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Lawal SA, Voisin A, Olof H, Bording-Jorgensen M, Armstrong H. Diversity of the microbiota communities found in the various regions of the intestinal tract in healthy individuals and inflammatory bowel diseases. Front Immunol 2023; 14:1242242. [PMID: 38022505 PMCID: PMC10654633 DOI: 10.3389/fimmu.2023.1242242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
The severe and chronic inflammatory bowel diseases (IBD), Crohn disease and ulcerative colitis, are characterized by persistent inflammation and gut damage. There is an increasing recognition that the gut microbiota plays a pivotal role in IBD development and progression. However, studies of the complete microbiota composition (bacteria, fungi, viruses) from precise locations within the gut remain limited. In particular, studies have focused primarily on the bacteriome, with available methods limiting evaluation of the mycobiome (fungi) and virome (virus). Furthermore, while the different segments of the small and large intestine display different functions (e.g., digestion, absorption, fermentation) and varying microenvironment features (e.g., pH, metabolites), little is known about the biogeography of the microbiota in different segments of the intestinal tract or how this differs in IBD. Here, we highlight evidence of the differing microbiota communities of the intestinal sub-organs in healthy and IBD, along with method summaries to improve future studies.
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Affiliation(s)
- Samuel Adefisoye Lawal
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Athalia Voisin
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Hana Olof
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | | | - Heather Armstrong
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
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2
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Fabian O, Bajer L, Drastich P, Harant K, Sticova E, Daskova N, Modos I, Tichanek F, Cahova M. A Current State of Proteomics in Adult and Pediatric Inflammatory Bowel Diseases: A Systematic Search and Review. Int J Mol Sci 2023; 24:ijms24119386. [PMID: 37298338 DOI: 10.3390/ijms24119386] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are systemic immune-mediated conditions with predilection for the gastrointestinal tract and include Crohn's disease and ulcerative colitis. Despite the advances in the fields of basic and applied research, the etiopathogenesis remains largely unknown. As a result, only one third of the patients achieve endoscopic remission. A substantial portion of the patients also develop severe clinical complications or neoplasia. The need for novel biomarkers that can enhance diagnostic accuracy, more precisely reflect disease activity, and predict a complicated disease course, thus, remains high. Genomic and transcriptomic studies contributed substantially to our understanding of the immunopathological pathways involved in disease initiation and progression. However, eventual genomic alterations do not necessarily translate into the final clinical picture. Proteomics may represent a missing link between the genome, transcriptome, and phenotypical presentation of the disease. Based on the analysis of a large spectrum of proteins in tissues, it seems to be a promising method for the identification of new biomarkers. This systematic search and review summarize the current state of proteomics in human IBD. It comments on the utility of proteomics in research, describes the basic proteomic techniques, and provides an up-to-date overview of available studies in both adult and pediatric IBD.
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Affiliation(s)
- Ondrej Fabian
- Clinical and Transplant Pathology Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Department of Pathology and Molecular Medicine, 3rd Faculty of Medicine, Charles University and Thomayer Hospital, 140 59 Prague, Czech Republic
| | - Lukas Bajer
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Pavel Drastich
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Karel Harant
- Proteomics Core Facility, Faculty of Science, Charles University, 252 50 Vestec, Czech Republic
| | - Eva Sticova
- Clinical and Transplant Pathology Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Department of Pathology, Royal Vinohrady Teaching Hospital, Srobarova 1150/50, 100 00 Prague, Czech Republic
| | - Nikola Daskova
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Istvan Modos
- Department of Informatics, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Filip Tichanek
- Department of Informatics, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Monika Cahova
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
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3
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Gut Microbiome Proteomics in Food Allergies. Int J Mol Sci 2023; 24:ijms24032234. [PMID: 36768555 PMCID: PMC9917015 DOI: 10.3390/ijms24032234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Food allergies (FA) have dramatically increased in recent years, particularly in developed countries. It is currently well-established that food tolerance requires the strict maintenance of a specific microbial consortium in the gastrointestinal (GI) tract microbiome as alterations in the gut microbiota can lead to dysbiosis, causing inflammation and pathogenic intestinal conditions that result in the development of FA. Although there is currently not enough knowledge to fully understand how the interactions between gut microbiota, host responses and the environment cause food allergies, recent advances in '-omics' technologies (i.e., proteomics, genomics, metabolomics) and in approaches involving systems biology suggest future headways that would finally allow the scientific understanding of the relationship between gut microbiome and FA. This review summarizes the current knowledge in the field of FA and insights into the future advances that will be achieved by applying proteomic techniques to study the GI tract microbiome in the field of FA and their medical treatment. Metaproteomics, a proteomics experimental approach of great interest in the study of GI tract microbiota, aims to analyze and identify all the proteins in complex environmental microbial communities; with shotgun proteomics, which uses liquid chromatography (LC) for separation and tandem mass spectrometry (MS/MS) for analysis, as it is the most promising technique in this field.
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Muacevic A, Adler JR, Zambrana-Valenzuela R, Iglesias-Escabi IM, Arciniegas-Medina NJ. Development of Very-Early-Onset Inflammatory Bowel Disease After Multiple Early-Life Antibiotic Exposures: A Case Report and Literature Review. Cureus 2023; 15:e33813. [PMID: 36819429 PMCID: PMC9930002 DOI: 10.7759/cureus.33813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2023] [Indexed: 01/17/2023] Open
Abstract
The use of antibiotics has increased drastically over the last few decades. Many antibiotics can target the commensal microbiota and promote gut dysbiosis. These alterations contribute to disease onset and exacerbation. Although the etiology of inflammatory bowel disease (IBD) is mostly unknown, it involves a complex interaction among host genetics, microbiota, environmental factors, and aberrant immune responses. Studies have shown a relationship between very-early-onset inflammatory bowel disease (VEO-IBD) and microbiota alterations. The case discussed in this report endorses the current clinical evidence for this interaction. This is an anonymous record review with no identifiers involving a 23-month-old female patient who was brought to the emergency department by her parents due to persistent bloody diarrhea. Eight days before the presentation, she had experienced watery diarrhea that progressed to bloody stools. The patient had a history of acute otitis media, acute enteritis, and right-arm cutaneous abscess, for which she had received multiple antibiotic therapies. Strategies to manipulate the microbiome through diet, probiotics, antibiotics, or fecal microbiota transplantation (FMT) may be used therapeutically to modulate disease activity. A high index of clinical suspicion for VEO-IBD should be maintained for patients with a history of multiple, recurrent antibiotic use. We believe this case report will raise awareness about the issue of early anaerobic antibiotic exposure and help prevent its unnecessary use and, consequently, prevent gut microbiota dysbiosis that can lead to VEO-IBD. Also, our literature review will hopefully prompt clinicians to consider alternative therapeutic options for this patient population, such as rebuilding intestinal microbiota composition to improve VEO-IBD activity.
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Jacobs JP, Goudarzi M, Lagishetty V, Li D, Mak T, Tong M, Ruegger P, Haritunians T, Landers C, Fleshner P, Vasiliauskas E, Ippoliti A, Melmed G, Shih D, Targan S, Borneman J, Fornace AJ, McGovern DPB, Braun J. Crohn's disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome. Genome Med 2022; 14:91. [PMID: 35971134 PMCID: PMC9377146 DOI: 10.1186/s13073-022-01099-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Crohn's disease (CD) patients demonstrate distinct intestinal microbial compositions and metabolic characteristics compared to unaffected controls. However, the impact of inflammation and underlying genetic risk on these microbial profiles and their relationship to disease phenotype are unclear. We used lavage sampling to characterize the colonic mucosal-luminal interface (MLI) microbiome of CD patients in endoscopic remission and unaffected controls relative to obesity, disease genetics, and phenotype. METHODS Cecum and sigmoid colon were sampled from 110 non-CD controls undergoing screening colonoscopy who were stratified by body mass index and 88 CD patients in endoscopic remission (396 total samples). CD polygenic risk score (GRS) was calculated using 186 known CD variants. MLI pellets were analyzed by 16S ribosomal RNA gene sequencing, and supernatants by untargeted liquid chromatography-mass spectrometry. RESULTS CD and obesity were each associated with decreased cecal and sigmoid MLI bacterial diversity and distinct bacterial composition compared to controls, including expansion of Escherichia/Shigella. Cecal and sigmoid dysbiosis indices for CD were significantly greater in obese controls than non-overweight controls. CD, but not obesity, was characterized by altered biogeographic relationship between the sigmoid and cecum. GRS was associated with select taxonomic shifts that overlapped with changes seen in CD compared to controls including Fusobacterium enrichment. Stricturing or penetrating Crohn's disease behavior was characterized by lower MLI bacterial diversity and altered composition, including reduced Faecalibacterium, compared to uncomplicated CD. Taxonomic profiles including reduced Parasutterella were associated with clinical disease progression over a mean follow-up of 3.7 years. Random forest classifiers using MLI bacterial abundances could distinguish disease state (area under the curve (AUC) 0.93), stricturing or penetrating Crohn's disease behavior (AUC 0.82), and future clinical disease progression (AUC 0.74). CD patients showed alterations in the MLI metabolome including increased cholate:deoxycholate ratio compared to controls. CONCLUSIONS Obesity, CD in endoscopic remission, and high CD genetic risk have overlapping colonic mucosal-luminal interface (MLI) microbiome features, suggesting a shared microbiome contribution to CD and obesity which may be influenced by genetic factors. Microbial profiling during endoscopic remission predicted Crohn's disease behavior and progression, supporting that MLI sampling could offer unique insight into CD pathogenesis and provide novel prognostic biomarkers.
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Affiliation(s)
- Jonathan P Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095-6949, USA.
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, USA.
| | | | - Venu Lagishetty
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095-6949, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Tytus Mak
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Maomeng Tong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Paul Ruegger
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Carol Landers
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Philip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Eric Vasiliauskas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Andrew Ippoliti
- Department of Medicine, Keck School of Medicine of USC, Los Angeles, USA
| | - Gil Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - David Shih
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, USA
| | - Albert J Fornace
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, USA
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Kumar S, Pollok R, Goldsmith D. Renal and Urological Disorders Associated With Inflammatory Bowel Disease. Inflamm Bowel Dis 2022:6658535. [PMID: 35942657 PMCID: PMC10393213 DOI: 10.1093/ibd/izac140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Indexed: 12/15/2022]
Abstract
Renal and urinary tract complications related to inflammatory bowel disease (IBD) have been relatively understudied in the literature compared with other extraintestinal manifestations. Presentation of these renal manifestations can be subtle, and their detection is complicated by a lack of clarity regarding the optimal screening and routine monitoring of renal function in IBD patients. Urolithiasis is the most common manifestation. Penetrating Crohn's disease involving the genitourinary system as an extraintestinal complication is rare but associated with considerable morbidity. Some biologic agents used to treat IBD have been implicated in progressive renal impairment, although differentiating between drug-related side effects and deteriorating kidney function due to extraintestinal manifestations can be challenging. The most common findings on renal biopsy of IBD patients with renal injury are tubulointerstitial nephritis and IgA nephropathy, the former also being associated with drug-induced nephrotoxicity related to IBD medication. Amyloidosis, albeit rare, must be diagnosed early to reduce the chance of progression to renal failure. In this review, we evaluate the key literature relating to renal and urological involvement in IBD and emphasize the high index of suspicion required for the prompt diagnosis and treatment of these manifestations and complications, considering the potential severity and implications of acute or chronic loss of renal function. We also provide suggestions for future research priorities.
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Affiliation(s)
- Shankar Kumar
- Centre for Medical Imaging, University College London, London, UK
| | - Richard Pollok
- Department of Gastroenterology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - David Goldsmith
- Renal and Transplantation Department, Guys and St Thomas' Hospitals NHS Foundation Trust, Great Maze Pond, London, UK
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Gonzales GB, Bourke CD, Sturgeon JP, Njunge JM, Robertson RC, Kelly PM, Berkley JA. Commentary: Mechanisms of kwashiorkor-associated immune suppression: Insights from human, mouse, and pig studies. Front Immunol 2022; 13:959465. [PMID: 35958616 PMCID: PMC9359071 DOI: 10.3389/fimmu.2022.959465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Gerard Bryan Gonzales
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, Netherlands
| | - Claire D. Bourke
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Jonathan P. Sturgeon
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - James M. Njunge
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
- Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Nairobi, Kenya
| | - Ruairi C. Robertson
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Paul M. Kelly
- Blizard Institute, Queen Mary University of London, London, United Kingdom
- Tropical Gastroenterology and Nutrition Group, University of Zambia, Lusaka, Zambia
| | - James A. Berkley
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
- Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Nairobi, Kenya
- Nuffield Department of Medicine, Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, United Kingdom
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8
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Michael H, Amimo JO, Rajashekara G, Saif LJ, Vlasova AN. Mechanisms of Kwashiorkor-Associated Immune Suppression: Insights From Human, Mouse, and Pig Studies. Front Immunol 2022; 13:826268. [PMID: 35585989 PMCID: PMC9108366 DOI: 10.3389/fimmu.2022.826268] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/31/2022] [Indexed: 12/11/2022] Open
Abstract
Malnutrition refers to inadequate energy and/or nutrient intake. Malnutrition exhibits a bidirectional relationship with infections whereby malnutrition increases risk of infections that further aggravates malnutrition. Severe malnutrition (SM) is the main cause of secondary immune deficiency and mortality among children in developing countries. SM can manifest as marasmus (non-edematous), observed most often (68.6% of all malnutrition cases), kwashiorkor (edematous), detected in 23.8% of cases, and marasmic kwashiorkor, identified in ~7.6% of SM cases. Marasmus and kwashiorkor occur due to calorie-energy and protein-calorie deficiency (PCD), respectively. Kwashiorkor and marasmic kwashiorkor present with reduced protein levels, protein catabolism rates, and altered levels of micronutrients leading to uncontrolled oxidative stress, exhaustion of anaerobic commensals, and proliferation of pathobionts. Due to these alterations, kwashiorkor children present with profoundly impaired immune function, compromised intestinal barrier, and secondary micronutrient deficiencies. Kwashiorkor-induced alterations contribute to growth stunting and reduced efficacy of oral vaccines. SM is treated with antibiotics and ready-to-use therapeutic foods with variable efficacy. Kwashiorkor has been extensively investigated in gnotobiotic (Gn) mice and piglet models to understand its multiple immediate and long-term effects on children health. Due to numerous physiological and immunological similarities between pigs and humans, pig represents a highly relevant model to study kwashiorkor pathophysiology and immunology. Here we summarize the impact of kwashiorkor on children's health, immunity, and gut functions and review the relevant findings from human and animal studies. We also discuss the reciprocal interactions between PCD and rotavirus-a highly prevalent enteric childhood pathogen due to which pathogenesis and immunity are affected by childhood SM.
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Affiliation(s)
- Husheem Michael
- Center for Food Animal Health, Department of Animal Sciences, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Joshua O. Amimo
- Center for Food Animal Health, Department of Animal Sciences, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Gireesh Rajashekara
- Center for Food Animal Health, Department of Animal Sciences, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Linda J. Saif
- Center for Food Animal Health, Department of Animal Sciences, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Anastasia N. Vlasova
- Center for Food Animal Health, Department of Animal Sciences, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
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Tanca A, Abbondio M, Fiorito G, Pira G, Sau R, Manca A, Muroni MR, Porcu A, Scanu AM, Cossu-Rocca P, De Miglio MR, Uzzau S. Metaproteomic Profile of the Colonic Luminal Microbiota From Patients With Colon Cancer. Front Microbiol 2022; 13:869523. [PMID: 35495697 PMCID: PMC9048685 DOI: 10.3389/fmicb.2022.869523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Recent studies have provided evidence of interactions among the gut microbiota (GM), local host immune cells, and intestinal tissues in colon carcinogenesis. However, little is known regarding the functions exerted by the GM in colon cancer (CC), particularly with respect to tumor clinical classification and lymphocyte infiltration. In addition, stool, usually employed as a proxy of the GM, cannot fully represent the original complexity of CC microenvironment. Here, we present a pilot study aimed at characterizing the metaproteome of CC-associated colonic luminal contents and identifying its possible associations with CC clinicopathological features. Colonic luminal contents were collected from 24 CC tissue specimens immediately after surgery. Samples were analyzed by shotgun metaproteomics. Almost 30,000 microbial peptides were quantified in the samples, enabling the achievement of the taxonomic and functional profile of the tumor-associated colonic luminal metaproteome. Upon sample aggregation based on tumor stage, grade, or tumor-infiltrating lymphocytes (TILs), peptide sets enabling discrimination of sample groups were identified through discriminant analysis (DA). As a result, Bifidobacterium and Bacteroides fragilis were significantly enriched in high-stage and high-grade CC, respectively. Among metabolic functions, formate-tetrahydrofolate ligase was significantly associated with high-stage CC. Finally, based on the results of this pilot study, we assessed the optimal sample size for differential metaproteomic studies analyzing colonic luminal contents. In conclusion, we provide a detailed picture of the microbial and host components of the colonic luminal proteome and propose promising associations between GM taxonomic/functional features and CC clinicopathological features. Future studies will be needed to verify the prognostic value of these data and to fully exploit the potential of metaproteomics in enhancing our knowledge concerning CC progression.
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Affiliation(s)
- Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giovanni Fiorito
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Medical Research Council (MRC), Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Giovanna Pira
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Rosangela Sau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Alessandra Manca
- Department of Pathology, Azienda Ospedaliero-Universitaria di Sassari, Sassari, Italy
| | - Maria Rosaria Muroni
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Alberto Porcu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Mario Scanu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Paolo Cossu-Rocca
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy.,Surgical Pathology Unit, Department of Diagnostic Services, "Giovanni Paolo II" Hospital, Area Socio-Sanitaria Locale (ASSL) Olbia-Azienda per la Tutela della Salute (ATS) Sardegna, Olbia, Italy
| | - Maria Rosaria De Miglio
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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10
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Baldan-Martin M, Chaparro M, Gisbert JP. Tissue Proteomic Approaches to Understand the Pathogenesis of Inflammatory Bowel Disease. Inflamm Bowel Dis 2021; 27:1184-1200. [PMID: 33529308 DOI: 10.1093/ibd/izaa352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel disease (IBD) has become a global disease encompassing a group of progressive disorders characterized by recurrent chronic inflammation of the gut with variable disease courses and complications. Despite recent advances in the knowledge of IBD pathophysiology, the elucidation of its etiopathology and progression is far from fully understood, requiring complex and multiple approaches. Therefore, limited clinical progress in diagnosis, assessment of disease activity, and optimal therapeutic regimens have been made over the past few decades. This review explores recent advances and challenges in tissue proteomics with an emphasis on biomarker discovery and better understanding of the molecular mechanisms underlying IBD pathogenesis. Future multi-omic studies are required for the comprehensive molecular characterization of disease biology in real time with a future impact on early detection, disease monitoring, and prediction of the clinical outcome.
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Affiliation(s)
- Montserrat Baldan-Martin
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
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11
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Ma M, Lu H, Yang Z, Chen L, Li Y, Zhang X. Differences in microbiota between acute and chronic perianal eczema. Medicine (Baltimore) 2021; 100:e25623. [PMID: 33879734 PMCID: PMC8078401 DOI: 10.1097/md.0000000000025623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/02/2021] [Indexed: 01/04/2023] Open
Abstract
Microbiota has been suggested to play a role in patients with intestinal and cutaneous diseases. However, the profiling of perianal eczema microbiota has not been described. We have explored the general profile and possible differences between acute and chronic perianal eczema. A total of 101 acute perianal eczema (APE) and 156 chronic perianal eczema (CPE) patients were enrolled in this study and the perianal microbiota was profiled via Illumina sequencing of the 16S rRNA V4 region.The microbial α-diversity and structure are similar in APE and CPE patients; however, the perianal microbiota of the APE patients had a higher content of Staphylococcus (22.2%, P < .01) than that of CPE patients. Top10 genera accounting for more than 60% (68.81% for APE and 65.47% for CPE) of the whole microbiota, including Prevotella, Streptococcus, and Bifidobacterium, show an upregulation trend in the case of APE without reaching statistically significant differences. This study compared the microbiota profiles of acute and chronic perianal eczema. Our results suggest that the microbiota of acute perianal eczema patients is enriched in Staphylococcus compared with that in the chronic group. Our findings provide data for further studies.
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Affiliation(s)
- Ming Ma
- Department of Dermatology, Beijing Coloproctological Hospital, Beijing Erlonglu Hospital, Beijing
| | - Hongmei Lu
- Department of Dermatology, Beijing Coloproctological Hospital, Beijing Erlonglu Hospital, Beijing
| | - Zuozhen Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang
- Cipher Gene LLC
| | - Li Chen
- Department of Dermatology, Beijing Coloproctological Hospital, Beijing Erlonglu Hospital, Beijing
| | | | - Xiu Zhang
- Department of Internal Medicine, Beijing Coloproctological Hospital, Beijing Erlonglu Hospital, Beijing, China
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12
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Revilla L, Mayorgas A, Corraliza AM, Masamunt MC, Metwaly A, Haller D, Tristán E, Carrasco A, Esteve M, Panés J, Ricart E, Lozano JJ, Salas A. Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis. PLoS One 2021; 16:e0246367. [PMID: 33556098 PMCID: PMC7870068 DOI: 10.1371/journal.pone.0246367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/18/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Personalized medicine requires finding relationships between variables that influence a patient's phenotype and predicting an outcome. Sparse generalized canonical correlation analysis identifies relationships between different groups of variables. This method requires establishing a model of the expected interaction between those variables. Describing these interactions is challenging when the relationship is unknown or when there is no pre-established hypothesis. Thus, our aim was to develop a method to find the relationships between microbiome and host transcriptome data and the relevant clinical variables in a complex disease, such as Crohn's disease. RESULTS We present here a method to identify interactions based on canonical correlation analysis. We show that the model is the most important factor to identify relationships between blocks using a dataset of Crohn's disease patients with longitudinal sampling. First the analysis was tested in two previously published datasets: a glioma and a Crohn's disease and ulcerative colitis dataset where we describe how to select the optimum parameters. Using such parameters, we analyzed our Crohn's disease data set. We selected the model with the highest inner average variance explained to identify relationships between transcriptome, gut microbiome and clinically relevant variables. Adding the clinically relevant variables improved the average variance explained by the model compared to multiple co-inertia analysis. CONCLUSIONS The methodology described herein provides a general framework for identifying interactions between sets of omic data and clinically relevant variables. Following this method, we found genes and microorganisms that were related to each other independently of the model, while others were specific to the model used. Thus, model selection proved crucial to finding the existing relationships in multi-omics datasets.
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Affiliation(s)
- Lluís Revilla
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Aida Mayorgas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Ana M. Corraliza
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Maria C. Masamunt
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Eva Tristán
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Anna Carrasco
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Maria Esteve
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Julian Panés
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Elena Ricart
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Juan J. Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
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13
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Li L, Figeys D. Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface. Mol Cell Proteomics 2020; 19:1409-1417. [PMID: 32581040 PMCID: PMC8143649 DOI: 10.1074/mcp.r120.002051] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/04/2020] [Indexed: 12/19/2022] Open
Abstract
Recent efforts in gut microbiome studies have highlighted the importance of explicitly describing the ecological processes beyond correlative analysis. However, we are still at the early stage of understanding the organizational principles of the gut ecosystem, partially because of the limited information provided by currently used analytical tools in ecological modeling practices. Proteomics and metaproteomics can provide a number of insights for ecological studies, including biomass, matter and energy flow, and functional diversity. In this Mini Review, we discuss proteomics and metaproteomics-based experimental strategies that can contribute to studying the ecology, in particular at the mucosal-luminal interface (MLI) where the direct host-microbiome interaction happens. These strategies include isolation protocols for different MLI components, enrichment methods to obtain designated array of proteins, probing for specific pathways, and isotopic labeling for tracking nutrient flow. Integration of these technologies can generate spatiotemporal and site-specific biological information that supports mathematical modeling of the ecosystem at the MLI.
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Affiliation(s)
- Leyuan Li
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.
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14
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Syed S, Stidham RW. Potential for Standardization and Automation for Pathology and Endoscopy in Inflammatory Bowel Disease. Inflamm Bowel Dis 2020; 26:1490-1497. [PMID: 32869844 PMCID: PMC7749192 DOI: 10.1093/ibd/izaa211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Indexed: 02/07/2023]
Abstract
Automated image analysis methods have shown potential for replicating expert interpretation of histology and endoscopy images, which traditionally require highly specialized and experienced reviewers. Inflammatory bowel disease (IBD) diagnosis, severity assessment, and treatment decision-making require multimodal expert data interpretation and integration, which could be significantly aided by applications of machine learning analyses. This review introduces fundamental concepts of machine learning for imaging analysis and highlights research and development of automated histology and endoscopy interpretation in IBD. Proof-of-concept studies strongly suggest that histologic and endoscopic images can be interpreted with similar accuracy as knowledge experts. Encouraging results support the potential of automating existing disease activity scoring instruments with high reproducibility, speed, and accessibility, therefore improving the standardization of IBD assessment. Though challenges surrounding ground truth definitions, technical barriers, and the need for extensive multicenter evaluation must be resolved before clinical implementation, automated image analysis is likely to both improve access to standardized IBD assessment and advance the fundamental concepts of how disease is measured.
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Affiliation(s)
- Sana Syed
- Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA, USA,Address correspondence to: Ryan W. Stidham, MD, MS, Assistant Professor of Medicine, Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, University of Michigan Medical School, 3912 Taubman Center, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA.
| | - Ryan W Stidham
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA,Michigan Integrated Center for Health Analytics and Medical Prediction (MiCHAMP), University of Michigan, Ann Arbor, MI, USA
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15
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Tang J, Mou M, Wang Y, Luo Y, Zhu F. MetaFS: Performance assessment of biomarker discovery in metaproteomics. Brief Bioinform 2020; 22:5854399. [PMID: 32510556 DOI: 10.1093/bib/bbaa105] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/17/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022] Open
Abstract
Metaproteomics suffers from the issues of dimensionality and sparsity. Data reduction methods can maximally identify the relevant subset of significant differential features and reduce data redundancy. Feature selection (FS) methods were applied to obtain the significant differential subset. So far, a variety of feature selection methods have been developed for metaproteomic study. However, due to FS's performance depended heavily on the data characteristics of a given research, the well-suitable feature selection method must be carefully selected to obtain the reproducible differential proteins. Moreover, it is critical to evaluate the performance of each FS method according to comprehensive criteria, because the single criterion is not sufficient to reflect the overall performance of the FS method. Therefore, we developed an online tool named MetaFS, which provided 13 types of FS methods and conducted the comprehensive evaluation on the complex FS methods using four widely accepted and independent criteria. Furthermore, the function and reliability of MetaFS were systematically tested and validated via two case studies. In sum, MetaFS could be a distinguished tool for discovering the overall well-performed FS method for selecting the potential biomarkers in microbiome studies. The online tool is freely available at https://idrblab.org/metafs/.
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16
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Metaproteomic analysis of human gut microbiome in digestive and metabolic diseases. Adv Clin Chem 2020; 97:1-12. [PMID: 32448430 DOI: 10.1016/bs.acc.2019.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metaproteomics, as a subfield of proteomics, has quickly emerged as a pivotal tool for global characterization of a microbiome system at a functional level. It has been increasingly applied in studying human digestive and metabolic diseases, and provides information-rich data to identify the dysbiosis of human gut microbiome related to healthy or disease states to elucidate the molecular events underlying host-microbiota interplays. While significant technical challenges still exist, this emerging technology has been demonstrated to provide essential information in interrogating functional changes in the human gut microbiome, complementary to metagenomics and metatranscriptomics. This chapter overviews the overall metaproteomic work flow and its recent applications in studying human gut microbiome relevant to digestive and metabolic diseases.
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17
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Wang Y, Zhou Y, Xiao X, Zheng J, Zhou H. Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota. J Proteomics 2020; 219:103737. [DOI: 10.1016/j.jprot.2020.103737] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
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18
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Zhuang X, Li T, Li M, Huang S, Qiu Y, Feng R, Zhang S, Chen M, Xiong L, Zeng Z. Systematic Review and Meta-analysis: Short-Chain Fatty Acid Characterization in Patients With Inflammatory Bowel Disease. Inflamm Bowel Dis 2019; 25:1751-1763. [PMID: 31498864 DOI: 10.1093/ibd/izz188] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Alterations in gut microbiota and short-chain fatty acids (SCFAs) have been reported in inflammatory bowel disease (IBD), but the results are conflicting. The aim of this study was to perform a meta-analysis to explore the characterization of SCFAs in IBD patients and their potential role in the occurrence and development of IBD. METHODS Case-control studies investigating SCFAs in IBD patients were identified from several English databases. The standardized mean difference (SMD) with 95% confidence interval (CI) was calculated using the random-effects model. RESULTS The SMDs of acetate, valerate, and total SCFAs in ulcerative colitis (UC) patients were -0.51 (95% CI, -0.90 to -0.13), -0.65 (95% CI, -1.02 to -0.28), and -0.51 (95% CI, -0.95 to -0.07), respectively. The SMDs of acetate, propionate, and butyrate in patients with active UC were -1.74 (95% CI, -3.15 to -0.33), -2.42 (95% CI, -4.24 to -0.60), and -1.99 (95% CI, -3.39 to -0.60), respectively. However, the SMD of butyrate in UC patients in remission was 0.72 (95% CI, 0.34 to 1.11). In addition, the SMDs of acetate, butyrate, and valerate in Crohn's disease (CD) patients were -1.43 (95% CI, -2.81 to -0.04), -0.77 (95% CI, -1.39 to -0.14), and -0.75 (95% CI, -1.47 to -0.02), respectively. Finally, the SMDs of acetate, propionate, butyrate, valerate, and lactate in IBD patients were -2.19 (95% CI, -3.98 to -0.39), -1.64 (95% CI, -3.02 to -0.25), -1.98 (95% CI, -3.93 to -0.03), -0.55 (95% CI, -0.93 to -0.18), and 4.02 (95% CI, 1.44 to 6.61), respectively. CONCLUSIONS There were alterations of SCFAs in IBD patients, and inconsistent SCFA alterations were found in CD and UC. More importantly, inverse SCFA alterations existed in patients with active UC and those in remission.
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Affiliation(s)
- Xiaojun Zhuang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Tong Li
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Manying Li
- Department of Medical Ultrasonics, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Shanshan Huang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yun Qiu
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Rui Feng
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Shenghong Zhang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Minhu Chen
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Lishou Xiong
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zhirong Zeng
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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19
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Klaassen MAY, Imhann F, Collij V, Fu J, Wijmenga C, Zhernakova A, Dijkstra G, Festen EAM, Gacesa R, Vich Vila A, Weersma RK. Anti-inflammatory Gut Microbial Pathways Are Decreased During Crohn's Disease Exacerbations. J Crohns Colitis 2019; 13:1439-1449. [PMID: 31066440 PMCID: PMC7142399 DOI: 10.1093/ecco-jcc/jjz077] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] is a chronic inflammatory disorder of the gastrointestinal tract characterised by alternating periods of exacerbation and remission. We hypothesised that changes in the gut microbiome are associated with CD exacerbations, and therefore aimed to correlate multiple gut microbiome features to CD disease activity. METHODS Faecal microbiome data generated using whole-genome metagenomic shotgun sequencing of 196 CD patients were of obtained from the 1000IBD cohort [one sample per patient]. Patient disease activity status at time of sampling was determined by re-assessing clinical records 3 years after faecal sample production. Faecal samples were designated as taken 'in an exacerbation' or 'in remission'. Samples taken 'in remission' were further categorised as 'before the next exacerbation' or 'after the last exacerbation', based on the exacerbation closest in time to the faecal production date. CD activity was correlated with gut microbial composition and predicted functional pathways via logistic regressions using MaAsLin software. RESULTS In total, 105 bacterial pathways were decreased during CD exacerbation (false-discovery rate [FDR] <0.1) in comparison with the gut microbiome of patients both before and after an exacerbation. Most of these decreased pathways exert anti-inflammatory properties facilitating the biosynthesis and fermentation of various amino acids [tryptophan, methionine, and arginine], vitamins [riboflavin and thiamine], and short-chain fatty acids [SCFAs]. CONCLUSIONS CD exacerbations are associated with a decrease in microbial genes involved in the biosynthesis of the anti-inflammatory mediators riboflavin, thiamine, and folate, and SCFAs, suggesting that increasing the intestinal abundances of these mediators might provide new treatment opportunities. These results were generated using bioinformatic analyses of cross-sectional data and need to be replicated using time-series and wet lab experiments.
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Affiliation(s)
- Marjolein A Y Klaassen
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Floris Imhann
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Valerie Collij
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Jingyuan Fu
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Alexandra Zhernakova
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Gerard Dijkstra
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Eleonora A M Festen
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Ranko Gacesa
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Arnau Vich Vila
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Rinse K Weersma
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands,Corresponding author: R. K. Weersma, MD, PhD, PO Box 30.001, 9700RB Groningen, The Netherlands. Tel.: +316 41132824; Fax 050 361 9306;
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20
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Issa Isaac N, Philippe D, Nicholas A, Raoult D, Eric C. Metaproteomics of the human gut microbiota: Challenges and contributions to other OMICS. CLINICAL MASS SPECTROMETRY 2019; 14 Pt A:18-30. [DOI: 10.1016/j.clinms.2019.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 12/22/2022]
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21
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Vlasova AN, Takanashi S, Miyazaki A, Rajashekara G, Saif LJ. How the gut microbiome regulates host immune responses to viral vaccines. Curr Opin Virol 2019; 37:16-25. [PMID: 31163292 PMCID: PMC6863389 DOI: 10.1016/j.coviro.2019.05.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023]
Abstract
The co-evolution of the microbiota and immune system has forged a mutually beneficial relationship. This relationship allows the host to maintain the balance between active immunity to pathogens and vaccines and tolerance to self-antigens and food antigens. In children living in low-income and middle-income countries, undernourishment and repetitive gastrointestinal infections are associated with the failure of oral vaccines. Intestinal dysbiosis associated with these environmental influences, as well as some host-related factors, compromises immune responses and negatively impacts vaccine efficacy. To understand how immune responses to viral vaccines can be optimally modulated, mechanistic studies of the relationship between the microbiome, host genetics, viral infections and the development and function of the immune system are needed. We discuss the potential role of the microbiome in modulating vaccine responses in the context of a growing understanding of the relationship between the gastrointestinal microbiota, host related factors (including histo-blood group antigens) and resident immune cell populations.
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Affiliation(s)
- Anastasia N Vlasova
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA.
| | - Sayaka Takanashi
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ayako Miyazaki
- Division of Viral Disease and Epidemiology, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan
| | - Gireesh Rajashekara
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA
| | - Linda J Saif
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA.
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22
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Danilova NA, Abdulkhakov SR, Grigoryeva TV, Markelova MI, Vasilyev IY, Boulygina EA, Ardatskaya MD, Pavlenko AV, Tyakht AV, Odintsova AK, Abdulkhakov RA. Markers of dysbiosis in patients with ulcerative colitis and Crohn's disease. TERAPEVT ARKH 2019; 91:17-24. [PMID: 31094471 DOI: 10.26442/00403660.2019.04.000211] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIM The aim of the study was to study the taxonomic and functional composition of the gut microbiota in ulcerative colitis (UC) and Crohn's disease (CD) patients to identify key markers of dysbiosis in IBD. MATERIALS AND METHODS Fecal samples obtained from 95 IBD patients (78 UC and 17 CD) as well as 96 healthy volunteers were used for whole-genome sequencing carried out on the SOLiD 5500 W platform. Taxonomic profiling was performed by aligning the reeds, not maped on hg19, on MetaPhlAn2 reference database. Reeds were mapped using the HUNAnN2 algorithm to the ChocoPhlAn database to assess the representation of microbial metabolic pathways. Short-chain fatty acids (SCFA) level were measured in fecal samples by gas-liquid chromatographic analysis. RESULTS Changes in IBD patients gut microbiota were characterized by an increase in the representation of Proteobacteria and Bacteroidetes phyla bacteria and decrease in the number of Firmicutes phylum bacteria and Euryarchaeota phylum archaea; a decrease in the alpha-diversity index, relative representation of butyrate-producing, hydrogen-utilizing bacteria, and Methanobrevibacter smithii; increase in the relative representation of Ruminococcus gnavus in UC and CD patients and Akkermansia muciniphila in CD patients. Reduction of Butyryl-CoA: acetate CoA transferase gene relative representation in CD patients, decrease of absolute content of SCFA total number as well as particular SCFAs and main SCFAs ratio in IBD patients may indicate inhibition of functional activity and number of anaerobic microflora and/or an change in SCFA utilization by colonocytes. CONCLUSION the revealed changes can be considered as typical signs of dysbiosis in IBD patients and can be used as potential targets for IBD patients personalized treatment development.
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Affiliation(s)
| | - S R Abdulkhakov
- Kazan Federal University, Kazan, Russia.,Kazan State Medical University of the Ministry of Health of the Russian Federation, Kazan, Russia
| | | | | | | | | | - M D Ardatskaya
- Central State Medical Academy of Administrative Department of the President of the Russian Federation, Moscow, Russia
| | - A V Pavlenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, Russia
| | - A V Tyakht
- Institute of Gene Biology of RAS, Moscow, Russi
| | - A Kh Odintsova
- Republican Clinical Hospital of the Ministry of Health of the Republic of Tatarstan, Kazan, Russia
| | - R A Abdulkhakov
- Kazan State Medical University of the Ministry of Health of the Russian Federation, Kazan, Russia
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23
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The mucosal-luminal interface: an ideal sample to study the mucosa-associated microbiota and the intestinal microbial biogeography. Pediatr Res 2019; 85:895-903. [PMID: 30758325 DOI: 10.1038/s41390-019-0326-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 12/22/2018] [Accepted: 01/28/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND Alterations in gastrointestinal microbial communities have been linked to human disease. Most studies use fecal samples as a proxy for the intestinal microbiota; however, the fecal microbiome is not fully representative of the mucosa-associated microbiota at the site of disease. While mucosal biopsies can be used instead, they often contain a high proportion of host DNA that can confound 16S ribosomal RNA (rRNA) gene sequencing studies. METHODS To overcome these limitations, we sampled the mucosal-luminal interface (MLI) to study the mucosa-associated microbiota. We also employed a simple bioinformatics workflow to remove contaminants from 16S rRNA gene profiling results. RESULTS Our results indicate that the microbial differences between individuals are greater than those between different microenvironments within the same individual. Moreover, biopsy samples frequently contained contaminants that could significantly impact biopsy profiling results. CONCLUSIONS Our findings highlight the utility of collecting MLI aspirates to complement biopsies and stools for characterizing human microbial communities.
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Gisbert JP, Chaparro M. Clinical Usefulness of Proteomics in Inflammatory Bowel Disease: A Comprehensive Review. J Crohns Colitis 2019; 13:374-384. [PMID: 30307487 DOI: 10.1093/ecco-jcc/jjy158] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The protein domain is probably the most ubiquitously affected in disease, response and recovery, and therefore proteomics holds special promise for biomarker discovery in general, and particularly in inflammatory bowel disease [IBD], i.e. ulcerative colitis and Crohn's disease. Tremendous progress has been made over the past decade in the development and refinement of proteomics technologies. These advances provide opportunities for a long-anticipated personalized medicine approach to the treatment of IBD. The present review examines the current state of IBD proteomics research and its usefulness in clinical practice. We performed a systematic bibliographic search to identify studies investigating the use of proteomics in patients with IBD, and we then summarized the current 'state of the art' in the applications of proteomic technologies in the study of IBD. In particular, in the present review we provide: [1] a brief introduction to proteomics in health and disease; [2] a review of the different stages from biomarker discovery to clinical application; and [3] a comprehensive review of the clinical usefulness and application of proteomics in IBD, including: [a] screening to differentiate IBD from healthy controls; [b] differentiating Crohn's disease from ulcerative colitis; [c] prediction of the behaviour or the IBD course; [d] prediction of IBD response to biological treatment; and [e] monitoring response to treatment. We also review the importance of the type of sample-blood vs intestinal tissue-for the study of proteomics in IBD patients. Finally, we emphasize the current limitations of proteomic studies in IBD.
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Affiliation(s)
- Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
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25
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Hobby GP, Karaduta O, Dusio GF, Singh M, Zybailov BL, Arthur JM. Chronic kidney disease and the gut microbiome. Am J Physiol Renal Physiol 2019; 316:F1211-F1217. [PMID: 30864840 DOI: 10.1152/ajprenal.00298.2018] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The gut microbiome is composed of a diverse population of bacteria that have beneficial and adverse effects on human health. The microbiome has recently gained attention and is increasingly noted to play a significant role in health and a number of disease states. Increasing urea concentration during chronic kidney disease (CKD) leads to alterations in the intestinal flora that can increase production of gut-derived toxins and alter the intestinal epithelial barrier. These changes can lead to an acceleration of the process of kidney injury. A number of strategies have been proposed to interrupt this pathway of injury in CKD. The purpose of this review is to summarize the role of the gut microbiome in CKD, tools used to study this microbial population, and attempts to alter its composition for therapeutic purposes.
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Affiliation(s)
- Gerren P Hobby
- Division of Nephrology, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Oleg Karaduta
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Giuseppina F Dusio
- Division of Nephrology, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Manisha Singh
- Division of Nephrology, University of Arkansas for Medical Sciences , Little Rock, Arkansas.,Central Arkansas Veterans Health System, Little Rock, Arkansas
| | - Boris L Zybailov
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - John M Arthur
- Division of Nephrology, University of Arkansas for Medical Sciences , Little Rock, Arkansas.,Central Arkansas Veterans Health System, Little Rock, Arkansas
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Manfredi M, Conte E, Barberis E, Buzzi A, Robotti E, Caneparo V, Cecconi D, Brandi J, Vanni E, Finocchiaro M, Astegiano M, Gariglio M, Marengo E, De Andrea M. Integrated serum proteins and fatty acids analysis for putative biomarker discovery in inflammatory bowel disease. J Proteomics 2019; 195:138-149. [DOI: 10.1016/j.jprot.2018.10.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/19/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022]
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Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease. mSystems 2019; 4:mSystems00337-18. [PMID: 30801026 PMCID: PMC6372841 DOI: 10.1128/msystems.00337-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/17/2019] [Indexed: 02/07/2023] Open
Abstract
Although genetic approaches are the standard in microbiome analysis, proteome-level information is largely absent. This discrepancy warrants a better understanding of the relationship between gene copy number and protein abundance, as this is crucial information for inferring protein-level changes from metagenomic data. As it remains unknown how metaproteomic systems evolve during dynamic disease states, we leveraged a 4.5-year fecal time series using samples from a single patient with colonic Crohn's disease. Utilizing multiplexed quantitative proteomics and shotgun metagenomic sequencing of eight time points in technical triplicate, we quantified over 29,000 protein groups and 110,000 genes and compared them to five protein biomarkers of disease activity. Broad-scale observations were consistent between data types, including overall clustering by principal-coordinate analysis and fluctuations in Gene Ontology terms related to Crohn's disease. Through linear regression, we determined genes and proteins fluctuating in conjunction with inflammatory metrics. We discovered conserved taxonomic differences relevant to Crohn's disease, including a negative association of Faecalibacterium and a positive association of Escherichia with calprotectin. Despite concordant associations of genera, the specific genes correlated with these metrics were drastically different between metagenomic and metaproteomic data sets. This resulted in the generation of unique functional interpretations dependent on the data type, with metaproteome evidence for previously investigated mechanisms of dysbiosis. An example of one such mechanism was a connection between urease enzymes, amino acid metabolism, and the local inflammation state within the patient. This proof-of-concept approach prompts further investigation of the metaproteome and its relationship with the metagenome in biologically complex systems such as the microbiome. IMPORTANCE A majority of current microbiome research relies heavily on DNA analysis. However, as the field moves toward understanding the microbial functions related to healthy and disease states, it is critical to evaluate how changes in DNA relate to changes in proteins, which are functional units of the genome. This study tracked the abundance of genes and proteins as they fluctuated during various inflammatory states in a 4.5-year study of a patient with colonic Crohn's disease. Our results indicate that despite a low level of correlation, taxonomic associations were consistent in the two data types. While there was overlap of the data types, several associations were uniquely discovered by analyzing the metaproteome component. This case study provides unique and important insights into the fundamental relationship between the genes and proteins of a single individual's fecal microbiome associated with clinical consequences.
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28
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Zacarías MF, Collado MC, Gómez-Gallego C, Flinck H, Aittoniemi J, Isolauri E, Salminen S. Pregestational overweight and obesity are associated with differences in gut microbiota composition and systemic inflammation in the third trimester. PLoS One 2018; 13:e0200305. [PMID: 30005082 PMCID: PMC6044541 DOI: 10.1371/journal.pone.0200305] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/22/2018] [Indexed: 12/13/2022] Open
Abstract
The obesity epidemic is a global challenge, and the velocity of propagation is high in the population at reproductive age. Overweight and obesity during pregnancy have been associated with high birth weight and an increased risk of childhood obesity, reinforcing the risk of other non-communicable diseases. Obesity involves chronic low-grade systemic inflammation. New biomarkers for early detection of obesity risk are urgently required. The aim of this study was to identify the connection between pregestational BMI (pre-BMI) status and inflammatory biomarkers during the third trimester of pregnancy and their association with intestinal microbiota composition. Fifty-four pregnant women were classified according to pre-pregnancy BMI as normoweight, overweight, or obese. Weight gain, inflammatory biomarkers (hs_CRP, haptoglobin, and suPAR), and microbiota composition were assessed during the third trimester. A significant lower weight gain for obese mothers and a positive correlation between pre-BMI and inflammatory biomarkers were detected (Spearman’s correlation). Haptoglobin levels were significantly higher in overweight and obese mothers. Higher Firmicutes levels and a higher ratio Firmicutes/Bacteroidetes were observed in the overweight and obese subjects. High hs_CRP and haptoglobin levels were also correlated with decreased microbiota diversity (Shannon index), whereas haptoglobin and hs_CRP values were correlated with several microbiota components, such as Ruminococcus gnavus and Faecalibacterium, and with specific phyla in the normoweight and overweight mothers; no significant associations with microbiota were found for suPAR. In conclusion, haptoglobin and hs_CRP reflected pregestational BMI status and related microbiota components, but haptoglobin was a better biomarker for microbiota associated with overweight. suPAR was associated with low grade inflammation dependent on pre-pregnancy BMI, but it was not related to deviated microbiota profiles.
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Affiliation(s)
| | - María Carmen Collado
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Department of Biotechnology, Valencia, Spain
| | - Carlos Gómez-Gallego
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Heini Flinck
- Department of Clinical Microbiology, Fimlab Laboratories, Tampere, Finland
| | - Janne Aittoniemi
- Department of Clinical Microbiology, Fimlab Laboratories, Tampere, Finland
| | - Erika Isolauri
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
- Department of Clinical Sciences, Faculty of Medicine, University of Turku, Turku, Finland
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
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29
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Mucosal-luminal interface proteomics reveals biomarkers of pediatric inflammatory bowel disease-associated colitis. Am J Gastroenterol 2018. [PMID: 29531307 DOI: 10.1038/s41395-018-0024-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Improved biomarkers are an unmet clinical need for suspected inflammatory bowel disease (IBD). Need is greatest for children, since current biomarkers suffers from low specificity, particularly in this population; thus, invasive testing methods, with the accompanying risk of complications, are necessary. Additionally, current biomarkers do not delineate disease extent assessment for ulcerative colitis (UC), a factor involved in therapeutic decisions. METHODS Intestinal mucosal-luminal interface (MLI) aspirates from the ascending colon (AC) and descending colon (DC) were collected during diagnostic colonoscopy from treatment-naïve children. The MLI proteomes of 18 non-IBD and 42 IBD patients were analyzed by liquid chromatography mass spectrometry. Analyses of proteomic data generated protein panels distinguishing IBD from non-IBD and pancolitis from non-pancolitis (UC disease extent). Select protein biomarkers were evaluated in stool samples by enzyme-linked immunosorbent assay (n = 24). RESULTS A panel of four proteins discriminated active IBD from non-IBD (discovery cohort) with a sensitivity of 0.954 (95% confidence interval (CI): 0.772-0.999) and >0.999 (95% CI: 0.824-1.00) for the AC and DC, respectively, and a specificity of >0.999 (AC, 95% CI: 0.815-1.00; DC, 95% CI:0.692-1.00) for both the AC and DC. A separate panel of four proteins distinguished pancolitis from non-pancolitis in UC patients with sensitivity >0.999 (95% CI: 0.590-1.00) and specificity >0.999 (95% CI: 0.715-1.00). Catalase (p < 0.0001) and LTA4H (p = 0.0002) were elevated in IBD stool samples compared to non-IBD stool samples. CONCLUSION This study identified panels of proteins that have significantly different expression levels and contribute to accurate IBD diagnosis and disease extent characterization in children with UC. Biomarkers identified from the MLI demonstrate transferable results in stool samples.
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30
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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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31
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Bambury A, Sandhu K, Cryan JF, Dinan TG. Finding the needle in the haystack: systematic identification of psychobiotics. Br J Pharmacol 2018; 175:4430-4438. [PMID: 29243233 DOI: 10.1111/bph.14127] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/24/2017] [Accepted: 11/30/2017] [Indexed: 12/13/2022] Open
Abstract
The brain-gut-microbiota axis is increasingly viewed as a novel paradigm in neuroscience with the capacity to generate innovative therapies for patients with psychiatric illnesses. Psychobiotics, defined as live bacteria, which when ingested in adequate amounts, confer mental health benefits, are increasingly of interest, as preclinical trials continue to show promising results. Particularly in stress-related, anxiety and depressive disorders, there is potential for psychobiotics to deliver new therapies. The question of which microbes may prove to be the most promising psychobiotic in delivering such therapies at a clinical level is of great importance. Here we look at the characteristics of psychobiotics, in an attempt to present an outline from which the identification of potential new psychobiotics may be possible. LINKED ARTICLES: This article is part of a themed section on When Pharmacology Meets the Microbiome: New Targets for Therapeutics? To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.24/issuetoc.
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Affiliation(s)
- Aisling Bambury
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Kiran Sandhu
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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Chronic Rhinosinusitis and the Evolving Understanding of Microbial Ecology in Chronic Inflammatory Mucosal Disease. Clin Microbiol Rev 2017; 30:321-348. [PMID: 27903594 DOI: 10.1128/cmr.00060-16] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Chronic rhinosinusitis (CRS) encompasses a heterogeneous group of debilitating chronic inflammatory sinonasal diseases. Despite considerable research, the etiology of CRS remains poorly understood, and debate on potential roles of microbial communities is unresolved. Modern culture-independent (molecular) techniques have vastly improved our understanding of the microbiology of the human body. Recent studies that better capture the full complexity of the microbial communities associated with CRS reintroduce the possible importance of the microbiota either as a direct driver of disease or as being potentially involved in its exacerbation. This review presents a comprehensive discussion of the current understanding of bacterial, fungal, and viral associations with CRS, with a specific focus on the transition to the new perspective offered in recent years by modern technology in microbiological research. Clinical implications of this new perspective, including the role of antimicrobials, are discussed in depth. While principally framed within the context of CRS, this discussion also provides an analogue for reframing our understanding of many similarly complex and poorly understood chronic inflammatory diseases for which roles of microbes have been suggested but specific mechanisms of disease remain unclear. Finally, further technological advancements on the horizon, and current pressing questions for CRS microbiological research, are considered.
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Zheng H, Chen M, Li Y, Wang Y, Wei L, Liao Z, Wang M, Ma F, Liao Q, Xie Z. Modulation of Gut Microbiome Composition and Function in Experimental Colitis Treated with Sulfasalazine. Front Microbiol 2017; 8:1703. [PMID: 28936203 PMCID: PMC5594074 DOI: 10.3389/fmicb.2017.01703] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022] Open
Abstract
Inflammatory bowel disease (IBD) results from alterations in intestinal flora and the immune system. Sulfasalazine (SASP) is a sulfa antimicrobial used to treat IBD in clinic for years. However, how SASP affects gut microbes and its potential functions remains unclear. To investigate the relationships of SASP, IBD, and gut microbiome, we used 2,4,6-trinitrobenzenesulfonic acid (TNBS) to induce experimental colitis in rats, and analyzed the microbiota in the fecal samples, which come from the control group (treated with ethanol + saline), the model group (treated with TNBS-ethanol + saline) and the SASP group (treated with TNBS-ethanol + SASP), with 16S gene sequencing and followed up a subset sample using shotgun sequencing. The study found that SASP treatment could not only restore the TNBS-induced gut dysbiosis, which was proved by the increasing amount of SCFAs-producing bacteria and lactic acid-producing bacteria as well as the decreasing amount of Proteobacteria, but also modulate the dysregulated function of the TNBS-induced colitis to resemble that of the control group, including an increased capacity for basic metabolism (carbohydrate metabolism, citrate cycle) and a decrease in the oxidative stress (riboflavin, sulfur, cysteine) as well as bacterial pathogenesis (cell motility and secretion, bacterial motility proteins, flagellar assembly). Moreover, a higher proportion of Mycoplasma was observed in the SASP group, which may associate with infertility. In all, the study provides insight into specific microbial clades and pathways linked with SASP treatment to elaborate the mechanism for treatment of IBD.
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Affiliation(s)
- Haihui Zheng
- School of Pharmaceutical Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Mingyi Chen
- School of Pharmaceutical Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Yuan Li
- School of Chinese Materia Medica, Guangzhou University of Chinese MedicineGuangzhou, China
| | | | - Lin Wei
- School of Pharmaceutical Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Ziqiong Liao
- School of Pharmaceutical Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Mengxia Wang
- School of Chinese Materia Medica, Guangzhou University of Chinese MedicineGuangzhou, China
| | - Fangli Ma
- Infinitus (China) Company Ltd.Guangzhou, China
| | - Qiongfeng Liao
- School of Chinese Materia Medica, Guangzhou University of Chinese MedicineGuangzhou, China
| | - Zhiyong Xie
- School of Pharmaceutical Sciences, Sun Yat-sen UniversityGuangzhou, China
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35
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Volkmann ER, Chang YL, Barroso N, Furst DE, Clements PJ, Gorn AH, Roth BE, Conklin JL, Getzug T, Borneman J, McGovern DPB, Tong M, Jacobs JP, Braun J. Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium. Arthritis Rheumatol 2017; 68:1483-92. [PMID: 26749064 PMCID: PMC5561666 DOI: 10.1002/art.39572] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/29/2015] [Indexed: 01/19/2023]
Abstract
OBJECTIVE To compare colonic microbial composition in systemic sclerosis (SSc) patients and healthy controls and to determine whether certain microbial genera are associated with gastrointestinal (GI) tract symptoms in patients with SSc. METHODS Healthy controls were age- and sex-matched (1:1) with adult SSc patients. Cecum and sigmoid mucosal lavage samples were obtained during colonoscopy. The microbiota in these samples were determined by Illumina HiSeq 2000 16S sequencing, and operational taxonomic units were selected. Linear discriminant analysis effect size was used to identify the genera that showed differential expression in SSc patients versus controls. Differential expression analysis for sequence count data was used to identify specific genera associated with GI tract symptoms. RESULTS Among 17 patients with SSc (88% female; median age 52.1 years), the mean ± SD total GI Tract 2.0 score was 0.7 ± 0.6. Principal coordinate analysis illustrated significant differences in microbial communities in the cecum and sigmoid regions in SSc patients versus healthy controls (both P = 0.001). Similar to the findings in inflammatory disease states, SSc patients had decreased levels of commensal bacteria, such as Faecalibacterium and Clostridium, and increased levels of pathobiont bacteria, such as Fusobacterium and γ-Proteobacteria, compared with healthy controls. Bifidobacterium and Lactobacillus, which are typically reduced under conditions of inflammation, were also increased in abundance in patients with SSc. In SSc patients with moderate/severe GI tract symptoms, the abundance of Bacteroides fragilis was decreased, and that of Fusobacterium was increased, compared with patients who had no or mild symptoms. CONCLUSION This study demonstrates a distinct colonic microbial signature in SSc patients compared with healthy controls. This unique ecologic change may perpetuate immunologic aberrations and contribute to clinical manifestations of SSc.
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Affiliation(s)
| | - Yu-Ling Chang
- University of California, Los Angeles David Geffen School of Medicine
| | - Nashla Barroso
- University of California, Los Angeles David Geffen School of Medicine
| | - Daniel E Furst
- University of California, Los Angeles David Geffen School of Medicine
| | - Philip J Clements
- University of California, Los Angeles David Geffen School of Medicine
| | - Alan H Gorn
- University of California, Los Angeles David Geffen School of Medicine
| | - Bennett E Roth
- University of California, Los Angeles David Geffen School of Medicine
| | - Jeffrey L Conklin
- University of California, Los Angeles David Geffen School of Medicine
| | - Terri Getzug
- University of California, Los Angeles David Geffen School of Medicine
| | | | | | - Maomeng Tong
- University of California, Los Angeles David Geffen School of Medicine
| | - Jonathan P Jacobs
- University of California, Los Angeles David Geffen School of Medicine
| | - Jonathan Braun
- University of California, Los Angeles David Geffen School of Medicine
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36
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Lee PY, Chin SF, Neoh HM, Jamal R. Metaproteomic analysis of human gut microbiota: where are we heading? J Biomed Sci 2017; 24:36. [PMID: 28606141 PMCID: PMC5469034 DOI: 10.1186/s12929-017-0342-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/01/2017] [Indexed: 02/08/2023] Open
Abstract
The human gut is home to complex microbial populations that change dynamically in response to various internal and external stimuli. The gut microbiota provides numerous functional benefits that are crucial for human health but in the setting of a disturbed equilibrium, the microbial community can cause deleterious outcomes such as diseases and cancers. Characterization of the functional activities of human gut microbiota is fundamental to understand their roles in human health and disease. Metaproteomics, which refers to the study of the entire protein collection of the microbial community in a given sample is an emerging area of research that provides informative details concerning functional aspects of the microbiota. In this mini review, we present a summary of the progress of metaproteomic analysis for studying the functional role of gut microbiota. This is followed by an overview of the experimental approaches focusing on fecal specimen for metaproteomics and is concluded by a discussion on the challenges and future directions of metaproteomic research.
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Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia.
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
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Yau YY, Leong RWL, Pudipeddi A, Redmond D, Wasinger VC. Serological Epithelial Component Proteins Identify Intestinal Complications in Crohn's Disease. Mol Cell Proteomics 2017; 16:1244-1257. [PMID: 28490445 DOI: 10.1074/mcp.m116.066506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/09/2017] [Indexed: 12/12/2022] Open
Abstract
Crohn's Disease (CD) is a relapsing inflammation of the gastrointestinal tract that affects a young working age population and is increasing in developing countries. Half of all sufferers will experience stricturing or fistulizing intestinal complications that require extensive surgical interventions and neither genes nor clinical risk factors can predict this debilitating natural history. We applied discovery and verification phase studies as part of an NCI-FDA modeled biomarker pipeline to identify differences in the low-mass (<25kDa) blood-serum proteome between CD behavioral phenotypes. A significant enrichment of epithelial component proteins was identified in CD patients with intestinal complications using quantitative proteomic profiling with label-free Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). DAVID 6.7 (NIH) was used for functional annotation analysis of detected proteins and immunoblotting and multiple reaction monitoring (MRM) to verify a priori findings in a secondary independent cohort of complicated CD (CCD), uncomplicated inflammatory CD (ICD), Th1/17 pathway inflammation controls (rheumatoid arthritis), inflammatory bowel disease controls (ulcerative colitis), and healthy controls. Seventy-six high-confidence serum proteins were modulated in CCD versus ICD by LC-MS/MS (p < 0.05, FDR q<0.01), annotating to pathways of epithelial barrier homeostasis (p < 0.01). In verification phase, a putative serology panel developed from discovery proteomics data consisting of desmoglein-1, desmoplakin, and fatty acid-binding protein 5 (FABP5) distinguished CCD from all other groups (p = 0.041) and discriminated complication in CD (70% sensitivity and 72.5% specificity at score ≥1.907, AUC = 0.777, p = 0.007). An MRM assay secondarily confirmed increased FABP5 levels in CCD (p < 0.001). In a longitudinal subanalysis-cohort, FABP5 levels were stable over a two-month period with no behavioral changes (p = 0.099). These studies along the biomarker development pipeline provide substantial proof-of-principle that a blood test can be developed specific to transmural intestinal injury. Data are available via the PRIDE proteomics data repository under identifier PXD001821 and PeptideAtlas with identifier PASS00661.
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Affiliation(s)
- Yunki Y Yau
- From the: ‡Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052 Australia.,§Concord Repatriation General Hospital, Gastroenterology and Liver Services, Hospital Rd, Concord, NSW 2139 Australia
| | - Rupert W L Leong
- §Concord Repatriation General Hospital, Gastroenterology and Liver Services, Hospital Rd, Concord, NSW 2139 Australia.,¶Department of Gastroenterology, Bankstown-Lidcombe Hospital, Eldridge Rd, Bankstown, NSW 2200 Australia
| | - Aviv Pudipeddi
- From the: ‡Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052 Australia
| | - Diane Redmond
- ¶Department of Gastroenterology, Bankstown-Lidcombe Hospital, Eldridge Rd, Bankstown, NSW 2200 Australia
| | - Valerie C Wasinger
- From the: ‡Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052 Australia;
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Volkmann ER, Hoffmann-Vold AM, Chang YL, Jacobs JP, Tillisch K, Mayer EA, Clements PJ, Hov JR, Kummen M, Midtvedt Ø, Lagishetty V, Chang L, Labus JS, Molberg Ø, Braun J. Systemic sclerosis is associated with specific alterations in gastrointestinal microbiota in two independent cohorts. BMJ Open Gastroenterol 2017; 4:e000134. [PMID: 28761687 PMCID: PMC5508636 DOI: 10.1136/bmjgast-2017-000134] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE To compare faecal microbial composition in patients with systemic sclerosis (SSc) from 2 independent cohorts with controls and to determine whether certain genera are associated with SSc-gastrointestinal tract (GIT) symptoms. DESIGN Adult patients with SSc from the University of California, Los Angeles (UCLA) and Oslo University Hospital (OUH) and healthy controls participated in this study (1:1:1). All participants provided stool specimens for 16S rRNA sequencing. Linear discriminant analysis effect size demonstrated genera with differential expression in SSc. Differential expression analysis for sequence count data identified specific genera associated with GIT symptoms as assessed by the GIT 2.0 questionnaire. RESULTS The UCLA-SSc and OUH-SSc cohorts were similar in age (52.1 and 60.5 years, respectively), disease duration (median (IQR): 6.6 (2.5-16.4) and 7.0 (1.0-19.2) years, respectively), gender distribution (88% and 71%, respectively), and GIT symptoms (mean (SD) total GIT 2.0 scores of 0.7 (0.6) and 0.6 (0.5), respectively). Principal coordinate analysis illustrated significant microbial community differences between SSc and controls (UCLA: p=0.001; OUH: p=0.002). Patients with SSc had significantly lower levels of commensal genera deemed to protect against inflammation, such as Bacteroides (UCLA and OUH), Faecalibacterium (UCLA), Clostridium (OUH); and significantly higher levels of pathobiont genera, such as Fusobacterium (UCLA), compared with controls. Increased abundance of Clostridium was associated with less severe GIT symptoms in both cohorts. CONCLUSIONS The present analysis detected specific aberrations in the lower GIT microbiota of patients with SSc from 2 geographically and ethnically distinct cohorts. These findings suggest that GIT dysbiosis may be a pathological feature of the SSc disease state.
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Affiliation(s)
- Elizabeth R Volkmann
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, USA
| | | | - Yu-Ling Chang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, USA
| | - Jonathan P Jacobs
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, USA
| | - Kirsten Tillisch
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, USA
| | - Emeran A Mayer
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, USA
| | - Philip J Clements
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, USA
| | - Johannes R Hov
- Division of Surgery, Inflammatory Diseases and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Division of Surgery, Inflammatory Diseases and Transplantation, Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Martin Kummen
- Division of Surgery, Inflammatory Diseases and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Division of Surgery, Inflammatory Diseases and Transplantation, Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Øyvind Midtvedt
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Venu Lagishetty
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, USA
| | - Lin Chang
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, USA
| | - Jennifer S Labus
- Department of Medicine, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, USA
| | - Øyvind Molberg
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, USA
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39
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Petriz BA, Franco OL. Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease. Front Chem 2017; 5:4. [PMID: 28184370 PMCID: PMC5266679 DOI: 10.3389/fchem.2017.00004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/13/2017] [Indexed: 12/20/2022] Open
Abstract
Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut. The advances in molecular separation methods coupled with mass spectrometry (e.g., LC-MS/MS) and proteome bioinformatics have been fundamental in these novel large-scale metaproteomic studies, which have further been performed in a wide range of samples including soil, plant and human environments. Metaproteomic studies will make major progress if a comprehensive database covering the genes and expresses proteins from all gut microbial species is developed. To this end, we here present some of the main limitations of metaproteomic studies in complex microbiota environments, such as the gut, also addressing the up-to-date pipelines in sample preparation prior to fractionation/separation and mass spectrometry analysis. In addition, a novel approach to the limitations of metagenomic databases is also discussed. Finally, prospects are addressed regarding the application of metaproteomic analysis using a unified host-microbiome gene database and other meta-OMICs platforms.
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Affiliation(s)
- Bernardo A Petriz
- Department of Health, Molecular and Physiologic Adaptations to Exercise, Centro Universitário do Distrito Federal Brasília, Brazil
| | - Octávio L Franco
- S-Inova Biotech, Universidade Católica Dom Bosco Campo Grande, Brazil
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40
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Mottawea W, Chiang CK, Mühlbauer M, Starr AE, Butcher J, Abujamel T, Deeke SA, Brandel A, Zhou H, Shokralla S, Hajibabaei M, Singleton R, Benchimol EI, Jobin C, Mack DR, Figeys D, Stintzi A. Altered intestinal microbiota-host mitochondria crosstalk in new onset Crohn's disease. Nat Commun 2016; 7:13419. [PMID: 27876802 PMCID: PMC5122959 DOI: 10.1038/ncomms13419] [Citation(s) in RCA: 273] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023] Open
Abstract
Intestinal microbial dysbiosis is associated with Crohn's disease (CD). However, the mechanisms leading to the chronic mucosal inflammation that characterizes this disease remain unclear. In this report, we use systems-level approaches to study the interactions between the gut microbiota and host in new-onset paediatric patients to evaluate causality and mechanisms of disease. We report an altered host proteome in CD patients indicative of impaired mitochondrial functions. In particular, mitochondrial proteins implicated in H2S detoxification are downregulated, while the relative abundance of H2S microbial producers is increased. Network correlation analysis reveals that Atopobium parvulum controls the central hub of H2S producers. A. parvulum induces pancolitis in colitis-susceptible interleukin-10-deficient mice and this phenotype requires the presence of the intestinal microbiota. Administrating the H2S scavenger bismuth mitigates A. parvulum-induced colitis in vivo. This study reveals that host–microbiota interactions are disturbed in CD and thus provides mechanistic insights into CD pathogenesis. Crohn's disease is associated with altered intestinal microbiota. Here, the authors show that the microbe Atopobium parvulum is associated with Crohn's disease patients, triggers colitis in a mouse model, and that scavenging microbe-induced hydrogen sulfide improved symptoms in mice.
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Affiliation(s)
- Walid Mottawea
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Cheng-Kang Chiang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Marcus Mühlbauer
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Florida, Gainesville, Florida 32611, USA
| | - Amanda E Starr
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - James Butcher
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Turki Abujamel
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Shelley A Deeke
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Annette Brandel
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Hu Zhou
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shadi Shokralla
- Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Mehrdad Hajibabaei
- Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Ruth Singleton
- Children's Hospital of Eastern Ontario (CHEO) Inflammatory Bowel Disease Centre and CHEO Research Institute, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8L1
| | - Eric I Benchimol
- Children's Hospital of Eastern Ontario (CHEO) Inflammatory Bowel Disease Centre and CHEO Research Institute, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8L1.,Department of Pediatrics, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Christian Jobin
- Department of Medicine, Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida 32611, USA
| | - David R Mack
- Children's Hospital of Eastern Ontario (CHEO) Inflammatory Bowel Disease Centre and CHEO Research Institute, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8L1.,Department of Pediatrics, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Department of Chemistry and Biomolecular Sciences, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
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41
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Lu Q, Liu C, Liu Y, Zhang N, Deng H, Zhang Z. Serum markers of pre-eclampsia identified on proteomics. J Obstet Gynaecol Res 2016; 42:1111-8. [PMID: 27279411 DOI: 10.1111/jog.13037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/24/2016] [Accepted: 03/26/2016] [Indexed: 12/13/2022]
Abstract
AIM Pre-eclampsia (PE) is a disorder of pregnancy associated with maternal and fetal mortality and morbidity. The aim of the present study was to use proteomics to identify biomarkers of, and elucidate the pathogenesis of, PE. METHODS Serum samples were analyzed using peptide ligand library beads (PLLB) on liquid chromatography-mass spectrometry/mass spectrometry. Retinol-binding protein 4 (RBP4) was used as the target protein for further validation on enzyme-linked immunosorbent assay, immunohistochemistry and real-time polymerase chain reaction. Transwell invasion assay was used to evaluate whether RBP4 affects the invasive ability of trophoblast tumor cells. RESULTS Twenty upregulated and 17 downregulated proteins were differentially expressed between severe PE patients and healthy pregnant women. Those proteins were further classified according to molecular function and biological process according to the gene ontology terms. RBP4 concentration was significantly lower in women with severe PE than in those with healthy pregnancy. CONCLUSIONS RBP4 is able to function as biomarker to distinguish severe PE from normal pregnancy. More importantly, these results may shed light on the role of RPB4 in the pathogenesis in PE. Further studies are required to validate these results, and determine the precise role of RBP4 in the pathogenesis of PE.
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Affiliation(s)
- Qi Lu
- Department of Obstetrics and Gynecology, Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing, China
| | - Chongdong Liu
- Department of Obstetrics and Gynecology, Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing, China
| | - Ye Liu
- Department of Obstetrics and Gynecology, Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing, China
| | - Nawei Zhang
- Department of Obstetrics and Gynecology, Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing, China
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhenyu Zhang
- Department of Obstetrics and Gynecology, Beijing Chaoyang Hospital Affiliated Capital Medical University, Beijing, China.
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42
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Valles-Colomer M, Darzi Y, Vieira-Silva S, Falony G, Raes J, Joossens M. Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines. J Crohns Colitis 2016; 10:735-46. [PMID: 26802086 DOI: 10.1093/ecco-jcc/jjw024] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/15/2016] [Indexed: 12/13/2022]
Abstract
Meta-omics [metagenomics, metatranscriptomics, and metaproteomics] are rapidly expanding our knowledge of the gut microbiota in health and disease. These technologies are increasingly used in inflammatory bowel disease [IBD] research. Yet, meta-omics data analysis, interpretation, and among-study comparison remain challenging. In this review we discuss the role these techniques are playing in IBD research, highlighting their strengths and limitations. We give guidelines on proper sample collection and preparation methods, and on performing the analyses and interpreting the results, reporting available user-friendly tools and pipelines.
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Affiliation(s)
- Mireia Valles-Colomer
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Youssef Darzi
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sara Vieira-Silva
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Marie Joossens
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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43
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Li J, Wei Z, Hakonarson H. Application of computational methods in genetic study of inflammatory bowel disease. World J Gastroenterol 2016; 22:949-960. [PMID: 26811639 PMCID: PMC4716047 DOI: 10.3748/wjg.v22.i3.949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/04/2015] [Accepted: 11/24/2015] [Indexed: 02/06/2023] Open
Abstract
Genetic factors play an important role in the etiology of inflammatory bowel disease (IBD). The launch of genome-wide association study (GWAS) represents a landmark in the genetic study of human complex disease. Concurrently, computational methods have undergone rapid development during the past a few years, which led to the identification of numerous disease susceptibility loci. IBD is one of the successful examples of GWAS and related analyses. A total of 163 genetic loci and multiple signaling pathways have been identified to be associated with IBD. Pleiotropic effects were found for many of these loci; and risk prediction models were built based on a broad spectrum of genetic variants. Important gene-gene, gene-environment interactions and key contributions of gut microbiome are being discovered. Here we will review the different types of analyses that have been applied to IBD genetic study, discuss the computational methods for each type of analysis, and summarize the discoveries made in IBD research with the application of these methods.
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44
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45
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Mayne J, Ning Z, Zhang X, Starr AE, Chen R, Deeke S, Chiang CK, Xu B, Wen M, Cheng K, Seebun D, Star A, Moore JI, Figeys D. Bottom-Up Proteomics (2013-2015): Keeping up in the Era of Systems Biology. Anal Chem 2015; 88:95-121. [PMID: 26558748 DOI: 10.1021/acs.analchem.5b04230] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Xu Zhang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Amanda E Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Rui Chen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Shelley Deeke
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Bo Xu
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Ming Wen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Kai Cheng
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Deeptee Seebun
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Alexandra Star
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Jasmine I Moore
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
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46
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The role of IL-10 in microbiome-associated immune modulation and disease tolerance. Cytokine 2015; 75:291-301. [DOI: 10.1016/j.cyto.2014.11.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 02/06/2023]
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47
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Wilmes P, Heintz-Buschart A, Bond PL. A decade of metaproteomics: where we stand and what the future holds. Proteomics 2015; 15:3409-17. [PMID: 26315987 PMCID: PMC5049639 DOI: 10.1002/pmic.201500183] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/06/2015] [Accepted: 08/05/2015] [Indexed: 12/21/2022]
Abstract
We are living through exciting times during which we are able to unravel the “microbial dark matter” in and around us through the application of high‐resolution “meta‐omics”. Metaproteomics offers the ability to resolve the major catalytic units of microbial populations and thereby allows the establishment of genotype‐phenotype linkages from in situ samples. A decade has passed since the term “metaproteomics” was first coined and corresponding analyses were carried out on mixed microbial communities. Since then metaproteomics has yielded many important insights into microbial ecosystem function in the various environmental settings where it has been applied. Although initial progress in analytical capacities and resulting numbers of proteins identified was extremely fast, this trend slowed rapidly. Here, we discuss several representative metaproteomic investigations of activated sludge, acid mine drainage biofilms, freshwater and seawater microbial communities, soil, and human gut microbiota. By using these case studies, we highlight current challenges and possible solutions for metaproteomics to realize its full potential, i.e. to enable conclusive links between microbial community composition, physiology, function, interactions, ecology, and evolution in situ.
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Affiliation(s)
- Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Philip L Bond
- Advanced Water Management Centre, University of Queensland, Brisbane, Australia
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Vázquez-Castellanos JF, Serrano-Villar S, Latorre A, Artacho A, Ferrús ML, Madrid N, Vallejo A, Sainz T, Martínez-Botas J, Ferrando-Martínez S, Vera M, Dronda F, Leal M, Del Romero J, Moreno S, Estrada V, Gosalbes MJ, Moya A. Altered metabolism of gut microbiota contributes to chronic immune activation in HIV-infected individuals. Mucosal Immunol 2015; 8:760-72. [PMID: 25407519 DOI: 10.1038/mi.2014.107] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 10/06/2014] [Indexed: 02/07/2023]
Abstract
Altered interplay between gut mucosa and microbiota during treated HIV infection may possibly contribute to increased bacterial translocation and chronic immune activation, both of which are predictors of morbidity and mortality. Although a dysbiotic gut microbiota has recently been reported in HIV+ individuals, the metagenome gene pool associated with HIV infection remains unknown. The aim of this study is to characterize the functional gene content of gut microbiota in HIV+ patients and to define the metabolic pathways of this bacterial community, which is potentially associated with immune dysfunction. We determined systemic markers of innate and adaptive immunity in a cohort of HIV-infected individuals on successful antiretroviral therapy without comorbidities and in healthy non-HIV-infected subjects. Metagenome sequencing revealed an altered functional profile, with enrichment of the genes involved in various pathogenic processes, lipopolysaccharide biosynthesis, bacterial translocation, and other inflammatory pathways. In contrast, we observed depletion of genes involved in amino acid metabolism and energy processes. Bayesian networks showed significant interactions between the bacterial community, their altered metabolic pathways, and systemic markers of immune dysfunction. This study reveals altered metabolic activity of microbiota and provides novel insight into the potential host-microbiota interactions driving the sustained inflammatory state in successfully treated HIV-infected patients.
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Affiliation(s)
- J F Vázquez-Castellanos
- 1] Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain [2] CIBER on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - S Serrano-Villar
- Department of Infectious Diseases, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - A Latorre
- 1] Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain [2] CIBER on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A Artacho
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - M L Ferrús
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain
| | - N Madrid
- Department of Infectious Diseases, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - A Vallejo
- Department of Infectious Diseases, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - T Sainz
- 1] Laboratory of Molecular Immune Biology, University Hospital Gregorio Marañón and Gregorio Marañón Research Institute, Madrid, Spain [2] CIBER on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - J Martínez-Botas
- 1] Department of Biochemistry, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain [2] CIBER on Obesity and Nutrition Pathophysiology (CIBEROBN), Madrid, Spain
| | - S Ferrando-Martínez
- 1] Laboratory of Molecular Immune Biology, University Hospital Gregorio Marañón and Gregorio Marañón Research Institute, Madrid, Spain [2] CIBER on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain [3] Laboratory of Immunovirology, Department of Infectious Diseases, Biomedicine Institute of Seville (IBIS), University Hospital Virgen del Rocío, Sevilla, Spain
| | - M Vera
- Centro Sandoval, Madrid, Spain
| | - F Dronda
- Department of Infectious Diseases, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - M Leal
- Laboratory of Immunovirology, Department of Infectious Diseases, Biomedicine Institute of Seville (IBIS), University Hospital Virgen del Rocío, Sevilla, Spain
| | | | - S Moreno
- Department of Infectious Diseases, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - V Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
| | - M J Gosalbes
- 1] Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain [2] CIBER on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A Moya
- 1] Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública) y el Instituto Cavanilles de Biodiversitad y Biología Evolutiva (Universitat de València), Valencia, Spain [2] CIBER on Epidemiology and Public Health (CIBERESP), Madrid, Spain
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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: 323] [Impact Index Per Article: 35.9] [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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50
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Xiong W, Abraham PE, Li Z, Pan C, Hettich RL. Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota. Proteomics 2015; 15:3424-38. [PMID: 25914197 DOI: 10.1002/pmic.201400571] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/08/2015] [Accepted: 04/21/2015] [Indexed: 01/12/2023]
Abstract
The human gastrointestinal tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome is not merely a collection of opportunistic parasites, but rather provides important functions to the host that are absolutely critical to many aspects of health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial metaproteomics provides the ability to characterize the human gut microbiota functions and metabolic activities at a remarkably deep level, revealing information about microbiome development and stability as well as their interactions with their human host. Generally, microbial and human proteins can be extracted and then measured by high performance MS-based proteomics technology. Here, we review the field of human gut microbiome metaproteomics, with a focus on the experimental and informatics considerations involved in characterizing systems ranging from low-complexity model gut microbiota in gnotobiotic mice, to the emerging gut microbiome in the GI tract of newborn human infants, and finally to an established gut microbiota in human adults.
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Affiliation(s)
- Weili Xiong
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Paul E Abraham
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zhou Li
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Chongle Pan
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert L Hettich
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
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