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Selvarajan R, Sibanda T, Venkatachalam S, Ogola HJO, Christopher Obieze C, Msagati TA. Distribution, Interaction and Functional Profiles of Epiphytic Bacterial Communities from the Rocky Intertidal Seaweeds, South Africa. Sci Rep 2019; 9:19835. [PMID: 31882618 PMCID: PMC6934600 DOI: 10.1038/s41598-019-56269-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/05/2019] [Indexed: 11/16/2022] Open
Abstract
Interrelations between epiphytic bacteria and macroalgae are multifaceted and complicated, though little is known about the community structure, interaction and functions of those epiphytic bacteria. This study comprehensively characterized the epiphytic bacterial communities associated with eight different common seaweeds collected from a rocky intertidal zone on the Indian Ocean at Cape Vidal, South Africa. High-throughput sequencing analyses indicated that seaweed-associated bacterial communities were dominated by the phyla Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Energy-dispersive X-ray (EDX) analysis showed the presence of elemental composition in the surface of examined seaweeds, in varying concentrations. Cluster analysis showed that bacterial communities of brown seaweeds (SW2 and SW4) were closely resembled those of green seaweeds (SW1) and red seaweeds (SW7) while those of brown seaweeds formed a separate branch. Predicted functional capabilities of epiphytic bacteria using PICRUSt analysis revealed abundance of genes related to metabolic and biosynthetic activities. Further important identified functional interactions included genes for bacterial chemotaxis, which could be responsible for the observed association and network of elemental-microbes interaction. The study concludes that the diversity of epiphytic bacteria on seaweed surfaces is greatly influenced by algal organic exudates as well as elemental deposits on their surfaces, which triggers chemotaxis responses from epiphytic bacteria with the requisite genes to metabolise those substrates.
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Affiliation(s)
- Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Johannesburg, South Africa.
| | - Timothy Sibanda
- Department of Biological Sciences, University of Namibia, Mandume Ndemufayo Ave, Pionierspark, Windhoek, Namibia
| | | | - Henry J O Ogola
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Johannesburg, South Africa.,Centre for Research, Innovation and Technology, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | | | - Titus A Msagati
- Nanotechnology and Water Sustainability Research Unit, College of Science, Engineering and Technology, University of South Africa-Science Campus, Florida, South Africa
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Zhang L, Li YY, Tang X, Zhao X. Faecal microbial dysbiosis in children with Wiskott-Aldrich syndrome. Scand J Immunol 2019; 91:e12805. [PMID: 31267543 DOI: 10.1111/sji.12805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022]
Abstract
Wiskott-Aldrich syndrome (WAS) is an X-linked primary immunodeficiency disease caused by a mutation in the WAS gene that encodes the WAS protein (WASp); up to 5-10% of these patients develop inflammatory bowel disease (IBD). The mechanisms by which WASp deficiency causes IBD are unclear. Intestinal microbial dysbiosis and imbalances in host immune responses play important roles in the pathogenesis of polygenetic IBD; however, few studies have conducted detailed examination of the microbial alterations and their relationship with IBD in WAS. Here, we collected faecal samples from 19 children (all less than 2 years old) with WAS and samples from WASp-KO mice with IBD and subjected them to 16S ribosomal RNA sequencing. We found that microbial community richness and structure in WAS children were different from those in controls; WAS children revealed reduced microbial community richness and diversity. Relative abundance of Bacteroidetes and Verrucomicrobiain in WAS children was significantly lower, while that of Proteobacteria was markedly higher. WASp-KO mice revealed a significantly decreased abundance of Firmicutes. Faecal microbial dysbiosis caused by WASp deficiency is similar to that observed for polygenetic IBD, suggesting that WASp may play crucial function in microbial homoeostasis and that microbial dysbiosis may contribute to IBD in WAS. These microbial alterations may be useful targets for monitoring and therapeutically managing intestinal inflammation in WAS.
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Affiliation(s)
- Liang Zhang
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ying Ying Li
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Tang
- Division of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaodong Zhao
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.,Division of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
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Ma HQ, Yu TT, Zhao XJ, Zhang Y, Zhang HJ. Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease. World J Gastroenterol 2018; 24:1464-1477. [PMID: 29632427 PMCID: PMC5889826 DOI: 10.3748/wjg.v24.i13.1464] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To analyze the alterations of fecal microbiota in Chinese patients with inflammatory bowel disease (IBD).
METHODS Fecal samples from 15 patients with Crohn’s disease (CD) (11 active CD, 4 inactive CD), 14 patients with active ulcerative colitis (UC) and 13 healthy individuals were collected and subjected to 16S ribosomal DNA (rDNA) gene sequencing. The V4 hypervariable regions of 16S rDNA gene were amplified from all samples and sequenced by the Illumina MiSeq platform. Quality control and operational taxonomic units classification of reads were calculated with QIIME software. Alpha diversity and beta diversity were displayed with R software.
RESULTS Community richness (chao) and microbial structure in both CD and UC were significantly different from those in normal controls. At the phyla level, analysis of the microbial compositions revealed a significantly greater abundance of Proteobacteria in IBD as compared to that in controls. At the genera level, 8 genera in CD and 23 genera in UC (in particular, the Escherichia genus) showed significantly greater abundance as compared to that in normal controls. The relative abundance of Bacteroidetes in the active CD group was markedly lower than that in the inactive CD group. The abundance of Proteobacteria in patients with active CD was nominally higher than that in patients with inactive CD; however, the difference was not statistically significant after correction. Furthermore, the relative abundance of Bacteroidetes showed a negative correlation with the CD activity index scores.
CONCLUSION Our study profiles specific characteristics and microbial dysbiosis in the gut of Chinese patients with IBD. Bacteroidetes may have a negative impact on inflammatory development.
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Affiliation(s)
- Hai-Qin Ma
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Ting-Ting Yu
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Xiao-Jing Zhao
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Yi Zhang
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - Hong-Jie Zhang
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
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The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe 2015; 16:276-89. [PMID: 25211071 PMCID: PMC5109542 DOI: 10.1016/j.chom.2014.08.014] [Citation(s) in RCA: 328] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Much has been learned about the diversity and distribution of human-associated microbial communities, but we still know little about the biology of the microbiome, how it interacts with the host, and how the host responds to its resident microbiota. The Integrative Human Microbiome Project (iHMP, http://hmp2.org), the second phase of the NIH Human Microbiome Project, will study these interactions by analyzing microbiome and host activities in longitudinal studies of disease-specific cohorts and by creating integrated data sets of microbiome and host functional properties. These data sets will serve as experimental test beds to evaluate new models, methods, and analyses on the interactions of host and microbiome. Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes, and their underlying hypotheses, as well as the multi-omic data types to be collected, integrated, and distributed through public repositories as a community resource.
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Millares L, Pérez-Brocal V, Ferrari R, Gallego M, Pomares X, García-Núñez M, Montón C, Capilla S, Monsó E, Moya A. Functional Metagenomics of the Bronchial Microbiome in COPD. PLoS One 2015; 10:e0144448. [PMID: 26632844 PMCID: PMC4669145 DOI: 10.1371/journal.pone.0144448] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 11/18/2015] [Indexed: 02/07/2023] Open
Abstract
The course of chronic obstructive pulmonary disease (COPD) is frequently aggravated by exacerbations, and changes in the composition and activity of the microbiome may be implicated in their appearance. The aim of this study was to analyse the composition and the gene content of the microbial community in bronchial secretions of COPD patients in both stability and exacerbation. Taxonomic data were obtained by 16S rRNA gene amplification and pyrosequencing, and metabolic information through shotgun metagenomics, using the Metagenomics RAST server (MG-RAST), and the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) programme, which predict metagenomes from 16S data. Eight severe COPD patients provided good quality sputum samples, and no significant differences in the relative abundance of any phyla and genera were found between stability and exacerbation. Bacterial biodiversity (Chao1 and Shannon indexes) did not show statistical differences and beta-diversity analysis (Bray-Curtis dissimilarity index) showed a similar microbial composition in the two clinical situations. Four functional categories showed statistically significant differences with MG-RAST at KEGG level 2: in exacerbation, Cell growth and Death and Transport and Catabolism decreased in abundance [1.6 (0.2-2.3) vs 3.6 (3.3-6.9), p = 0.012; and 1.8 (0-3.3) vs 3.6 (1.8-5.1), p = 0.025 respectively], while Cancer and Carbohydrate Metabolism increased [0.8 (0-1.5) vs 0 (0-0.5), p = 0.043; and 7 (6.4-9) vs 5.9 (6.3-6.1), p = 0.012 respectively]. In conclusion, the bronchial microbiome as a whole is not significantly modified when exacerbation symptoms appear in severe COPD patients, but its functional metabolic capabilities show significant changes in several pathways.
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Affiliation(s)
- Laura Millares
- Fundació Parc Taulí, Sabadell, Spain
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Fundació Insitut d’Investigació Germans Trias i Pujol, Badalona, Spain
- * E-mail:
| | - Vicente Pérez-Brocal
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Evolutionary Genetics Unit, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Rafaela Ferrari
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Evolutionary Genetics Unit, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Miguel Gallego
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Xavier Pomares
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Marian García-Núñez
- Fundació Parc Taulí, Sabadell, Spain
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Fundació Insitut d’Investigació Germans Trias i Pujol, Badalona, Spain
| | - Concepción Montón
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Silvia Capilla
- Department of Microbiology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Eduard Monsó
- CIBER de Enfermedades Respiratorias, CIBERES, Bunyola, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Andrés Moya
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Evolutionary Genetics Unit, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
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Abstract
: The human intestinal microbiome plays a critical role in human health and disease, including the pathogenesis of inflammatory bowel disease (IBD). Numerous studies have identified altered bacterial diversity and abundance at varying taxonomic levels through biopsies and fecal samples of patients with IBD and diseased model animals. However, inconsistent observations regarding the microbial compositions of such patients have hindered the efforts in assessing the etiological role of specific bacterial species in the pathophysiology of IBD. These observations highlight the importance of minimizing the confounding factors associated with IBD and the need for a standardized methodology to analyze well-defined microbial sampling sources in early IBD diagnosis. Furthermore, establishing the linkage between microbiota compositions with their function within the host system can provide new insights on the pathogenesis of IBD. Such research has been greatly facilitated by technological advances that include functional metagenomics coupled with proteomic and metabolomic profiling. This review provides updates on the composition of the microbiome in IBD and emphasizes microbiota dysbiosis-involved mechanisms. We highlight functional roles of specific bacterial groups in the development and management of IBD. Functional analyses of the microbiome may be the key to understanding the role of microbiota in the development and chronicity of IBD and reveal new strategies for therapeutic intervention.
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Davenport M, Poles J, Leung JM, Wolff MJ, Abidi WM, Ullman T, Mayer L, Cho I, Loke P. Metabolic alterations to the mucosal microbiota in inflammatory bowel disease. Inflamm Bowel Dis 2014; 20:723-31. [PMID: 24583479 PMCID: PMC4158619 DOI: 10.1097/mib.0000000000000011] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Inflammation during inflammatory bowel disease may alter nutrient availability to adherent mucosal bacteria and impact their metabolic function. Microbial metabolites may regulate intestinal CD4 T-cell homeostasis. We investigated the relationship between inflammation and microbial function by inferred metagenomics of the mucosal microbiota from colonic pinch biopsies of patients with inflammatory bowel disease. METHODS Paired pinch biopsy samples of known inflammation states were analyzed from ulcerative colitis (UC) (23), Crohn's disease (CD) (21), and control (24) subjects by 16S ribosomal sequencing, histopathologic assessment, and flow cytometry. PICRUSt was used to generate metagenomic data and derive relative Kyoto Encyclopedia of Genes and Genomes Pathway abundance information. Leukocytes were isolated from paired biopsy samples and analyzed by multicolor flow cytometry. Active inflammation was defined by neutrophil infiltration into the epithelium. RESULTS Carriage of metabolic pathways in the mucosal microbiota was relatively stable among patients with inflammatory bowel disease, despite large variations in individual bacterial community structures. However, microbial function was significantly altered in inflamed tissue of UC patients, with a reduction in carbohydrate and nucleotide metabolism in favor of increased lipid and amino acid metabolism. These differences were not observed in samples from CD patients. In CD, microbial lipid, carbohydrate, and amino acid metabolism tightly correlated with the frequency of CD4Foxp3 Tregs, whereas in UC, these pathways correlated with the frequency of CD4IL-22 (TH22) cells. CONCLUSIONS Metabolic pathways of the mucosal microbiota in CD do not vary as much as UC with inflammation state, indicating a more systemic perturbation of host-bacteria interactions in CD compared with more localized dysfunction in UC.
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Affiliation(s)
- Michael Davenport
- Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Jordan Poles
- Department of Microbiology, New York University School of Medicine, New York, NY, 10010, United States
| | - Jacqueline M. Leung
- Department of Microbiology, New York University School of Medicine, New York, NY, 10010, United States
| | - Martin J. Wolff
- Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Wasif M. Abidi
- Department of Medicine, Division of Gastroenterology, Mount Sinai School of Medicine, New York, NY, United States
- Immunology Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
| | - Thomas Ullman
- Department of Medicine, Division of Gastroenterology, Mount Sinai School of Medicine, New York, NY, United States
| | - Lloyd Mayer
- Immunology Institute, Mount Sinai School of Medicine, New York, New York 10029, USA
| | - Ilseung Cho
- Department of Medicine, New York University School of Medicine, New York, NY, United States
- VA New York Harbor Healthcare System, New York, NY, United States
| | - P'ng Loke
- Department of Microbiology, New York University School of Medicine, New York, NY, 10010, United States
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