with 2% DSS in water for 7 days, followed by 5 days colitis recovery. In colitic mice, both ASP and RUT upregulated mediators of improved barrier integrity and enhanced mucosal injury repair (e.g. Muc1, IL-22, Rho-A, Rac1, and Reg3γ), increased the proportion of mouse survival, and improved disease activity index. RUT had the greatest effect in attenuating DSS-induced colonic damage indicated by increased crypt and goblet cell restitution, reduced colonic myeloperoxidase, as well as attenuated DSS-induced microbial dysbiosis (reduced Enterobacteriaceae and Bacteroides, and increased unassigned Clostridales, Oscillospira, Lactobacillus, and Bifidobacterium). CONCLUSION These findings demonstrate that dietary cooked ASP and its flavonoid glycoside, RUT, may be useful in attenuating colitis severity by modulating the colonic microenvironment resulting in reduced colonic inflammation, promotion of colonic mucosal injury repair, and attenuation of colitis-associated microbial dysbiosis.
Collapse
Affiliation(s)
- Krista A Power
- Guelph Food Research Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada
| | - Jenifer T Lu
- Guelph Food Research Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada
| | - Jennifer M Monk
- Guelph Food Research Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada
| | - Dion Lepp
- Guelph Food Research Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Wenqing Wu
- Guelph Food Research Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Claire Zhang
- Guelph Food Research Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada
| | - Ronghua Liu
- Guelph Food Research Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Rong Tsao
- Guelph Food Research Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Lindsay E Robinson
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada
| | - Geoffrey A Wood
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - David J Wolyn
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
110
|
Budden KF, Gellatly SL, Wood DLA, Cooper MA, Morrison M, Hugenholtz P, Hansbro PM. Emerging pathogenic links between microbiota and the gut-lung axis. Nat Rev Microbiol 2016; 15:55-63. [PMID: 27694885 DOI: 10.1038/nrmicro.2016.142] [Citation(s) in RCA: 870] [Impact Index Per Article: 108.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The microbiota is vital for the development of the immune system and homeostasis. Changes in microbial composition and function, termed dysbiosis, in the respiratory tract and the gut have recently been linked to alterations in immune responses and to disease development in the lungs. In this Opinion article, we review the microbial species that are usually found in healthy gastrointestinal and respiratory tracts, their dysbiosis in disease and interactions with the gut-lung axis. Although the gut-lung axis is only beginning to be understood, emerging evidence indicates that there is potential for manipulation of the gut microbiota in the treatment of lung diseases.
Collapse
Affiliation(s)
- Kurtis F Budden
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia
| | - Shaan L Gellatly
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia
| | - David L A Wood
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland 4072, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, and the Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia; and The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, Queensland 4102, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales 2305, Australia
| |
Collapse
|
111
|
Oral exposure to environmental pollutant benzo[a]pyrene impacts the intestinal epithelium and induces gut microbial shifts in murine model. Sci Rep 2016; 6:31027. [PMID: 27503127 PMCID: PMC4977522 DOI: 10.1038/srep31027] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/13/2016] [Indexed: 02/07/2023] Open
Abstract
Gut microbiota dysbiosis are associated with a wide range of human diseases, including inflammatory bowel diseases. The physiopathology of these diseases has multifactorial aetiology in which environmental factors, particularly pollution could play a crucial role. Among the different pollutants listed, Polycyclic Aromatic Hydrocarbons (PAHs) are subject to increased monitoring due to their wide distribution and high toxicity on Humans. Here, we used 16S rRNA gene sequencing to investigate the impact of benzo[a]pyrene (BaP, most toxic PAH) oral exposure on the faecal and intestinal mucosa-associated bacteria in C57BL/6 mice. Intestinal inflammation was also evaluated by histological observations. BaP oral exposure significantly altered the composition and the abundance of the gut microbiota and led to moderate inflammation in ileal and colonic mucosa. More severe lesions were observed in ileal segment. Shifts in gut microbiota associated with moderate inflammatory signs in intestinal mucosa would suggest the establishment of a pro-inflammatory intestinal environment following BaP oral exposure. Therefore, under conditions of genetic susceptibility and in association with other environmental factors, exposure to this pollutant could trigger and/or accelerate the development of inflammatory pathologies.
Collapse
|
112
|
Wang H, Li Y, Feng X, Li Y, Wang W, Qiu C, Xu J, Yang Z, Li Z, Zhou Q, Yao K, Wang H, Li Y, Li D, Dai W, Zheng Y. Dysfunctional gut microbiota and relative co-abundance network in infantile eczema. Gut Pathog 2016; 8:36. [PMID: 27453732 PMCID: PMC4957860 DOI: 10.1186/s13099-016-0118-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/11/2016] [Indexed: 12/20/2022] Open
Abstract
Background Infantile eczema is an immunological disease that is characterized by itchy and dry skin. Recent studies have suggested that gut microbiota (GM) plays a role in the development and progression of eczema. To further evaluate this potential link, we collected feces from 19 infants with eczema and 14 infants without eczema and analyzed the molecular discrepancies between the two groups using 16S rDNA analysis. Results Bacteroidaceae and Deinococcaceae were significantly enriched in eczema infants, and Bacteroidaceae was potentially involved in autoimmune diseases by promoting the Th17 (T helper cell 17) secretion of IL-17 (interleukin-17). In the infants without eczema, the co-abundance network featured three core nodes: Clostridiaceae, Veillonellaceae, and Lactobacillaceae, all of which were lacking in the infants with eczema. Furthermore, our data suggested that Enterobacteriaceae was the core of the co-abundance network for the diseased subjects. Conclusions GM is closely connected to the human immune system, and the dysbiotic GM network plays a role in eczema. This study furthered our understanding of the dynamic GM network and its correlation to the occurrence of eczema. Electronic supplementary material The online version of this article (doi:10.1186/s13099-016-0118-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Heping Wang
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Shenzhen, 518026 China
| | - Yinhu Li
- WeHealthGene, No. 118 Wuhe Road, Shenzhen, 518129 China
| | - Xin Feng
- WeHealthGene, No. 118 Wuhe Road, Shenzhen, 518129 China
| | - Yufeng Li
- Dongguan Maternal and Child Healthcare Hospital, No. 99 Zhenxing Road, Dongguan, 523000 China
| | - Wenjian Wang
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Shenzhen, 518026 China
| | | | - Jianqiang Xu
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Shenzhen, 518026 China
| | - Zhenyu Yang
- WeHealthGene, No. 118 Wuhe Road, Shenzhen, 518129 China
| | - Zhichuan Li
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Shenzhen, 518026 China
| | - Qian Zhou
- WeHealthGene, No. 118 Wuhe Road, Shenzhen, 518129 China
| | - Kaihu Yao
- Beijing Children's Hospital, No. 56 Nanlishi Road, Beijing, 100045 China
| | - Hongmei Wang
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Shenzhen, 518026 China
| | - Yuzheng Li
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Shenzhen, 518026 China
| | - Dongfang Li
- WeHealthGene, No. 118 Wuhe Road, Shenzhen, 518129 China
| | - Wenkui Dai
- WeHealthGene, No. 118 Wuhe Road, Shenzhen, 518129 China
| | - Yuejie Zheng
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Shenzhen, 518026 China
| |
Collapse
|
113
|
Li F, Henderson G, Sun X, Cox F, Janssen PH, Guan LL. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches. Front Microbiol 2016; 7:987. [PMID: 27446027 PMCID: PMC4916217 DOI: 10.3389/fmicb.2016.00987] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022] Open
Abstract
Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data.
Collapse
Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| | - Gemma Henderson
- AgResearch Ltd., Grasslands Research Centre Palmerston North, New Zealand
| | - Xu Sun
- Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| | - Faith Cox
- AgResearch Ltd., Grasslands Research Centre Palmerston North, New Zealand
| | - Peter H Janssen
- AgResearch Ltd., Grasslands Research Centre Palmerston North, New Zealand
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| |
Collapse
|
114
|
Zhang Q, Wu Y, Wang J, Wu G, Long W, Xue Z, Wang L, Zhang X, Pang X, Zhao Y, Zhao L, Zhang C. Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium. Sci Rep 2016; 6:27572. [PMID: 27264309 PMCID: PMC4893749 DOI: 10.1038/srep27572] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/23/2016] [Indexed: 12/13/2022] Open
Abstract
Butyrate-producing bacteria (BPB) are potential probiotic candidates for inflammatory bowel diseases as they are often depleted in the diseased gut microbiota. However, here we found that augmentation of a human-derived butyrate-producing strain, Anaerostipes hadrus BPB5, significantly aggravated colitis in dextran sulphate sodium (DSS)-treated mice while exerted no detrimental effect in healthy mice. We explored how the interaction between BPB5 and gut microbiota may contribute to this differential impact on the hosts. Butyrate production and severity of colitis were assessed in both healthy and DSS-treated mice, and gut microbiota structural changes were analysed using high-throughput sequencing. BPB5-inoculated healthy mice showed no signs of colitis, but increased butyrate content in the gut. In DSS-treated mice, BPB5 augmentation did not increase butyrate content, but induced significantly more severe disease activity index and much higher mortality. BPB5 didn't induce significant changes of gut microbiota in healthy hosts, but expedited the structural shifts 3 days earlier toward the disease phase in BPB5-augmented than DSS-treated animals. The differential response of gut microbiota in healthy and DSS-treated mice to the same potentially beneficial bacterium with drastically different health consequences suggest that animals with dysbiotic gut microbiota should also be employed for the safety assessment of probiotic candidates.
Collapse
Affiliation(s)
- Qianpeng Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Yanqiu Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Jing Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Guojun Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Wenmin Long
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Zhengsheng Xue
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Linghua Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Xiaoyan Pang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Yufeng Zhao
- Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240.,Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China, 200240
| |
Collapse
|
115
|
Ferguson JF, Allayee H, Gerszten RE, Ideraabdullah F, Kris-Etherton PM, Ordovás JM, Rimm EB, Wang TJ, Bennett BJ. Nutrigenomics, the Microbiome, and Gene-Environment Interactions: New Directions in Cardiovascular Disease Research, Prevention, and Treatment: A Scientific Statement From the American Heart Association. CIRCULATION. CARDIOVASCULAR GENETICS 2016; 9:291-313. [PMID: 27095829 PMCID: PMC7829062 DOI: 10.1161/hcg.0000000000000030] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cardiometabolic diseases are the leading cause of death worldwide and are strongly linked to both genetic and nutritional factors. The field of nutrigenomics encompasses multiple approaches aimed at understanding the effects of diet on health or disease development, including nutrigenetic studies investigating the relationship between genetic variants and diet in modulating cardiometabolic risk, as well as the effects of dietary components on multiple "omic" measures, including transcriptomics, metabolomics, proteomics, lipidomics, epigenetic modifications, and the microbiome. Here, we describe the current state of the field of nutrigenomics with respect to cardiometabolic disease research and outline a direction for the integration of multiple omics techniques in future nutrigenomic studies aimed at understanding mechanisms and developing new therapeutic options for cardiometabolic disease treatment and prevention.
Collapse
|
116
|
Rokhsefat S, Lin A, Comelli EM. Mucin-Microbiota Interaction During Postnatal Maturation of the Intestinal Ecosystem: Clinical Implications. Dig Dis Sci 2016; 61:1473-86. [PMID: 26792279 DOI: 10.1007/s10620-016-4032-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023]
Abstract
The mucus layer and gut microbiota interplay contributes to host homeostasis. The mucus layer serves as a scaffold and a carbon source for gut microorganisms; conversely, gut microorganisms, including mucin degraders, influence mucin gene expression, glycosylation, and secretion. Conjointly they shield the epithelium from luminal pathogens, antigens, and toxins. Importantly, the mucus layer and gut microbiota are established in parallel during early postnatal life. During this period, the development of gut microbiota and mucus layer is coupled with that of the immune system. Developmental changes of different mucin types can impact the age-dependent patterns of intestinal infection in terms of incidence and severity. Altered mucus layer, dysbiotic microbiota, and abnormal mucus-gut microbiota interaction have the potential for inducing systemic effects, and accompany several intestinal diseases such as inflammatory bowel disease, colorectal cancer, and radiation-induced mucositis. Early life provides a pivotal window of opportunity to favorably modulate the mucus-microbiota interaction. The support of a health-compatible mucin-microbiota maturation in early life is paramount for long-term health and serves as an important opportunity for clinical intervention.
Collapse
Affiliation(s)
- Sana Rokhsefat
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, FitzGerald Building Room 308a, 150 College Street, Toronto, ON, M5S3E2, Canada
| | - Aifeng Lin
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, FitzGerald Building Room 308a, 150 College Street, Toronto, ON, M5S3E2, Canada
- Division of Genetics and Development, Toronto Western Research Institute, Toronto, Canada
- Faculty of Medicine, Institute of Medical Sciences, University of Toronto, Toronto, Canada
| | - Elena M Comelli
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, FitzGerald Building Room 308a, 150 College Street, Toronto, ON, M5S3E2, Canada.
- Centre for Child Nutrition and Health, Faculty of Medicine, University of Toronto, Ontario, Canada.
| |
Collapse
|
117
|
Munyaka PM, Rabbi MF, Khafipour E, Ghia JE. Acute dextran sulfate sodium (DSS)-induced colitis promotes gut microbial dysbiosis in mice. J Basic Microbiol 2016; 56:986-98. [PMID: 27112251 DOI: 10.1002/jobm.201500726] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/18/2016] [Indexed: 12/20/2022]
Abstract
UNLABELLED The most widely used and characterized experimental model of ulcerative colitis (UC) is the epithelial erosion, dextran sulfate sodium (DSS)-induced colitis, which is developed by administration of DSS in drinking water. We investigated fecal and colonic mucosa microbial composition and functional changes in mice treated with DSS. C57Bl/6 mice received 5% DSS in drinking water for 5 days. Inflammation was evaluated clinically and by analysis of colonic tissue cytokine levels and C-reactive protein (CRP) in the serum. Colonic mucosa and fecal samples were used for DNA extraction and the V4 region of bacterial 16S rRNA gene was subjected to MiSeq Illumina sequencing. Alpha- and beta-diversities, and compositional differences at phylum and genus levels were determined, and bacterial functional pathways were predicted. DSS increased disease severity, serum CRP and cytokines IL-1β and IL-6, but decreased bacterial species richness, and shifted bacterial community composition. Bacteroides, Turicibacter, Escherichia, Clostridium, Enterobacteriaceae, Clostridiaceae, Bacteroidaceae, Bacteroidales, among other taxa were associated with DSS treatment in fecal and colonic samples. Also, DSS altered microbial functional pathways in both colonic mucosa and fecal samples. CONCLUSIONS The development of colitis in DSS model was accompanied with reduced microbial diversity and dysbiosis of gut microbiota at lower taxonomical levels.
Collapse
Affiliation(s)
- Peris Mumbi Munyaka
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada. .,Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Jean-Eric Ghia
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada. .,Department of Internal Medicine, Section of Gastroenterology, University of Manitoba, Winnipeg, Manitoba, Canada. .,Inflammatory Bowel Disease Clinical & Research Centre, University of Manitoba, Winnipeg, Manitoba, Canada.
| |
Collapse
|
118
|
The Roles of Inflammation, Nutrient Availability and the Commensal Microbiota in Enteric Pathogen Infection. Microbiol Spectr 2016; 3. [PMID: 26185088 DOI: 10.1128/microbiolspec.mbp-0008-2014] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The healthy human intestine is colonized by as many as 1014 bacteria belonging to more than 500 different species forming a microbial ecosystem of unsurpassed diversity, termed the microbiota. The microbiota's various bacterial members engage in a physiological network of cooperation and competition within several layers of complexity. Within the last 10 years, technological progress in the field of next-generation sequencing technologies has tremendously advanced our understanding of the wide variety of physiological and pathological processes that are influenced by the commensal microbiota (1, 2). An increasing number of human disease conditions, such as inflammatory bowel diseases (IBD), type 2 diabetes, obesity, allergies and colorectal cancer are linked with altered microbiota composition (3). Moreover, a clearer picture is emerging of the composition of the human microbiota in healthy individuals, its variability over time and between different persons and how the microbiota is shaped by environmental factors (i.e., diet) and the host's genetic background (4). A general feature of a normal, healthy gut microbiota can generate conditions in the gut that disfavor colonization of enteric pathogens. This is termed colonization-resistance (CR). Upon disturbance of the microbiota, CR can be transiently disrupted, and pathogens can gain the opportunity to grow to high levels. This disruption can be caused by exposure to antibiotics (5, 6), changes in diet (7, 8), application of probiotics and drugs (9), and a variety of diseases (3). Breakdown of CR can boost colonization by intrinsic pathogens or increase susceptibility to infections (10). One consequence of pathogen expansion is the triggering of inflammatory host responses and pathogen-mediated disease. Interestingly, human enteric pathogens are part of a small group of bacterial families that belong to the Proteobacteria: the Enterobacteriaceae (E. coli, Yersinia spp., Salmonella spp., Shigella spp.), the Vibrionaceae (Vibrio cholerae) and the Campylobacteriaceae (Campylobacter spp.). In general, members of these families (be it commensals or pathogens) only constitute a minority of the intestinal microbiota. However, proteobacterial "blooms" are a characteristic trait of an abnormal microbiota such as in the course of antibiotic therapy, dietary changes or inflammation (11). It has become clear that the gut microbiota not only plays a major role in priming and regulating mucosal and systemic immunity, but that the immune system also contributes to host control over microbiota composition. These two ways of mutual communication between the microbiota and the immune system were coined as "outside-in" and "inside-out," respectively (12). The significance of those interactions for human health is particularly evident in Crohn's disease (CD) and Ulcerative Colitis (UC). The symptoms of these recurrent, chronic types of gut inflammation are caused by an excessive immune response against one's own commensal microbiota (13). It is assumed that deregulated immune responses can be caused by a genetic predisposition, leading to, for example, the impairment of intestinal barrier function or disruption of mucosal T-cell homeostasis. In CD or UC patients, an abnormally composed microbiota, referred to as "dysbiosis," is commonly observed (discussed later). This is often characterized by an increased relative abundance of facultative anaerobic bacteria (e.g., Enterobacteriaeceae, Bacilli) and, at the same time, depletion of obligate anaerobic bacteria of the classes Bacteroidia and Clostridia. So far, it is unclear whether dysbiosis is a cause or a consequence of inflammatory bowel disease (IBD). In fact, both scenarios are equally conceivable. Recent work suggests that inflammatory immune responses in the gut (both IBD and pathogen-induced) can alter the gut luminal milieu in a way that favors dysbiosis (14). In this chapter, I present a survey on our current state of understanding of the characteristics and mechanisms underlying gut inflammation-associated dysbiosis. The role of dysbiosis in enteric infections and human IBD is discussed. In addition, I will focus on competition of enteric pathogens and the gut microbiota in the inflamed gut and the role of dysbiotic microbiota alterations (e.g., "Enterobacterial blooms" (11)) for the evolution of pathogenicity.
Collapse
|
119
|
Robertson SJ, Geddes K, Maisonneuve C, Streutker CJ, Philpott DJ. Resilience of the intestinal microbiota following pathogenic bacterial infection is independent of innate immunity mediated by NOD1 or NOD2. Microbes Infect 2016; 18:460-71. [PMID: 27083475 DOI: 10.1016/j.micinf.2016.03.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/24/2016] [Accepted: 03/30/2016] [Indexed: 12/15/2022]
Abstract
The innate immune receptors, NOD1 and NOD2, are key regulators of intestinal homeostasis. NOD2 deficiency is linked to increased risk for Crohn's disease, a type of inflammatory bowel disease characterized by chronic inflammatory pathology and dysbiosis within resident microbial communities. However, the relationship between NOD protein-regulated immune functions and dysbiosis remains unclear. We hypothesized that the relationship between NOD1 or NOD2 deficiency and altered community structure during chronic disease may arise via NOD-dependent impairment of community resilience over time. Using the Salmonella ΔaroA model of chronic colitis with littermate mice to control for environmental influences on the microbiota, we show that NOD proteins exert a relatively minor impact on the chronic inflammatory environment and do not significantly contribute to bacterial abundance or community resilience following infection. Rather, temporal shifts in relative abundance of targeted bacterial groups correlated with inflammatory phenotype driven by presence of the pathogen and the ensuing complex immune response.
Collapse
Affiliation(s)
- Susan J Robertson
- Department of Immunology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Kaoru Geddes
- Department of Immunology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Charles Maisonneuve
- Department of Immunology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Catherine J Streutker
- Surgical Pathology, Department of Pathology and Laboratory Medicine, St. Michael's Hospital, Toronto, Ontario, M5B 1W8, Canada
| | - Dana J Philpott
- Department of Immunology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.
| |
Collapse
|
120
|
Del Bel Belluz L, Guidi R, Pateras IS, Levi L, Mihaljevic B, Rouf SF, Wrande M, Candela M, Turroni S, Nastasi C, Consolandi C, Peano C, Tebaldi T, Viero G, Gorgoulis VG, Krejsgaard T, Rhen M, Frisan T. The Typhoid Toxin Promotes Host Survival and the Establishment of a Persistent Asymptomatic Infection. PLoS Pathog 2016; 12:e1005528. [PMID: 27055274 PMCID: PMC4824513 DOI: 10.1371/journal.ppat.1005528] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 03/04/2016] [Indexed: 02/06/2023] Open
Abstract
Bacterial genotoxins, produced by several Gram-negative bacteria, induce DNA damage in the target cells. While the responses induced in the host cells have been extensively studied in vitro, the role of these effectors during the course of infection remains poorly characterized. To address this issue, we assessed the effects of the Salmonella enterica genotoxin, known as typhoid toxin, in in vivo models of murine infection. Immunocompetent mice were infected with isogenic S. enterica, serovar Typhimurium (S. Typhimurium) strains, encoding either a functional or an inactive typhoid toxin. The presence of the genotoxic subunit was detected 10 days post-infection in the liver of infected mice. Unexpectedly, its expression promoted the survival of the host, and was associated with a significant reduction of severe enteritis in the early phases of infection. Immunohistochemical and transcriptomic analysis confirmed the toxin-mediated suppression of the intestinal inflammatory response. The presence of a functional typhoid toxin further induced an increased frequency of asymptomatic carriers. Our data indicate that the typhoid toxin DNA damaging activity increases host survival and favours long-term colonization, highlighting a complex cross-talk between infection, DNA damage response and host immune response. These findings may contribute to understand why such effectors have been evolutionary conserved and horizontally transferred among Gram-negative bacteria.
Collapse
Affiliation(s)
- Lisa Del Bel Belluz
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Riccardo Guidi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ioannis S. Pateras
- Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
| | - Laura Levi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Boris Mihaljevic
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Syed Fazle Rouf
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marie Wrande
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Claudia Nastasi
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, Italian National Research Council, Segrate, Milan, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, Italian National Research Council, Segrate, Milan, Italy
| | - Toma Tebaldi
- Centre for Integrative Biology University of Trento, Trento, Italy
| | | | - Vassilis G. Gorgoulis
- Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Institute for Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Manchester Centre for Cellular Metabolism, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Thorbjørn Krejsgaard
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Mikael Rhen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Teresa Frisan
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
121
|
Identification of Commensal Species Positively Correlated with Early Stress Responses to a Compromised Mucus Barrier. Inflamm Bowel Dis 2016; 22:826-40. [PMID: 26926038 DOI: 10.1097/mib.0000000000000688] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Our aims were (1) to correlate changes in the microbiota to intestinal gene expression before and during the development of colitis in Muc2 mice and (2) to investigate whether the heterozygote Muc2 mouse would reveal host markers of gut barrier stress. METHODS Colon histology, transcriptomics, and microbiota profiling of faecal samples was performed on wild type, Muc2, and Muc2 mice at 2, 4, and 8 weeks of age. RESULTS Muc2 mice develop colitis in proximal colon after weaning, resulting in inflammatory and adaptive immune responses, and expression of genes associated with human inflammatory bowel disease. Muc2 mice do not develop colitis, but produce a thinner mucus layer. The transcriptome of Muc2 mice revealed differential expression of genes participating in mucosal stress responses and exacerbation of a transient inflammatory state around the time of weaning. Young wild type and Muc2 mice have a more constrained group of bacteria as compared with the Muc2 mice, but at 8 weeks the microbiota composition is more similar in all mice. At all ages, microbiota composition discriminated the groups of mice according to their genotype. Specific bacterial clusters correlated with altered gene expression responses to stress and bacteria, before colitis development, including colitogenic members of the genus Bacteroides. CONCLUSIONS The abundance of Bacteroides pathobionts increased before histological signs of pathology suggesting they may play a role in triggering the development of colitis. The Muc2 mouse produces a thinner mucus layer and can be used to study mucus barrier stress in the absence of colitis.
Collapse
|
122
|
Ilott NE, Bollrath J, Danne C, Schiering C, Shale M, Adelmann K, Krausgruber T, Heger A, Sims D, Powrie F. Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling. ISME JOURNAL 2016; 10:2389-404. [PMID: 27003245 PMCID: PMC5030693 DOI: 10.1038/ismej.2016.40] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 02/06/2016] [Accepted: 02/10/2016] [Indexed: 12/23/2022]
Abstract
The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess modifications to both bacterial community structure and transcriptional activity in a mouse model of colitis. By using transcriptomic analysis of colonic tissue and luminal RNA derived from the host, we have also characterised how host transcription relates to the microbial transcriptional response in inflammation. In colitis, increased abundance and transcription of diverse microbial gene families involved in responses to nutrient deprivation, antimicrobial peptide production and oxidative stress support an adaptation of multiple commensal genera to withstand a diverse set of environmental stressors in the inflammatory environment. These data are supported by a transcriptional signature of activated macrophages and granulocytes in the gut lumen during colitis, a signature that includes the transcription of the key antimicrobial genes S100a8 and S100a9 (calprotectin). Genes involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase were identified as changing to a greater extent at the level of transcription than would be predicted by DNA abundance changes, implicating a role for increased oxygen tension and/or host-derived reactive oxygen species in driving transcriptional changes in commensal microbes.
Collapse
Affiliation(s)
| | - Julia Bollrath
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.,Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Camille Danne
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Chris Schiering
- The Francis Crick Institute, Mill Hill Laboratory, London, UK
| | - Matthew Shale
- Translational Gastroenterology Unit, Experimental Medicine, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, UK
| | - Krista Adelmann
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Heger
- Computational Genomics Analysis and Training (CGAT), MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - David Sims
- Computational Genomics Analysis and Training (CGAT), MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| |
Collapse
|
123
|
Rausch P, Basic M, Batra A, Bischoff SC, Blaut M, Clavel T, Gläsner J, Gopalakrishnan S, Grassl GA, Günther C, Haller D, Hirose M, Ibrahim S, Loh G, Mattner J, Nagel S, Pabst O, Schmidt F, Siegmund B, Strowig T, Volynets V, Wirtz S, Zeissig S, Zeissig Y, Bleich A, Baines JF. Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities. Int J Med Microbiol 2016; 306:343-355. [PMID: 27053239 DOI: 10.1016/j.ijmm.2016.03.004] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 12/18/2022] Open
Abstract
The intestinal microbiota is involved in many physiological processes and it is increasingly recognized that differences in community composition can influence the outcome of a variety of murine models used in biomedical research. In an effort to describe and account for the variation in intestinal microbiota composition across the animal facilities of participating members of the DFG Priority Program 1656 "Intestinal Microbiota", we performed a survey of C57BL/6J mice from 21 different mouse rooms/facilities located at 13 different institutions across Germany. Fresh feces was sampled from five mice per room/facility using standardized procedures, followed by extraction and 16S rRNA gene profiling (V1-V2 region, Illumina MiSeq) at both the DNA and RNA (reverse transcribed to cDNA) level. In order to determine the variables contributing to bacterial community differences, we collected detailed questionnaires of animal husbandry practices and incorporated this information into our analyses. We identified considerable variation in a number of descriptive aspects including the proportions of major phyla, alpha- and beta diversity, all of which displayed significant associations to specific aspects of husbandry. Salient findings include a reduction in alpha diversity with the use of irradiated chow, an increase in inter-individual variability (beta diversity) with respect to barrier access and open cages and an increase in bacterial community divergence with time since importing from a vendor. We further observe a high degree of facility-level individuality, which is likely due to each facility harboring its own unique combination of multiple varying attributes of animal husbandry. While it is important to account and control for such differences between facilities, the documentation of such diversity may also serve as a valuable future resource for investigating the origins of microbial-driven host phenotypes.
Collapse
Affiliation(s)
- Philipp Rausch
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, August-Thienemann-Str. 2, 24306, Plön, Germany; Institute for Experimental Medicine, Evolutionary Genomics, Christian-Albrechts-University of Kiel, Arnold-Heller-Str. 3, Haus 17, 24105 Kiel, Germany
| | - Marijana Basic
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany
| | - Arvind Batra
- Charité-Universitätsklinikum Berlin, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Stephan C Bischoff
- Department of Nutritional Medicine, University of Hohenheim, Fruwirthstr. 12, 70593 Stuttgart, Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Thomas Clavel
- ZIEL Institute for Food and Health, Technische Universität München, Gregor-Mendel-Str. 2, 85354, Freising-Weihenstephan, Germany
| | - Joachim Gläsner
- Institute for Medical Microbiology and Hygiene, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Shreya Gopalakrishnan
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 3, 24105 Kiel, Germany
| | - Guntram A Grassl
- German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Carl-Neuberg-Str. 1, 30625 Hannover, Germany; Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany; Research Center Borstel, Parkallee 1-40, 23845, Borstel, Germany
| | - Claudia Günther
- Medical Clinic 1, Friedrich Alexander University, Ulmenweg 18, 91054 Erlangen, Germany
| | - Dirk Haller
- ZIEL Institute for Food and Health, Technische Universität München, Gregor-Mendel-Str. 2, 85354, Freising-Weihenstephan, Germany; Chair of Nutrition and Immunology, Technische Universität München, Gregor-Mendel-Str. 2, 85354 Freising-Weihenstephan, Germany
| | - Misa Hirose
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Saleh Ibrahim
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Gunnar Loh
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Jochen Mattner
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Lehrstuhl für Mikrobiologie und Infektionsimmunologie, Wasserturmstr. 3/5, 91054 Erlangen, Germany
| | - Stefan Nagel
- Charité - Universitätsklinikum Berlin, Research Institutes for Experimental Medicine, Krahmerstr. 6-10, 12207 Berlin, Germany
| | - Oliver Pabst
- Institute of Molecular Medicine, RWTH University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Franziska Schmidt
- Charité-Universitätsklinikum Berlin, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Britta Siegmund
- Charité-Universitätsklinikum Berlin, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Valentina Volynets
- Department of Nutritional Medicine, University of Hohenheim, Fruwirthstr. 12, 70593 Stuttgart, Germany
| | - Stefan Wirtz
- Medical Clinic 1, Friedrich Alexander University, Ulmenweg 18, 91054 Erlangen, Germany
| | - Sebastian Zeissig
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 3, 24105 Kiel, Germany; Department of Medicine I, University Medical Center Dresden and Center for Regenerative Therapies, Technical University Dresden, 01307 Dresden, Germany
| | - Yvonne Zeissig
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 3, 24105 Kiel, Germany; Department of General Pediatrics, University Medical Center Dresden, Technical University Dresden, 01307 Dresden, Germany
| | - André Bleich
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, August-Thienemann-Str. 2, 24306, Plön, Germany; Institute for Experimental Medicine, Evolutionary Genomics, Christian-Albrechts-University of Kiel, Arnold-Heller-Str. 3, Haus 17, 24105 Kiel, Germany.
| |
Collapse
|
124
|
Podany AB, Wright J, Lamendella R, Soybel DI, Kelleher SL. ZnT2-Mediated Zinc Import Into Paneth Cell Granules Is Necessary for Coordinated Secretion and Paneth Cell Function in Mice. Cell Mol Gastroenterol Hepatol 2016; 2:369-383. [PMID: 28174721 PMCID: PMC5042355 DOI: 10.1016/j.jcmgh.2015.12.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 12/22/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS Defects in Paneth cell (PC) function are associated with microbial dysbiosis and intestinal inflammation. PC granules contain antimicrobial peptides, cytokines, and substantial stores of zinc (Zn). We hypothesized that Zn, transported into the granule through the Zn transporter (ZnT)2, is critical for signature PC functions. METHODS ZnT2 was localized to PC granules using immunofluorescence and sucrose gradient fractionation in wild-type (wt) mice, and consequences of ZnT2 loss were characterized in ZnT2 knockout (ZnT2ko) mice. Terminal ilea were harvested for immunofluorescence, electron microscopy, and fluorescent imaging with the Zn reporter Zinpyr-1. Alterations in fecal microbiota were characterized using 16s ribosomal RNA sequencing. PC degranulation, bacterial translocation, cytokine response to Escherichia coli endotoxin lipopolysaccharide, crypt viability after exposure to the oxidant monochloramine (NH2Cl), and bactericidal activity of luminal contents of terminal ilea against enteropathogenic E coli were assessed. RESULTS ZnT2 was localized to the membrane of PC granules. In ZnT2ko mice, spontaneous degranulation was observed more frequently than among wt mice. Secretory granules were hypodense with less active lysozyme, and there was evidence of autophagosome accumulation and granule degradation in PCs from ZnT2ko mice. Gut microbiota of ZnT2ko mice were enriched in Bacteroidales S24-7 and relatively depleted of species commonly found in wt mice. Evidence of PC dysfunction in ZnT2ko mice included impaired granule secretion and increased inflammatory response to lipopolysaccharide, less bactericidal activity, and greater susceptibility to cell death from NH2Cl. CONCLUSIONS ZnT2 is critical for Zn import into PC granules, and the inability to import Zn leads to profound defects in PC function and uncoordinated granule secretion.
Collapse
Key Words
- CFU, colony forming unit
- EPEC, enteropathogenic Escherichia coli
- ER, endoplasmic reticulum
- IF, immunofluorescent
- IL, interleukin
- IP, intraperitoneal
- LPS, lipopolysaccharide
- Microbiota
- NEC, necrotizing enterocolitis
- OTU, organizational taxonomic unit
- PBS, phosphate-buffered saline
- PC, Paneth cell
- PCR, polymerase chain reaction
- Small Intestine
- TNF, tumor necrosis factor
- ZIP, ZRT, IRT-like protein
- Zinc Transporter
- Zn, zinc
- ZnT, zinc transporter
- ko, knockout
- wt, wild-type
Collapse
Affiliation(s)
- Abigail B. Podany
- Department of Surgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania,Department of Cellular and Molecular Physiology, Penn State Hershey College of Medicine, Hershey, Pennsylvania
| | - Justin Wright
- Department of Biology, Juniata College, Huntingdon, Pennsylvania
| | | | - David I. Soybel
- Department of Surgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania,Department of Cellular and Molecular Physiology, Penn State Hershey College of Medicine, Hershey, Pennsylvania
| | - Shannon L. Kelleher
- Department of Surgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania,Department of Cellular and Molecular Physiology, Penn State Hershey College of Medicine, Hershey, Pennsylvania,Department of Pharmacology, Penn State Hershey College of Medicine, Hershey, Pennsylvania,Correspondence Address correspondence to: Shannon L. Kelleher, PhD, Penn State Hershey College of Medicine, 500 University Drive, Hershey, Pennsylvania 17033. fax: (717) 531-5393.Penn State Hershey College of Medicine500 University DriveHersheyPennsylvania 17033
| |
Collapse
|
125
|
Berry D, Kuzyk O, Rauch I, Heider S, Schwab C, Hainzl E, Decker T, Müller M, Strobl B, Schleper C, Urich T, Wagner M, Kenner L, Loy A. Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis. Front Microbiol 2015; 6:1408. [PMID: 26697002 PMCID: PMC4678223 DOI: 10.3389/fmicb.2015.01408] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 11/27/2015] [Indexed: 12/20/2022] Open
Abstract
Acute colitis causes alterations in the intestinal microbiota, but the microbiota is thought to recover after such events. Extreme microbiota alterations are characteristic of human chronic inflammatory bowel diseases, although alterations reported in different studies are divergent and sometimes even contradictory. To better understand the impact of periodic disturbances on the intestinal microbiota and its compositional difference between acute and relapsing colitis, we investigated the beginnings of recurrent inflammation using the dextran sodium sulfate (DSS) mouse model of chemically induced colitis. Using bacterial 16S rRNA gene-targeted pyrosequencing as well as quantitative fluorescence in situ hybridization, we profiled the intestinal and stool microbiota of mice over the course of three rounds of DSS-induced colitis and recovery. We found that characteristic inflammation-associated microbiota could be detected in recovery-phase mice. Successive inflammation episodes further drove the microbiota into an increasingly altered composition post-inflammation, and signatures of colitis history were detectable in the microbiota more sensitively than by pathology analysis. Bacterial indicators of murine colitis history were identified in intestinal and stool samples, with a high degree of consistency between both sample types. Stool may therefore be a promising non-invasive source of bacterial biomarkers that are highly sensitive to inflammation state and history.
Collapse
Affiliation(s)
- David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of ViennaVienna, Austria
| | - Orest Kuzyk
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of ViennaVienna, Austria
| | - Isabella Rauch
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of ViennaVienna, Austria
| | - Susanne Heider
- Clinical Institute of Pathology, Medical University of ViennaVienna, Austria
| | - Clarissa Schwab
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Eva Hainzl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine ViennaVienna, Austria
| | - Thomas Decker
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of ViennaVienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine ViennaVienna, Austria
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine ViennaVienna, Austria
| | - Christa Schleper
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Tim Urich
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of ViennaVienna, Austria
| | - Lukas Kenner
- Clinical Institute of Pathology, Medical University of ViennaVienna, Austria
- Ludwig Boltzmann Institute for Cancer ResearchVienna, Austria
- Department of Laboratory Animal Pathology, University of Veterinary Medicine ViennaVienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of ViennaVienna, Austria
| |
Collapse
|
126
|
Hainzl E, Stockinger S, Rauch I, Heider S, Berry D, Lassnig C, Schwab C, Rosebrock F, Milinovich G, Schlederer M, Wagner M, Schleper C, Loy A, Urich T, Kenner L, Han X, Decker T, Strobl B, Müller M. Intestinal Epithelial Cell Tyrosine Kinase 2 Transduces IL-22 Signals To Protect from Acute Colitis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 195:5011-24. [PMID: 26432894 PMCID: PMC4635564 DOI: 10.4049/jimmunol.1402565] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 09/07/2015] [Indexed: 12/12/2022]
Abstract
In the intestinal tract, IL-22 activates STAT3 to promote intestinal epithelial cell (IEC) homeostasis and tissue healing. The mechanism has remained obscure, but we demonstrate that IL-22 acts via tyrosine kinase 2 (Tyk2), a member of the Jak family. Using a mouse model for colitis, we show that Tyk2 deficiency is associated with an altered composition of the gut microbiota and exacerbates inflammatory bowel disease. Colitic Tyk2(-/-) mice have less p-STAT3 in colon tissue and their IECs proliferate less efficiently. Tyk2-deficient primary IECs show reduced p-STAT3 in response to IL-22 stimulation, and expression of IL-22-STAT3 target genes is reduced in IECs from healthy and colitic Tyk2(-/-) mice. Experiments with conditional Tyk2(-/-) mice reveal that IEC-specific depletion of Tyk2 aggravates colitis. Disease symptoms can be alleviated by administering high doses of rIL-22-Fc, indicating that Tyk2 deficiency can be rescued via the IL-22 receptor complex. The pivotal function of Tyk2 in IL-22-dependent colitis was confirmed in Citrobacter rodentium-induced disease. Thus, Tyk2 protects against acute colitis in part by amplifying inflammation-induced epithelial IL-22 signaling to STAT3.
Collapse
Affiliation(s)
- Eva Hainzl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, 1210 Vienna, Austria
| | - Silvia Stockinger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, 1210 Vienna, Austria;
| | - Isabella Rauch
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Susanne Heider
- Ludwig Boltzmann Institute for Cancer Research, 1090 Vienna, Austria
| | - David Berry
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Caroline Lassnig
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, 1210 Vienna, Austria; Biomodels Austria, University of Veterinary Medicine, Vienna, 1210 Vienna, Austria
| | - Clarissa Schwab
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Felix Rosebrock
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Gabriel Milinovich
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | | | - Michael Wagner
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Christa Schleper
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Lukas Kenner
- Ludwig Boltzmann Institute for Cancer Research, 1090 Vienna, Austria; Institute for Clinical Pathology, Medical University Vienna, 1090 Vienna, Austria; Unit of Pathology of Laboratory Animals, University of Veterinary Medicine, Vienna, 1210 Vienna, Austria; and
| | - Xiaonan Han
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Thomas Decker
- Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, 1210 Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, 1210 Vienna, Austria; Biomodels Austria, University of Veterinary Medicine, Vienna, 1210 Vienna, Austria;
| |
Collapse
|
127
|
Abstract
Animals assemble and maintain a diverse but host-specific gut microbial community. In addition to characteristic microbial compositions along the longitudinal axis of the intestines, discrete bacterial communities form in microhabitats, such as the gut lumen, colonic mucus layers and colonic crypts. In this Review, we examine how the spatial distribution of symbiotic bacteria among physical niches in the gut affects the development and maintenance of a resilient microbial ecosystem. We consider novel hypotheses for how nutrient selection, immune activation and other mechanisms control the biogeography of bacteria in the gut, and we discuss the relevance of this spatial heterogeneity to health and disease.
Collapse
|
128
|
Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJY, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Dworzynski P, Nielsen HB, Bäckhed F, Doré J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Madsen L, Kristiansen K. A catalog of the mouse gut metagenome. Nat Biotechnol 2015; 33:1103-8. [PMID: 26414350 DOI: 10.1038/nbt.3353] [Citation(s) in RCA: 330] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/20/2015] [Indexed: 12/28/2022]
Abstract
We established a catalog of the mouse gut metagenome comprising ∼2.6 million nonredundant genes by sequencing DNA from fecal samples of 184 mice. To secure high microbiome diversity, we used mouse strains of diverse genetic backgrounds, from different providers, kept in different housing laboratories and fed either a low-fat or high-fat diet. Similar to the human gut microbiome, >99% of the cataloged genes are bacterial. We identified 541 metagenomic species and defined a core set of 26 metagenomic species found in 95% of the mice. The mouse gut microbiome is functionally similar to its human counterpart, with 95.2% of its Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups in common. However, only 4.0% of the mouse gut microbial genes were shared (95% identity, 90% coverage) with those of the human gut microbiome. This catalog provides a useful reference for future studies.
Collapse
Affiliation(s)
- Liang Xiao
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Qiang Feng
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Suisha Liang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Si Brask Sonne
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zhongkui Xia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Xinmin Qiu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Xiaoping Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Hua Long
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Jianfeng Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Dongya Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Chuan Liu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Zhiwei Fang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Joyce Chou
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Jacob Glanville
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Qin Hao
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dorota Kotowska
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Colding
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Donghai Wu
- Key Laboratory of Regenerative Biology, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences (Chinese University Hong Kong), Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Jao Yiu Sung
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences (Chinese University Hong Kong), Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Qiaoyi Liang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences (Chinese University Hong Kong), Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Junhua Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Huijue Jia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Zhou Lan
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Valentina Tremaroli
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Piotr Dworzynski
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - H Bjørn Nielsen
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden.,The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Joël Doré
- Institut National de la Recherche Agronomique (Microbiologie de l'Alimentation au Service de la Santé), Jouy en Josas, France.,Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France
| | | | - S Dusko Ehrlich
- Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, UK
| | - John C Lin
- Pfizer Experimental Medicine, Pfizer Inc., South San Francisco, California, USA
| | - Manimozhiyan Arumugam
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jun Wang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, China
| | - Lise Madsen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,National Institute of Nutrition and Seafood Research, Bergen, Norway
| | - Karsten Kristiansen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
129
|
Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, Bruley des Varannes S, Massart S, Moreau P, Potel G, de La Cochetière MF, Batard E, Knights D. Chemotherapy-driven dysbiosis in the intestinal microbiome. Aliment Pharmacol Ther 2015; 42:515-28. [PMID: 26147207 DOI: 10.1111/apt.13302] [Citation(s) in RCA: 312] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 04/16/2015] [Accepted: 06/12/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Chemotherapy is commonly used as myeloablative conditioning treatment to prepare patients for haematopoietic stem cell transplantation (HSCT). Chemotherapy leads to several side effects, with gastrointestinal (GI) mucositis being one of the most frequent. Current models of GI mucositis pathophysiology are generally silent on the role of the intestinal microbiome. AIM To identify functional mechanisms by which the intestinal microbiome may play a key role in the pathophysiology of GI mucositis, we applied high-throughput DNA-sequencing analysis to identify microbes and microbial functions that are modulated following chemotherapy. METHODS We amplified and sequenced 16S rRNA genes from faecal samples before and after chemotherapy in 28 patients with non-Hodgkin's lymphoma who received the same myeloablative conditioning regimen and no other concomitant therapy such as antibiotics. RESULTS We found that faecal samples collected after chemotherapy exhibited significant decreases in abundances of Firmicutes (P = 0.0002) and Actinobacteria (P = 0.002) and significant increases in abundances of Proteobacteria (P = 0.0002) compared to samples collected before chemotherapy. Following chemotherapy, patients had reduced capacity for nucleotide metabolism (P = 0.0001), energy metabolism (P = 0.001), metabolism of cofactors and vitamins (P = 0.006), and increased capacity for glycan metabolism (P = 0.0002), signal transduction (P = 0.0002) and xenobiotics biodegradation (P = 0.002). CONCLUSIONS Our study identifies a severe compositional and functional imbalance in the gut microbial community associated with chemotherapy-induced GI mucositis. The functional pathways implicated in our analysis suggest potential directions for the development of intestinal microbiome-targeted interventions in cancer patients.
Collapse
Affiliation(s)
- E Montassier
- EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, Nantes, France.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - T Gastinne
- Department of Hematology, Nantes University Hospital, Nantes, France
| | - P Vangay
- Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA
| | - G A Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.,Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA
| | - S Bruley des Varannes
- Institut des Maladies de l'Appareil Digestif, Nantes University Hospital, Nantes, France
| | - S Massart
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - P Moreau
- Department of Hematology, Nantes University Hospital, Nantes, France
| | - G Potel
- EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, Nantes, France
| | - M F de La Cochetière
- EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, INSERM, Université de Nantes, Nantes, France
| | - E Batard
- EA 3826 Thérapeutiques Cliniques et Expérimentales des Infections, Faculté de Médecine, Université de Nantes, Nantes, France
| | - D Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.,BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| |
Collapse
|
130
|
Killing of Escherichia coli by Crohn's Disease Monocyte-derived Macrophages and Its Enhancement by Hydroxychloroquine and Vitamin D. Inflamm Bowel Dis 2015; 21:1499-510. [PMID: 25839777 PMCID: PMC4894789 DOI: 10.1097/mib.0000000000000387] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Crohn's disease (CD) is associated with defective innate immunity, including impaired neutrophil chemotaxis, and mucosal invasion by bacteria, particularly adherent and invasive Escherichia coli that replicate inside macrophage phagolysosomes. We compared CD and healthy control (HC) macrophages for their abilities to kill E. coli and generate neutrophil chemoattractants and also assessed the effects of hydroxychloroquine (HCQ) and vitamin D on killing of phagocytosed E. coli. METHODS Peripheral blood monocyte-derived macrophages from CD and HC were compared for bacterial killing and generation of neutrophil chemoattractants in response to CD-derived E. coli. Escherichia coli replication was also assessed in the presence and absence of HCQ, alone and with antibiotics, and vitamin D. RESULTS Monocyte-derived macrophages from patients with CD were similar to HC in allowing replication of phagocytosed CD-derived E. coli: HM605 {CD: N = 10, mean fold replication in 3 hr = 1.08 (95% confidence interval [CI], 0.39-1.78); HC: N = 9, 1.50 (95% CI, 1.02-1.97); P = 0.15} and also in generation of neutrophil chemoattractants in response to E. coli (mean fold chemotaxis relative to control: CD = 2.55 [95% CI, 2.31-2.80]; HC = 2.65 [95% CI, 2.46-2.85], P = 0.42). HCQ and 1,25 OH2-vitamin D3 both caused dose-dependent inhibition of intramacrophage E. coli replication 3-hour postinfection; HCQ: 73.9% inhibition (P < 0.001) at 1 μg/mL, accompanied by raised intraphagosomal pH, and 1,25 OH2-vitamin D3: 80.7% inhibition (P < 0.05) at 80 nM. HCQ had synergistic effects with doxycycline and ciprofloxacin. CONCLUSIONS CD and HC macrophages perform similarly in allowing replication of phagocytosed E. coli and generating neutrophil chemoattractants. Replication of phagocytosed E. coli was substantially decreased by HCQ and vitamin D. These warrant further therapeutic trials in CD in combination with relevant antibiotics.
Collapse
|
131
|
Slížová M, Nemcová R, Mad’ar M, Hadryová J, Gancarčíková S, Popper M, Pistl J. Analysis of biofilm formation by intestinal lactobacilli. Can J Microbiol 2015; 61:437-46. [DOI: 10.1139/cjm-2015-0007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, the biofilm-forming potential of intestinal Lactobacillus reuteri strains under different culture conditions was characterized by microtiter plate biofilm assays. Moreover, the spatial organization of exogenously applied L. reuteri L2/6 (a pig isolate) at specific locations in gastrointestinal tract of monoassociated mice was investigated by fluorescence in situ hybridization. We did not detect biofilm formation by tested strains in nutrient-rich de Man–Rogosa–Sharpe (MRS) medium. On the contrary, a highly positive biofilm formation was observed in medium with lower accessibility to the carbon sources and lack of salts. The results obtained confirmed the significant role of Tween 80 and the quantity and nature of the sugars in the growth medium in biofilm formation. The omission of Tween 80 in MRS medium favored the formation of biofilm. Abundant biofilm formation was detected in the presence of lactose, galactose, and glucose. However, a gradual increase in sugar concentration triggered a significant decrease in biofilm formation. In addition, conditions related to the gastrointestinal environment, such as low pH and the presence of bile and mucins, highly modulated biofilm production. This effect seems to be dependent on the specificity and properties of the medium used for cultivation. From the evidence provided by this study we conclude that the biofilm formation capacity of L. reuteri is strongly dependent on the environmental factors and culture medium used.
Collapse
Affiliation(s)
- Magdaléna Slížová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
| | - Radomíra Nemcová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
| | - Marián Mad’ar
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
| | - Jana Hadryová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
| | - Soňa Gancarčíková
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
| | - Miroslav Popper
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
| | - Juraj Pistl
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
| |
Collapse
|
132
|
Nasrollahzadeh D, Malekzadeh R, Ploner A, Shakeri R, Sotoudeh M, Fahimi S, Nasseri-Moghaddam S, Kamangar F, Abnet CC, Winckler B, Islami F, Boffetta P, Brennan P, Dawsey SM, Ye W. Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia. Sci Rep 2015; 5:8820. [PMID: 25743945 PMCID: PMC4351546 DOI: 10.1038/srep08820] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/27/2015] [Indexed: 02/06/2023] Open
Abstract
Observational studies revealed a relationship between changes in gastric mucosa and risk of esophageal squamous cell carcinoma (ESCC) which suggested a possible role for gastric microbiota in ESCC carcinogenesis. In this study we aimed to compare pattern of gastric corpus microbiota in ESCC with normal esophagus. Cases were included subjects with early ESCC (stage I-II) and esophageal squamous dysplasia (ESD) as the cancer precursor. Control groups included age and sex-matched subjects with mid-esophagus esophagitis (diseased-control), and histologically normal esophagus (healthy-control). DNA was extracted from snap-frozen gastric corpus tissues and 16S rRNA was sequenced on GS-FLX Titanium. After noise removal, an average of 3004 reads per sample was obtained from 93 subjects. We applied principal coordinate analysis to ordinate distances from beta diversity data. Pattern of gastric microbiota using Unifrac (p = 0.004) and weighted Unifrac distances (p = 0.018) statistically varied between cases and healthy controls. Sequences were aligned to SILVA database and Clostridiales and Erysipelotrichales orders were more abundant among cases after controling for multiple testing (p = 0.011). No such difference was observed between mid-esophagitis and healthy controls. This study is the first to show that composition of gastric corpus mucosal microbiota differs in early ESCC and ESD from healthy esophagus.
Collapse
Affiliation(s)
- Dariush Nasrollahzadeh
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Ramin Shakeri
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Sotoudeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Saman Fahimi
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Siavosh Nasseri-Moghaddam
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Farin Kamangar
- Department of Public Health Analysis, School of Community Health and Policy, Morgan State University, Baltimore, Maryland, USA
| | - Christian C. Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda MD 20892-7335, USA
| | - Björn Winckler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Farhad Islami
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Institute for Translational Epidemiology and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, NY 10029-6574, USA
| | - Paolo Boffetta
- Institute for Translational Epidemiology and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, NY 10029-6574, USA
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Sanford M. Dawsey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda MD 20892-7335, USA
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| |
Collapse
|
133
|
Tuning the Brain-Gut Axis in Health and Disease. CURRENT STEM CELL REPORTS 2015. [DOI: 10.1007/s40778-014-0004-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
134
|
Azad MB, Konya T, Guttman DS, Field CJ, Sears MR, HayGlass KT, Mandhane PJ, Turvey SE, Subbarao P, Becker AB, Scott JA, Kozyrskyj AL. Infant gut microbiota and food sensitization: associations in the first year of life. Clin Exp Allergy 2015; 45:632-43. [DOI: 10.1111/cea.12487] [Citation(s) in RCA: 276] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/22/2014] [Accepted: 12/21/2014] [Indexed: 12/20/2022]
Affiliation(s)
- M. B. Azad
- Department of Pediatrics; School of Public Health; University of Alberta; Edmonton AB Canada
- Department of Pediatrics & Child Health; Children's Hospital Research Institute of Manitoba; University of Manitoba; Winnipeg MB Canada
| | - T. Konya
- Dalla Lana School of Public Health; University of Toronto; Toronto ON Canada
| | - D. S. Guttman
- Centre for the Analysis of Genome Evolution and Function; University of Toronto; Toronto ON Canada
| | - C. J. Field
- Department of Agricultural, Food & Nutritional Science; University of Alberta; Edmonton AB Canada
| | - M. R. Sears
- Department of Medicine; McMaster University; Hamilton ON Canada
| | - K. T. HayGlass
- Department of Immunology; University of Manitoba; Winnipeg MB Canada
| | - P. J. Mandhane
- Department of Pediatrics; School of Public Health; University of Alberta; Edmonton AB Canada
| | - S. E. Turvey
- Department of Pediatrics, Child & Family Research Institute; BC Children's Hospital; University of British Columbia; Vancouver BC Canada
| | - P. Subbarao
- Department of Pediatrics; Hospital for Sick Children; University of Toronto; Toronto ON Canada
| | - A. B. Becker
- Department of Pediatrics & Child Health; Children's Hospital Research Institute of Manitoba; University of Manitoba; Winnipeg MB Canada
| | - J. A. Scott
- Dalla Lana School of Public Health; University of Toronto; Toronto ON Canada
| | - A. L. Kozyrskyj
- Department of Pediatrics; School of Public Health; University of Alberta; Edmonton AB Canada
- Department of Community Health Sciences; University of Manitoba; Winnipeg MB Canada
| | | |
Collapse
|
135
|
Galley JD, Yu Z, Kumar P, Dowd SE, Lyte M, Bailey MT. The structures of the colonic mucosa-associated and luminal microbial communities are distinct and differentially affected by a prolonged murine stressor. Gut Microbes 2014; 5:748-60. [PMID: 25536463 PMCID: PMC4615309 DOI: 10.4161/19490976.2014.972241] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The commensal microbiota of the human gastrointestinal tract live in a largely stable community structure, assisting in host physiological and immunological functions. Changes to this structure can be injurious to the health of the host, a concept termed dysbiosis. Psychological stress is a factor that has been implicated in causing dysbiosis, and studies performed by our lab have shown that restraint stress can indeed shift the cecal microbiota structure as well as increase the severity of a colonic infection caused by Citrobacter rodentium. However, this study, like many others, have focused on fecal contents when examining the effect of dysbiosis-causing stimuli (e.g. psychological stress) upon the microbiota. Since the mucosa-associated microbiota have unique properties and functions that can act upon the host, it is important to understand how stressor exposure might affect this niche of bacteria. To begin to understand whether chronic restraint stress changes the mucosa-associated and/or luminal microbiota mice underwent 7 16-hour cycles of restraint stress, and the microbiota of both colonic tissue and fecal contents were analyzed by sequencing using next-gen bacterial tag-encoded FLX amplicon technology (bTEFAP) pyrosequencing. Both control and stress groups had significantly different mucosa-associated and luminal microbiota communities, highlighting the importance of focusing gastrointestinal community structure analysis by microbial niche. Furthermore, restraint stress was able to disrupt both the mucosa-associated and luminally-associated colonic microbiota by shifting the relative abundances of multiple groups of bacteria. Among these changes, there was a significant reduction in the immunomodulatory commensal genus Lactobacillus associated with colonic mucosa. The relative abundance of Lactobacillus spp. was not affected in the lumen. These results indicate that stressor-exposure can have distinct effects upon the colonic microbiota situated at the mucosal epithelium in comparison to the luminal-associated microbiota.
Collapse
Affiliation(s)
- Jeffrey D Galley
- Division of Oral Biolog; College of Dentistry; The Ohio State University; Columbus, OH USA
| | - Zhongtang Yu
- Department of Animal Sciences; College of Food; Agricultural and Environmental Sciences; The Ohio State University, Columbus, OH USA
| | - Purnima Kumar
- Division of Periodontology; College of Dentistry; The Ohio State University; Columbus, OH USA
| | - Scot E Dowd
- Research and Testing Laboratory; Lubbock, TX USA
| | - Mark Lyte
- Department of Immunotherapeutics and Biotechnology; School of Pharmacy; Texas Tech University Health Sciences Center; Abilene, TX USA
| | - Michael T Bailey
- Division of Oral Biolog; College of Dentistry; The Ohio State University; Columbus, OH USA,Institute for Behavioral Medicine Research; College of Medicine; The Ohio State University; Columbus, OH USA,Department of Pediatrics; Wexner Medical Center; The Ohio State University; Columbus, OH USA,Correspondence to: Michael T Bailey;
| |
Collapse
|
136
|
O’Connor A, Quizon PM, Albright JE, Lin FT, Bennett BJ. Responsiveness of cardiometabolic-related microbiota to diet is influenced by host genetics. Mamm Genome 2014; 25:583-99. [PMID: 25159725 PMCID: PMC4239785 DOI: 10.1007/s00335-014-9540-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/04/2014] [Indexed: 01/04/2023]
Abstract
Intestinal microbial community structure is driven by host genetics in addition to environmental factors such as diet. In comparison with environmental influences, the effect of host genetics on intestinal microbiota, and how host-driven differences alter host metabolism is unclear. Additionally, the interaction between host genetics and diet, and the impact on the intestinal microbiome and possible down-stream effect on host metabolism is not fully understood, but represents another aspects of inter-individual variation in disease risk. The objectives of this study were to investigate how diet and genetic background shape microbial communities, and how these diet- and genetic-driven microbial differences relate to cardiometabolic phenotypes. To determine these effects, we used the 8 progenitor strains of the collaborative cross/diversity outbred mapping panels (C57BL/6J, A/J, NOD/ShiLtJ, NZO/HILtJ, WSB/EiJ, CAST/EiJ, PWK/PhJ, and 129S1/SvImJ). 16s rRNA profiling of enteric microbial communities in addition to the assessment of phenotypes central to cardiometabolic health was conducted under baseline nutritional conditions and in response to diets varying in atherogenic nutrient (fat, cholesterol, cholic acid) composition. These studies revealed strain-driven differences in enteric microbial communities which were retained with dietary intervention. Diet–strain interactions were seen for a core group of cardiometabolic-related microbial taxa. In conclusion, these studies highlight diet and genetically regulated cardiometabolic-related microbial taxa. Furthermore, we demonstrate the progenitor model is useful for nutrigenomic-based studies and screens seeking to investigate the interaction between genetic background and the phenotypic and microbial response to diet.
Collapse
Affiliation(s)
- Annalouise O’Connor
- UNC Chapel Hill Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC 28081 USA
| | - Pamela M. Quizon
- UNC Chapel Hill Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC 28081 USA
| | - Jody E. Albright
- UNC Chapel Hill Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC 28081 USA
| | - Fred T. Lin
- UNC Chapel Hill Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC 28081 USA
| | - Brian J. Bennett
- UNC Chapel Hill Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC 28081 USA
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Nutrition, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| |
Collapse
|
137
|
Rauch I, Hainzl E, Rosebrock F, Heider S, Schwab C, Berry D, Stoiber D, Wagner M, Schleper C, Loy A, Urich T, Müller M, Strobl B, Kenner L, Decker T. Type I interferons have opposing effects during the emergence and recovery phases of colitis. Eur J Immunol 2014; 44:2749-60. [PMID: 24975266 DOI: 10.1002/eji.201344401] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 05/23/2014] [Accepted: 06/25/2014] [Indexed: 12/22/2022]
Abstract
The contribution of the innate immune system to inflammatory bowel disease (IBD) is under intensive investigation. Research in animal models has demonstrated that type I interferons (IFN-Is) protect from IBD. In contrast, studies of patients with IBD have produced conflicting results concerning the therapeutic potential of IFN-Is. Here, we present data suggesting that IFN-Is play dual roles as regulators of intestinal inflammation in dextran sodium sulfate (DSS)-treated C57BL/6 mice. Though IFN-Is reduced acute intestinal damage and the abundance of colitis-associated intestinal bacteria caused by treatment with a high dose of DSS, they also inhibited the resolution of inflammation after DSS treatment. IFN-Is played an anti-inflammatory role by suppressing the release of IL-1β from the colon MHC class II(+) cells. Consistently, IL-1 receptor blockade reduced the severity of inflammation in IFN-I receptor-deficient mice and myeloid cell-restricted ablation of the IFN-I receptor was detrimental. The proinflammatory role of IFN-Is during recovery from DSS treatment was caused by IFN-I-dependent cell apoptosis as well as an increase in chemokine production and infiltrating inflammatory monocytes and neutrophils. Thus, IFN-Is play opposing roles in specific phases of intestinal injury and inflammation, which may be important for guiding treatment strategies in patients.
Collapse
Affiliation(s)
- Isabella Rauch
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
138
|
Berry D, Widder S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol 2014; 5:219. [PMID: 24904535 PMCID: PMC4033041 DOI: 10.3389/fmicb.2014.00219] [Citation(s) in RCA: 809] [Impact Index Per Article: 80.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 04/26/2014] [Indexed: 01/17/2023] Open
Abstract
Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.
Collapse
Affiliation(s)
- David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Stefanie Widder
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| |
Collapse
|
139
|
Increasing phytoremediation efficiency and reliability using novel omics approaches. Trends Biotechnol 2014; 32:271-80. [DOI: 10.1016/j.tibtech.2014.02.008] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 02/12/2014] [Accepted: 02/26/2014] [Indexed: 01/19/2023]
|
140
|
Schwab C, Tveit AT, Schleper C, Urich T. Gene expression of lactobacilli in murine forestomach biofilms. Microb Biotechnol 2014; 7:347-59. [PMID: 24702817 PMCID: PMC4241727 DOI: 10.1111/1751-7915.12126] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/20/2014] [Accepted: 03/02/2014] [Indexed: 02/01/2023] Open
Abstract
Lactobacilli populate the gastro-intestinal tract of vertebrates, and are used in food fermentations and as probiotics. Lactobacilli are also major constituents of stable biofilms in the forestomach of rodents. In order to investigate the lifestyle of these biofilm lactobacilli in C57BL/6 mice, we applied metatranscriptomics to analyse gene expression (assessed by mRNA) and community composition (assessed by rRNA). Lactobacillales were the major biofilm inhabitants (62–82% of rRNA reads), followed by Clostridiales (8–31% of rRNA reads). To identify mRNA transcripts specific for the forestomach, we compared forestomach and hindgut metatranscriptomes. Gene expression of the biofilm microbiota was characterized by high abundance of transcripts related to glucose and maltose utilization, peptide degradation, and amino acid transport, indicating their major catabolic and anabolic pathways. The microbiota transcribed genes encoding pathways enhancing oxidative stress (glutathione synthesis) and acid tolerance. Various pathways, including metabolite formation (urea degradation, arginine pathway, γ-aminobutyrate) and cell wall modification (DltA, cyclopropane-fatty-acyl-phospholipid synthase), contributed to acid tolerance, as judged from the transcript profile. In addition, the biofilm microbiota expressed numerous genes encoding extracellular proteins involved in adhesion and/or biofilm formation (e.g. MucBP, glycosyl hydrolase families 68 and 70). This study shed light on the lifestyle and specific adaptations of lactobacilli in the murine forestomach that might also be relevant for lactobacilli biofilms in other vertebrates, including humans.
Collapse
Affiliation(s)
- Clarissa Schwab
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Wien, Austria
| | | | | | | |
Collapse
|