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Kiran A, Hanachi M, Alsayed N, Fassatoui M, Oduaran OH, Allali I, Maslamoney S, Meintjes A, Zass L, Rocha JD, Kefi R, Benkahla A, Ghedira K, Panji S, Mulder N, Fadlelmola FM, Souiai O. The African Human Microbiome Portal: a public web portal of curated metagenomic metadata. Database (Oxford) 2024; 2024:baad092. [PMID: 38204360 PMCID: PMC10782148 DOI: 10.1093/database/baad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/03/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various public repositories prior to cleaning, curation and harmonization according to a pre-established guideline and using ontology terms. These metadata sets can be accessed at https://microbiome.h3abionet.org/. This web portal is open access and offers an interactive visualization of 14 889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user's applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome. Database URL: https://microbiome.h3abionet.org/.
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Affiliation(s)
| | - Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
- Faculty of Science of Bizerte, University of Carthage, Tunis, Tunisia
| | - Nihad Alsayed
- Kush Centre for Genomics and Biomedical Informatics, Biotechnology Perspectives Organization, Khartoum, Sudan
| | - Meriem Fassatoui
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Ovokeraye H Oduaran
- The Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Suresh Maslamoney
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Ayton Meintjes
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Jorge Da Rocha
- The Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Rym Kefi
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Faisal M Fadlelmola
- Kush Centre for Genomics and Biomedical Informatics, Biotechnology Perspectives Organization, Khartoum, Sudan
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
- Malawi-Liverpool-Wellcome Trust, Blantyre 3, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK
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2
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El Ouafi Z, Rhalem W, Habib N, Idrissi Azami A, Sehli S, Al Idrissi N, Bakkali F, Abderrazak R, Merzouki M, Allali I, Amzazi S, Nejjari C, Ghazal H. Molecular Modeling Targeting the ACE2 Receptor with Cannabis sativa's Active Ingredients for Antiviral Drug Discovery against SARS-CoV-2 Infections. Bioinform Biol Insights 2022; 16:11779322221145380. [PMID: 36582392 PMCID: PMC9793058 DOI: 10.1177/11779322221145380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/25/2022] [Indexed: 12/25/2022] Open
Abstract
The emergence of a novel coronavirus that later on rendered a global pandemic, caused desperation within the communities and drove increased interest in exploring medicinal plant-based therapeutics to treat and prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infections. Many medicinal plants have been reported to have antiviral, anti-inflammatory, and immunomodulatory effects that hinder, cure, or ease the symptoms of COVID-19 infection. This exploratory study seeks to dock the active components of Cannabis sativa, a natural plant with several pharmacological and biological properties, with the angiotensin-converting enzyme II (ACE2) receptor. A total of 3 C. sativa active components have been found to bind to the ACE2 protein active site and could inhibit spike binding, although they do not compete directly with the receptor-binding domain (RBD) of SARS-CoV-2. 6-Prenylapigenin, cannabivarin (CBN-C3), and Δ8-tetrahydrocannabinolic acid-A (Δ8-THCA) have a greater affinity (-8.3, -8.3, and -8.0 kcal/mol, respectively) and satisfactory interaction with ACE2 than its inhibitor MLN-4760 (-7.1 kcal/mol). These potential drugs with higher affinity for the ACE2 receptor and adequate absorption, distribution, metabolism, excretion, and toxicity (ADMET) values are candidates for treating or preventing SARS-CoV-2 infections. In vitro and in vivo investigations are needed to evaluate further the efficacy and toxicity of these hit compounds.
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Affiliation(s)
- Zainab El Ouafi
- Laboratory of Genomics and
Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences
Casablanca, Casablanca, Morocco
| | - Wajih Rhalem
- Electronic Systems, Sensors and
Nanobiotechnologies (E2SN), École Nationale Supérieure des Arts et Métiers (ENSAM),
Mohammed V University, Rabat, Morocco
| | - Nihal Habib
- Laboratory of Genomics and
Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences
Casablanca, Casablanca, Morocco
| | - Abdellah Idrissi Azami
- Laboratory of Genomics and
Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences
Casablanca, Casablanca, Morocco
| | - Sofia Sehli
- Laboratory of Genomics and
Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences
Casablanca, Casablanca, Morocco
| | - Najib Al Idrissi
- Department of Surgery, School of
Medicine, Mohammed VI University of Health Sciences Casablanca, Casablanca,
Morocco
| | - Fadil Bakkali
- Toxicology Laboratory, School of
Medicine, Mohammed VI University of Health Sciences (UM6SS) Casablanca, Casablanca,
Morocco
| | - Rfaki Abderrazak
- National Center for Scientific and
Technical Research (CNRST), Rabat, Morocco
| | - Mohamed Merzouki
- Bioengineering Laboratory, Faculty of
Science and Technologies, University of Sultan Moulay Slimane, Beni Mellal,
Morocco
| | - Imane Allali
- Laboratory of Human Pathologies
Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human
Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat,
Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of Human Pathologies
Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human
Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat,
Rabat, Morocco
| | - Chakib Nejjari
- Department of Epidemiology and
Biostatistics, International School of Public Health, Mohammed VI University of
Health Sciences Casablanca, Casablanca, Morocco,Department of Epidemiology and Public
Health, Faculty of Medicine, University Sidi Mohammed Ben Abdellah, Fes,
Morocco
| | - Hassan Ghazal
- Laboratory of Genomics and
Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences
Casablanca, Casablanca, Morocco,Electronic Systems, Sensors and
Nanobiotechnologies (E2SN), École Nationale Supérieure des Arts et Métiers (ENSAM),
Mohammed V University, Rabat, Morocco,National Center for Scientific and
Technical Research (CNRST), Rabat, Morocco,Hassan Ghazal, Laboratory of Genomics and
Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences
Casablanca, Bld Mohammed Taieb Naciri, Hay Hassani, Casablanca, 82 403, Morocco.
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3
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Delgado-Diaz DJ, Jesaveluk B, Hayward JA, Tyssen D, Alisoltani A, Potgieter M, Bell L, Ross E, Iranzadeh A, Allali I, Dabee S, Barnabas S, Gamieldien H, Blackburn JM, Mulder N, Smith SB, Edwards VL, Burgener AD, Bekker LG, Ravel J, Passmore JAS, Masson L, Hearps AC, Tachedjian G. Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression. Microbiome 2022; 10:141. [PMID: 36045402 PMCID: PMC9429363 DOI: 10.1186/s40168-022-01337-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Women with a cervicovaginal microbiota dominated by Lactobacillus spp. are at reduced risk of acquiring sexually transmitted infections including HIV, but the biological mechanisms involved remain poorly defined. Here, we performed metaproteomics on vaginal swab samples from young South African women (n = 113) and transcriptomics analysis of cervicovaginal epithelial cell cultures to examine the ability of lactic acid, a metabolite produced by cervicovaginal lactobacilli, to modulate genital epithelial barrier function. RESULTS Compared to women with Lactobacillus-depleted microbiota, women dominated by vaginal lactobacilli exhibit higher abundance of bacterial lactate dehydrogenase, a key enzyme responsible for lactic acid production, which is independently associated with an increased abundance of epithelial barrier proteins. Physiological concentrations of lactic acid enhance epithelial cell culture barrier integrity and increase intercellular junctional molecule expression. CONCLUSIONS These findings reveal a novel ability of vaginal lactic acid to enhance genital epithelial barrier integrity that may help prevent invasion by sexually transmitted pathogens. Video abstract.
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Affiliation(s)
- David Jose Delgado-Diaz
- Life Sciences Discipline, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia
- Department of Microbiology, Monash University, Clayton, VIC, 3168, Australia
| | - Brianna Jesaveluk
- Life Sciences Discipline, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia
- Department of Microbiology, Monash University, Clayton, VIC, 3168, Australia
| | - Joshua A Hayward
- Life Sciences Discipline, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia
- Department of Microbiology, Monash University, Clayton, VIC, 3168, Australia
| | - David Tyssen
- Life Sciences Discipline, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia
| | - Arghavan Alisoltani
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, 92521, USA
| | - Matthys Potgieter
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Liam Bell
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Elizabeth Ross
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, 1014, Rabat, Morocco
| | - Smritee Dabee
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98101, USA
| | - Shaun Barnabas
- Family Centre for Research with Ubuntu, Stellenbosch University, Cape Town, 7505, South Africa
| | - Hoyam Gamieldien
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Jonathan M Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Centre for Infectious Diseases Research (CIDRI) in Africa Wellcome Trust Centre, University of Cape Town, Cape Town, 7925, South Africa
| | - Steven B Smith
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vonetta L Edwards
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Adam D Burgener
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Obstetrics and Gynecology, University of Manitoba, Winnipeg, Canada
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Linda-Gail Bekker
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, 7925, South Africa
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jo-Ann S Passmore
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, 4013, South Africa
- National Health Laboratory Service, Cape Town, 7925, South Africa
| | - Lindi Masson
- Life Sciences Discipline, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, 4013, South Africa
- Central Clinical School, Monash University, Melbourne, 3004, Australia
| | - Anna C Hearps
- Life Sciences Discipline, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia
- Central Clinical School, Monash University, Melbourne, 3004, Australia
| | - Gilda Tachedjian
- Life Sciences Discipline, Burnet Institute, 85 Commercial Road, Melbourne, VIC, 3004, Australia.
- Department of Microbiology, Monash University, Clayton, VIC, 3168, Australia.
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia.
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4
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Alisoltani A, Manhanzva MT, Potgieter M, Balle C, Bell L, Ross E, Iranzadeh A, du Plessis M, Radzey N, McDonald Z, Calder B, Allali I, Mulder N, Dabee S, Barnabas S, Gamieldien H, Godzik A, Blackburn JM, Tabb DL, Bekker LG, Jaspan HB, Passmore JAS, Masson L. Correction to: Microbial function and genital inflammation in young South African women at high risk of HIV infection. Microbiome 2022; 10:42. [PMID: 35264249 PMCID: PMC8905787 DOI: 10.1186/s40168-022-01245-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Arghavan Alisoltani
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, 92521, USA
| | - Monalisa T Manhanzva
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Matthys Potgieter
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Christina Balle
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Liam Bell
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Elizabeth Ross
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | | | - Nina Radzey
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Zac McDonald
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Bridget Calder
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology and Genomic Center of Human Pathologies, Mohammed V University, Rabat, Morocco
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Centre for Infectious Diseases Research (CIDRI) in Africa Wellcome Trust Centre, University of Cape Town, Cape Town, 7925, South Africa
| | - Smritee Dabee
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Seattle Children's Research Institute, University of Washington, Seattle, WA, 98101, USA
| | - Shaun Barnabas
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Hoyam Gamieldien
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Adam Godzik
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, 92521, USA
| | - Jonathan M Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
| | - David L Tabb
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Stellenbosch, 7602, South Africa
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Linda-Gail Bekker
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, 7925, South Africa
| | - Heather B Jaspan
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Seattle Children's Research Institute, University of Washington, Seattle, WA, 98101, USA
| | - Jo-Ann S Passmore
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, 4013, South Africa
- National Health Laboratory Service, Cape Town, 7925, South Africa
| | - Lindi Masson
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa.
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, 4013, South Africa.
- Disease Elimination Program, Life Sciences Discipline, Burnet Institute, 85 Commercial Road, Melbourne, Victoria, 3004, Australia.
- Central Clinical School, Monash University, Melbourne, 3004, Australia.
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5
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Correction to: Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. Microbiome 2022; 10:10. [PMID: 35045873 PMCID: PMC8772064 DOI: 10.1186/s40168-022-01226-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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6
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. Microbiome 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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7
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Awany D, Allali I, Chimusa ER. Dissecting genome-wide studies for microbiome-related metabolic diseases. Hum Mol Genet 2021; 29:R73-R80. [PMID: 32478833 DOI: 10.1093/hmg/ddaa105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 05/14/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
Despite the meteoric rise in genome-wide association studies for metabolic diseases (MetD) over the last few years, our understanding of the pathogenesis of these diseases is still far from complete. Recent developments have established that MetD arises from complex interactions between host genetics, the gut microbiome and the environment. However, our knowledge of the genetic and microbiome components involved and the underlying molecular mechanisms remains limited. Here, we review and summarize recent studies investigating the genetic and microbiome basis of MetD. Then, given the critical importance of study-individual's ancestry in these studies, we leverage 4932 whole-genome sequence samples from 18 worldwide ethnic groups to examine genetic diversity in currently reported variants associated with MetD. The analyses show marked differences in gene-specific proportion of pathogenic single-nucleotide polymorphisms (SNPs) and gene-specific SNPs MAFs across ethnic groups, highlighting the importance of population- and ethnic-specific investigations in pinpointing the causative factors for MetD. We conclude with a discussion of research areas where further investigation on interactions between host genetics, microbiome and the environment is needed.
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Affiliation(s)
- Denis Awany
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, Cape Town, South Africa
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Agdal Rabat, B.P, 8007 N.U, Morocco
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, Cape Town, South Africa
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8
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Abstract
African populations are diverse in their ethnicity, language, culture, and genetics. Although plagued by high disease burdens, until recently the continent has largely been excluded from biomedical studies. Along with limitations in research and clinical infrastructure, human capacity, and funding, this omission has resulted in an underrepresentation of African data and disadvantaged African scientists. This review interrogates the relative abundance of biomedical data from Africa, primarily in genomics and other omics. The visibility of African science through publications is also discussed. A challenge encountered in this review is the relative lack of annotation of data on their geographical or population origin, with African countries represented as a single group. In addition to the abovementioned limitations,the global representation of African data may also be attributed to the hesitation to deposit data in public repositories. Whatever the reason, the disparity should be addressed, as African data have enormous value for scientists in Africa and globally.
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Affiliation(s)
- Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; .,Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-AFRICA), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics and Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, University of Tunis El Manar, 1002 Tunis, Tunisia
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 1014 Rabat, Morocco
| | - Yasmina Jaufeerally Fakim
- Biotechnology Unit, Department of Agricultural and Food Science, Faculty of Agriculture, University of Mauritius, Réduit 80837, Mauritius
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9
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Fadlelmola FM, Ghedira K, Hamdi Y, Hanachi M, Radouani F, Allali I, Kiran A, Zass L, Alsayed N, Fassatoui M, Samtal C, Ahmed S, Da Rocha J, Chaqsare S, Sallam RM, Chaouch M, Farahat MA, Ssekagiri A, Parker Z, Adil M, Turkson M, Benchaalia A, Benkahla A, Panji S, Kassim S, Souiai O, Mulder N. H3ABioNet genomic medicine and microbiome data portals hackathon proceedings. Database (Oxford) 2021; 2021:baab016. [PMID: 33864455 PMCID: PMC8052916 DOI: 10.1093/database/baab016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/12/2021] [Accepted: 03/29/2021] [Indexed: 12/23/2022]
Abstract
African genomic medicine and microbiome datasets are usually not well characterized in terms of their origin, making it difficult to find and extract data for specific African ethnic groups or even countries. The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for developing data portals for African genomic medicine and African microbiomes to address this and ran a hackathon to initiate their development. The two portals were designed and significant progress was made in their development during the hackathon. All the participants worked in a very synergistic and collaborative atmosphere in order to achieve the hackathon's goals. The participants were divided into content and technical teams and worked over a period of 6 days. In response to one of the survey questions of what the participants liked the most during the hackathon, 55% of the hackathon participants highlighted the familial and friendly atmosphere, the team work and the diversity of team members and their expertise. This paper describes the preparations for the portals hackathon and the interaction between the participants and reflects upon the lessons learned about its impact on successfully developing the two data portals as well as building scientific expertise of younger African researchers. Database URL: The code for developing the two portals was made publicly available in GitHub repositories: [https://github.com/codemeleon/Database; https://github.com/codemeleon/AfricanMicrobiomePortal].
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Affiliation(s)
- Faisal M Fadlelmola
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Al-Gamaa Ave, Khartoum 11115, Sudan
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis (IPT), 13, Place Pasteur BP 74, Tunis 1002, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, Tunis 1002, Tunisia
| | - Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis (IPT), 13, Place Pasteur BP 74, Tunis 1002, Tunisia
- Faculty of Science of Bizerte, University of Carthage, Zarzouna, Bizerte 7021, Tunisia
| | - Fouzia Radouani
- Research Department, Chlamydiae and Mycoplasmas Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, Casablanca 20360, Morocco
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University, 4 Ibn Battouta Avenue, Rabat, BP 1014 RP, Morocco
- Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Anmol Kiran
- Malawi-Liverpool Wellcome Trust, Clinical Research Programme, PO Box 30096, Chichiri, Blantyre 3, Blantyre, Malawi
| | - Lyndon Zass
- Computational Biology Division, N1.05 Werner Beit North, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Nihad Alsayed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Al-Gamaa Ave, Khartoum 11115, Sudan
| | - Meriem Fassatoui
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, Tunis 1002, Tunisia
| | - Chaimae Samtal
- Faculty of Sciences Dhar El Mahraz, Department of Biology, Genetics Unit, Atlas-Fez 1796, Morocco
| | - Samah Ahmed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Al-Gamaa Ave, Khartoum 11115, Sudan
| | - Jorge Da Rocha
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, 9 Jubilee Road, Parktown, Johannesburg 2193, South Africa
| | - Souad Chaqsare
- National Institute of Health, Informatics Unit, 27 Ibn Batouta Avenue, Agdal, Rabat BP 769, Morocco
| | - Reem M Sallam
- Medical Biochemistry & Molecular Biology, Faculty of Medicine, Ain Shams University, Abassia, Cairo 11381, Egypt
- Department of Basic Medical Sciences, Faculty of Medicine, Galala University, Galala City, Suez 43511, Egypt
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis (IPT), 13, Place Pasteur BP 74, Tunis 1002, Tunisia
| | - Mohammed A Farahat
- Information Systems Department, Faculty of Computers and Artificial Intelligence, Helwan University, Ain Helwan, PO Box 11795, Cairo, Egypt
| | - Alfred Ssekagiri
- Division of Entomology and core molecular Biology/Bioinformatics facility, Uganda Virus Research Institute, 51/59, Nakiwogo Road, Entebbe 31301, Uganda
| | - Ziyaad Parker
- Computational Biology Division, N1.05 Werner Beit North, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Mai Adil
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Al-Gamaa Ave, Khartoum 11115, Sudan
| | - Michael Turkson
- National Institute for Mathematical Sciences, PMB Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Aymen Benchaalia
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis (IPT), 13, Place Pasteur BP 74, Tunis 1002, Tunisia
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis (IPT), 13, Place Pasteur BP 74, Tunis 1002, Tunisia
| | - Sumir Panji
- Computational Biology Division, N1.05 Werner Beit North, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Samar Kassim
- Medical Biochemistry & Molecular Biology, Faculty of Medicine, Ain Shams University, Abassia, Cairo 11381, Egypt
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis (IPT), 13, Place Pasteur BP 74, Tunis 1002, Tunisia
| | - Nicola Mulder
- Computational Biology Division, N1.05 Werner Beit North, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Anzio Road, Observatory, Cape Town 7925, South Africa
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10
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Hamdi Y, Zass L, Othman H, Radouani F, Allali I, Hanachi M, Okeke CJ, Chaouch M, Tendwa MB, Samtal C, Mohamed Sallam R, Alsayed N, Turkson M, Ahmed S, Benkahla A, Romdhane L, Souiai O, Tastan Bishop Ö, Ghedira K, Mohamed Fadlelmola F, Mulder N, Kamal Kassim S. Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects. OMICS 2021; 25:213-233. [PMID: 33794662 DOI: 10.1089/omi.2021.0004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Following the publication of the first human genome, OMICs research, including genomics, transcriptomics, proteomics, and metagenomics, has been on the rise. OMICs studies revealed the complex genetic diversity among human populations and challenged our understandings of genotype-phenotype correlations. Africa, being the cradle of the first modern humans, is distinguished by a large genetic diversity within its populations and rich ethnolinguistic history. However, the available human OMICs tools and databases are not representative of this diversity, therefore creating significant gaps in biomedical research. African scientists, students, and publics are among the key contributors to OMICs systems science. This expert review examines the pressing issues in human OMICs research, education, and development in Africa, as seen through a lens of computational biology, public health relevant technology innovation, critically-informed science governance, and how best to harness OMICs data to benefit health and societies in Africa and beyond. We underscore the disparities between North and Sub-Saharan Africa at different levels. A harmonized African ethnolinguistic classification would help address annotation challenges associated with population diversity. Finally, building on the existing strategic research initiatives, such as the H3Africa and H3ABioNet Consortia, we highly recommend addressing large-scale multidisciplinary research challenges, strengthening research collaborations and knowledge transfer, and enhancing the ability of African researchers to influence and shape national and international research, policy, and funding agendas. This article and analysis contribute to a deeper understanding of past and current challenges in the African OMICs innovation ecosystem, while also offering foresight on future innovation trajectories.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Fouzia Radouani
- Chlamydiae and Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Faculty of Science of Bizerte, Zarzouna, University of Carthage, Tunis, Tunisia
| | - Chiamaka Jessica Okeke
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Maureen Bilinga Tendwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Chaimae Samtal
- Laboratory of Biotechnology, Environment, Agri-food and Health, Faculty of Sciences Dhar El Mahraz-Sidi Mohammed Ben Abdellah University, Fez, Morocco.,University of Mohamed Premier, Oujda, Morocco
| | - Reem Mohamed Sallam
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.,Department of Basic Medical Sciences, Faculty of Medicine, Galala University, Suez, Egypt
| | - Nihad Alsayed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Michael Turkson
- The National Institute for Mathematical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samah Ahmed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Faculty of Science of Bizerte, Zarzouna, University of Carthage, Tunis, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Faisal Mohamed Fadlelmola
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Samar Kamal Kassim
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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11
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Sehli S, Allali I, Chahboune R, Bakri Y, Al Idrissi N, Hamdi S, Nejjari C, Amzazi S, Ghazal H. Metagenomics Approaches to Investigate the Gut Microbiome of COVID-19 Patients. Bioinform Biol Insights 2021; 15:1177932221999428. [PMID: 33786001 PMCID: PMC7961713 DOI: 10.1177/1177932221999428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Over the last decade, it has become increasingly apparent that the microbiome is a central component in human well-being and illness. However, to establish innovative therapeutic methods, it is crucial to learn more about the microbiota. Thereby, the area of metagenomics and associated bioinformatics methods and tools has become considerable in the study of the human microbiome biodiversity. The application of these metagenomics approaches to studying the gut microbiome in COVID-19 patients could be one of the promising areas of research in the fight against the SARS-CoV-2 infection and disparity. Therefore, understanding how the gut microbiome is affected by or could affect the SARS-CoV-2 is very important. Herein, we present an overview of approaches and methods used in the current published studies on COVID-19 patients and the gut microbiome. The accuracy of these researches depends on the appropriate choice and the optimal use of the metagenomics bioinformatics platforms and tools. Interestingly, most studies reported that COVID-19 patients' microbiota are enriched with opportunistic microorganisms. The choice and use of appropriate computational tools and techniques to accurately investigate the gut microbiota is therefore critical in determining the appropriate microbiome profile for diagnosis and the most reliable antiviral or preventive microbial composition.
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Affiliation(s)
- Sofia Sehli
- Department of fundamental sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Rajaa Chahboune
- School of Medicine and Pharmacy, University Abdelmalek Essaâdi, Tangier, Morocco
| | - Youssef Bakri
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Najib Al Idrissi
- Department of Surgery, School of medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Salsabil Hamdi
- Environmental Health Laboratory, Department of Research, Institut Pasteur Du Maroc, Casablanca, Morocco
| | - Chakib Nejjari
- Department of Epidemiology and Biostatistics, International School of Public Health, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Department of Epidemiology and Public Health, Faculty of Medicine, University Sidi Mohammed Ben Abdellah, Fez, Morocco
| | - Saaïd Amzazi
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Hassan Ghazal
- Department of fundamental sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Scientific Department, National Centre for Scientific and Technical Research, Rabat, Morocco
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12
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El Jaddaoui I, Allali I, Sehli S, Ouldim K, Hamdi S, Al Idrissi N, Nejjari C, Amzazi S, Bakri Y, Ghazal H. Cancer Omics in Africa: Present and Prospects. Front Oncol 2020; 10:606428. [PMID: 33425763 PMCID: PMC7793679 DOI: 10.3389/fonc.2020.606428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022] Open
Abstract
During the last century, cancer biology has been arguably one of the most investigated research fields. To gain deeper insight into cancer mechanisms, scientists have been attempting to integrate multi omics data in cancer research. Cancer genomics, transcriptomics, metabolomics, proteomics, and metagenomics are the main multi omics strategies used currently in the diagnosis, prognosis, treatment, and biomarker discovery in cancer. In this review, we describe the use of different multi omics strategies in cancer research in the African continent and discuss the main challenges facing the implementation of these approaches in African countries such as the lack of training programs in bioinformatics in general and omics strategies in particular and suggest paths to address deficiencies. As a way forward, we advocate for the establishment of an "African Cancer Genomics Consortium" to promote intracontinental collaborative projects and enhance engagement in research activities that address indigenous aspects for cancer precision medicine.
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Affiliation(s)
- Islam El Jaddaoui
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Sofia Sehli
- Department of Fundamental Sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | | | - Salsabil Hamdi
- Environmental Health Laboratory, Pasteur Institute, Casablanca, Morocco
| | - Najib Al Idrissi
- Department of Surgery, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Chakib Nejjari
- Department of Medicine, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Saaïd Amzazi
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Youssef Bakri
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Hassan Ghazal
- Department of Fundamental Sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- National Center for Scientific and Technical Research, Rabat, Morocco
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13
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Hassan R, Allali I, Agamah FE, Elsheikh SSM, Thomford NE, Dandara C, Chimusa ER. Drug response in association with pharmacogenomics and pharmacomicrobiomics: towards a better personalized medicine. Brief Bioinform 2020; 22:6012864. [PMID: 33253350 DOI: 10.1093/bib/bbaa292] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/19/2020] [Accepted: 10/03/2020] [Indexed: 12/15/2022] Open
Abstract
Researchers have long been presented with the challenge imposed by the role of genetic heterogeneity in drug response. For many years, Pharmacogenomics and pharmacomicrobiomics has been investigating the influence of an individual's genetic background to drug response and disposition. More recently, the human gut microbiome has proven to play a crucial role in the way patients respond to different therapeutic drugs and it has been shown that by understanding the composition of the human microbiome, we can improve the drug efficacy and effectively identify drug targets. However, our knowledge on the effect of host genetics on specific gut microbes related to variation in drug metabolizing enzymes, the drug remains limited and therefore limits the application of joint host-microbiome genome-wide association studies. In this paper, we provide a historical overview of the complex interactions between the host, human microbiome and drugs. While discussing applications, challenges and opportunities of these studies, we draw attention to the critical need for inclusion of diverse populations and the development of an innovative and combined pharmacogenomics and pharmacomicrobiomics approach, that may provide an important basis in personalized medicine.
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Affiliation(s)
- Radia Hassan
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | - Imane Allali
- Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Morocco
| | - Francis E Agamah
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | | | - Nicholas E Thomford
- Lecturers at the Department of Medical Biochemistry School of Medical Sciences, University of Cape Coast, Ghana
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town
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14
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Alosaimi S, Bandiang A, van Biljon N, Awany D, Thami PK, Tchamga MSS, Kiran A, Messaoud O, Hassan RIM, Mugo J, Ahmed A, Bope CD, Allali I, Mazandu GK, Mulder NJ, Chimusa ER. A broad survey of DNA sequence data simulation tools. Brief Funct Genomics 2020; 19:49-59. [PMID: 31867604 DOI: 10.1093/bfgp/elz033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 10/27/2019] [Accepted: 11/04/2019] [Indexed: 11/12/2022] Open
Abstract
In silico DNA sequence generation is a powerful technology to evaluate and validate bioinformatics tools, and accordingly more than 35 DNA sequence simulation tools have been developed. With such a diverse array of tools to choose from, an important question is: Which tool should be used for a desired outcome? This question is largely unanswered as documentation for many of these DNA simulation tools is sparse. To address this, we performed a review of DNA sequence simulation tools developed to date and evaluated 20 state-of-art DNA sequence simulation tools on their ability to produce accurate reads based on their implemented sequence error model. We provide a succinct description of each tool and suggest which tool is most appropriate for the given different scenarios. Given the multitude of similar yet non-identical tools, researchers can use this review as a guide to inform their choice of DNA sequence simulation tool. This paves the way towards assessing existing tools in a unified framework, as well as enabling different simulation scenario analysis within the same framework.
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Affiliation(s)
- Shatha Alosaimi
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Armand Bandiang
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Noelle van Biljon
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Denis Awany
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Prisca K Thami
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Milaine S S Tchamga
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anmol Kiran
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Edinburgh University, Edinburgh, UK
| | - Olfa Messaoud
- Université de Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 Génomique Biomédicale et Oncogénétique, Tunis, 1002, Tunisia
| | - Radia Ismaeel Mohammed Hassan
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jacquiline Mugo
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Azza Ahmed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Sudan
| | - Christian D Bope
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gaston K Mazandu
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,African Institute for Mathematical Sciences (AIMS), Cape Town, South Africa
| | - Nicola J Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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15
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Alisoltani A, Manhanzva MT, Potgieter M, Balle C, Bell L, Ross E, Iranzadeh A, du Plessis M, Radzey N, McDonald Z, Calder B, Allali I, Mulder N, Dabee S, Barnabas S, Gamieldien H, Godzik A, Blackburn JM, Tabb DL, Bekker LG, Jaspan HB, Passmore JAS, Masson L. Microbial function and genital inflammation in young South African women at high risk of HIV infection. Microbiome 2020; 8:165. [PMID: 33220709 PMCID: PMC7679981 DOI: 10.1186/s40168-020-00932-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Female genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile; however, the relative importance of microbial activities has not been established. Since proteins are key elements representing actual microbial functions, this study utilized metaproteomics to evaluate the relationship between FGT microbial function and inflammation in 113 young and adolescent South African women at high risk of HIV infection. Women were grouped as having low, medium, or high FGT inflammation by K-means clustering according to pro-inflammatory cytokine concentrations. RESULTS A total of 3186 microbial and human proteins were identified in lateral vaginal wall swabs using liquid chromatography-tandem mass spectrometry, while 94 microbial taxa were included in the taxonomic analysis. Both metaproteomics and 16S rRNA gene sequencing analyses showed increased non-optimal bacteria and decreased lactobacilli in women with FGT inflammatory profiles. However, differences in the predicted relative abundance of most bacteria were observed between 16S rRNA gene sequencing and metaproteomics analyses. Bacterial protein functional annotations (gene ontology) predicted inflammatory cytokine profiles more accurately than bacterial relative abundance determined by 16S rRNA gene sequence analysis, as well as functional predictions based on 16S rRNA gene sequence data (p < 0.0001). The majority of microbial biological processes were underrepresented in women with high inflammation compared to those with low inflammation, including a Lactobacillus-associated signature of reduced cell wall organization and peptidoglycan biosynthesis. This signature remained associated with high FGT inflammation in a subset of 74 women 9 weeks later, was upheld after adjusting for Lactobacillus relative abundance, and was associated with in vitro inflammatory cytokine responses to Lactobacillus isolates from the same women. Reduced cell wall organization and peptidoglycan biosynthesis were also associated with high FGT inflammation in an independent sample of ten women. CONCLUSIONS Both the presence of specific microbial taxa in the FGT and their properties and activities are critical determinants of FGT inflammation. Our findings support those of previous studies suggesting that peptidoglycan is directly immunosuppressive, and identify a possible avenue for biotherapeutic development to reduce inflammation in the FGT. To facilitate further investigations of microbial activities, we have developed the FGT-DB application that is available at http://fgtdb.org/ . Video Abstract.
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Affiliation(s)
- Arghavan Alisoltani
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, 92521, USA
| | - Monalisa T Manhanzva
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Matthys Potgieter
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Christina Balle
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Liam Bell
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Elizabeth Ross
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | | | - Nina Radzey
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Zac McDonald
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Bridget Calder
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology and Genomic Center of Human Pathologies, Mohammed V University, Rabat, Morocco
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Centre for Infectious Diseases Research (CIDRI) in Africa Wellcome Trust Centre, University of Cape Town, Cape Town, 7925, South Africa
| | - Smritee Dabee
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Seattle Children's Research Institute, University of Washington, Seattle, WA, 98101, USA
| | - Shaun Barnabas
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Hoyam Gamieldien
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Adam Godzik
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, 92521, USA
| | - Jonathan M Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
| | - David L Tabb
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Stellenbosch, 7602, South Africa
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Linda-Gail Bekker
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, 7925, South Africa
| | - Heather B Jaspan
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Seattle Children's Research Institute, University of Washington, Seattle, WA, 98101, USA
| | - Jo-Ann S Passmore
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, 4013, South Africa
- National Health Laboratory Service, Cape Town, 7925, South Africa
| | - Lindi Masson
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa.
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, 4013, South Africa.
- Disease Elimination Program, Life Sciences Discipline, Burnet Institute, 85 Commercial Road, Melbourne, Victoria, 3004, Australia.
- Central Clinical School, Monash University, Melbourne, 3004, Australia.
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16
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Laamarti M, Alouane T, Kartti S, Chemao-Elfihri MW, Hakmi M, Essabbar A, Laamarti M, Hlali H, Bendani H, Boumajdi N, Benhrif O, Allam L, El Hafidi N, El Jaoudi R, Allali I, Marchoudi N, Fekkak J, Benrahma H, Nejjari C, Amzazi S, Belyamani L, Ibrahimi A. Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. PLoS One 2020; 15:e0240345. [PMID: 33170902 PMCID: PMC7654798 DOI: 10.1371/journal.pone.0240345] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (http://covid-19.medbiotech.ma) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.
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Affiliation(s)
- Meriem Laamarti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Tarek Alouane
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - M. W. Chemao-Elfihri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Abdelomunim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Mohamed Laamarti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Haitam Hlali
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Houda Bendani
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Nassma Boumajdi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Oussama Benhrif
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Loubna Allam
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Naima El Hafidi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Rachid El Jaoudi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | | | - Jamal Fekkak
- Anoual Laboratory of Radio-Immuno Analysis, Casablanca, Morocco
| | - Houda Benrahma
- Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Chakib Nejjari
- International School of Public Health, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Saaid Amzazi
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
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17
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Shome S, Parra RG, Fatima N, Monzon AM, Cuypers B, Moosa Y, Coimbra NDR, Assis J, Giner-Delgado C, Dönertaş HM, Cuesta-Astroz Y, Saarunya G, Allali I, Gupta S, Srivastava A, Kalsan M, Valdivia C, J Olguin-Orellana G, Papadimitriou S, Parisi D, Kristensen NP, Rib L, Guebila MB, Bauer E, Zaffaroni G, Bekkar A, Ashano E, Paladin L, Necci M, Moreyra NN, Rydén M, Villalobos-Solís J, Papadopoulos N, Rafael C, Karakulak T, Kaya Y, Gladbach Y, Dhanda SK, Šoštarić N, Alex A, DeBlasio D, Rahman F. Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers. F1000Res 2019; 8. [PMID: 31508204 PMCID: PMC6720036 DOI: 10.12688/f1000research.20408.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/26/2019] [Indexed: 11/20/2022] Open
Abstract
Regional Student Groups (RSGs) of the International Society for Computational Biology Student Council (ISCB-SC) have been instrumental to connect computational biologists globally and to create more awareness about bioinformatics education. This article highlights the initiatives carried out by the RSGs both nationally and internationally to strengthen the present and future of the bioinformatics community. Moreover, we discuss the future directions the organization will take and the challenges to advance further in the ISCB-SC main mission: "Nurture the new generation of computational biologists".
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Affiliation(s)
- Sayane Shome
- Bioinformatics and Computational Biology Program, Iowa State University, Iowa, USA
| | - R Gonzalo Parra
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Nazeefa Fatima
- Science for Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Upsala, Sweden
| | | | - Bart Cuypers
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Yumna Moosa
- KZN Research and Innovation Sequencing Platform, University of KwaZulu Natal, Durban, South Africa
| | - Nilson Da Rocha Coimbra
- Graduate Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana Assis
- Graduate Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Carla Giner-Delgado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Yesid Cuesta-Astroz
- School of Microbiology, Universidad de Antioquía, Medellín, Colombia.,Colombian Tropical Medicine Institute (ICMT), Universidad CES, Medellín, Colombia
| | - Geetha Saarunya
- Department of Biological Sciences, University of South Carolina, South Caroli a, USA
| | - Imane Allali
- Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.,Division of Computational Biology, Department of Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shruti Gupta
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ambuj Srivastava
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Manisha Kalsan
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Catalina Valdivia
- Ecosystem's Health Laboratory, Universidad Andres, Bello Santiago, Chile
| | | | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
| | | | | | - Leonor Rib
- The Bioinformatics Center, Biology and Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Marouen Ben Guebila
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Eugen Bauer
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Gaia Zaffaroni
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Amel Bekkar
- Swiss Institute of Bioinformatics (SIB), University of Lausanne, Lausanne, Switzerland
| | - Efejiro Ashano
- Molecular Diagnostics, Laboratory Services, APIN Public Health Initiatives, Abuja, Nigeria
| | - Lisanna Paladin
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Marco Necci
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Nicolás N Moreyra
- Genetics and Evolution of Buenos Aires (IEGEBA), CONICET-UBA, Institute of Ecology, Buenos Aires, Argentina
| | - Martin Rydén
- Biomedical Centre, Faculty of Medicine, Lund University, Lund, Sweden
| | - Jordan Villalobos-Solís
- Laboratorio de Biotenología de Plantas, Universidad Nacional de Costa Rica (UNA), Heredia, Costa Rica
| | - Nikolaos Papadopoulos
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Candice Rafael
- Research Unit for Bioinformatics, Rhodes University, Grahamstown, South Africa
| | - Tülay Karakulak
- Izmir Biomedicine and Genome Center, Dokuz Eylül University, Izmir, Turkey
| | - Yasin Kaya
- Hacettepe University, Faculty of Science, Department of Biology, Ankara, Turkey
| | - Yvonne Gladbach
- University Medical Center Rostock, University Heidelberg, Heidelberg, Germany
| | - Sandeep Kumar Dhanda
- La Jolla Institute for Allergy and Immunology, La Jolla Institute for Immunology, California, USA
| | | | - Aishwarya Alex
- Roche Diagnostics Automation Solutions GmbH, Roche, Waiblingen, Germany
| | - Dan DeBlasio
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, USA
| | - Farzana Rahman
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, UK.,School of Human and Life Sciences, Canterbury Christ Church University, Kent, UK
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18
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Awany D, Allali I, Dalvie S, Hemmings S, Mwaikono KS, Thomford NE, Gomez A, Mulder N, Chimusa ER. Host and Microbiome Genome-Wide Association Studies: Current State and Challenges. Front Genet 2019; 9:637. [PMID: 30723493 PMCID: PMC6349833 DOI: 10.3389/fgene.2018.00637] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022] Open
Abstract
The involvement of the microbiome in health and disease is well established. Microbiome genome-wide association studies (mGWAS) are used to elucidate the interaction of host genetic variation with the microbiome. The emergence of this relatively new field has been facilitated by the advent of next generation sequencing technologies that enable the investigation of the complex interaction between host genetics and microbial communities. In this paper, we review recent studies investigating host-microbiome interactions using mGWAS. Additionally, we highlight the marked disparity in the sampling population of mGWAS carried out to date and draw attention to the critical need for inclusion of diverse populations.
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Affiliation(s)
- Denis Awany
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shareefa Dalvie
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Sian Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kilaza S Mwaikono
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicholas E Thomford
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Andres Gomez
- Department of Animal Science, University of Minnesota-Twin Cities, St. Paul, MN, United States
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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19
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Chimusa ER, Defo J, Thami PK, Awany D, Mulisa DD, Allali I, Ghazal H, Moussa A, Mazandu GK. Dating admixture events is unsolved problem in multi-way admixed populations. Brief Bioinform 2018; 21:144-155. [PMID: 30462157 DOI: 10.1093/bib/bby112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022] Open
Abstract
Advances in human sequencing technologies, coupled with statistical and computational tools, have fostered the development of methods for dating admixture events. These methods have merits and drawbacks in estimating admixture events in multi-way admixed populations. Here, we first provide a comprehensive review and comparison of current methods pertinent to dating admixture events. Second, we assess various admixture dating tools. We do so by performing various simulations. Third, we apply the top two assessed methods to real data of a uniquely admixed population from South Africa. Results reveal that current dating admixture models are not sufficiently equipped to estimate ancient admixtures events and to identify multi-faceted admixture events in complex multi-way admixed populations. We conclude with a discussion of research areas where further work on dating admixture-based methods is needed.
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Affiliation(s)
- Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Joel Defo
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Prisca K Thami
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa.,Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Denis Awany
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Delesa D Mulisa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Imane Allali
- Division of Computational Biology, Department of Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | | | - Ahmed Moussa
- Abdelmalek Essaadi University ENSA, Tangier, Morocco
| | - Gaston K Mazandu
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa.,Division of Computational Biology, Department of Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa.,African Institute for Mathematical Sciences (AIMS),Muizenberg, Cape Town, South Africa
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20
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Awany D, Allali I, Chimusa ER. Tantalizing dilemma in risk prediction from disease scoring statistics. Brief Funct Genomics 2018; 18:211-219. [PMID: 30605512 PMCID: PMC6609536 DOI: 10.1093/bfgp/ely040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 08/17/2018] [Accepted: 11/29/2018] [Indexed: 02/01/2023] Open
Abstract
Over the past decade, human host genome-wide association studies (GWASs) have contributed greatly to our understanding of the impact of host genetics on phenotypes. Recently, the microbiome has been recognized as a complex trait in host genetic variation, leading to microbiome GWAS (mGWASs). For these, many different statistical methods and software tools have been developed for association mapping. Applications of these methods and tools have revealed several important findings; however, the establishment of causal factors and the direction of causality in the interactive role between human genetic polymorphisms, the microbiome and the host phenotypes are still a huge challenge. Here, we review disease scoring approaches in host and mGWAS and their underlying statistical methods and tools. We highlight the challenges in pinpointing the genetic-associated causal factors in host and mGWAS and discuss the role of multi-omic approach in disease scoring statistics that may provide a better understanding of human phenotypic variation by enabling further system biological experiment to establish causality.
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Affiliation(s)
- Denis Awany
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
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21
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Allali I, Arnold JW, Roach J, Cadenas MB, Butz N, Hassan HM, Koci M, Ballou A, Mendoza M, Ali R, Azcarate-Peril MA. A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome. BMC Microbiol 2017; 17:194. [PMID: 28903732 PMCID: PMC5598039 DOI: 10.1186/s12866-017-1101-8] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 08/29/2017] [Indexed: 12/16/2022] Open
Abstract
Background Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Results Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150–199 for GS FLX+ and bases 90–99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. Conclusions The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies. Electronic supplementary material The online version of this article (10.1186/s12866-017-1101-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Imane Allali
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA.,Laboratory of Biochemistry & Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Jason W Arnold
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, USA
| | - Maria Belen Cadenas
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Natasha Butz
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Hosni M Hassan
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Matthew Koci
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Anne Ballou
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Mary Mendoza
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Rizwana Ali
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA.
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22
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Becker-Dreps S, Allali I, Monteagudo A, Vilchez S, Hudgens MG, Rogawski ET, Carroll IM, Zambrana LE, Espinoza F, Azcarate-Peril MA. Gut Microbiome Composition in Young Nicaraguan Children During Diarrhea Episodes and Recovery. Am J Trop Med Hyg 2015; 93:1187-93. [PMID: 26350452 DOI: 10.4269/ajtmh.15-0322] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/23/2015] [Indexed: 12/16/2022] Open
Abstract
Understanding how the gut microbiota is affected by diarrhea episodes may help explain alterations in intestinal function among children in low-income settings. This study examined the composition of the gut microbiome of Nicaraguan children both during diarrhea episodes and while free of diarrhea for at least 2 months. Relative abundances of bacterial taxa, phylogenetic diversity, and species richness were determined by 16S amplicon sequencing and compared between paired diarrhea and recovery samples. A total of 66 stools were provided by 25 children enrolled in a 1-year cohort study of diarrhea etiologies. Children in our cohort had a mean age of 21.9 months; 64% were breast-fed, and 10% had received an antibiotic during the diarrhea episode. Overall, phylogenetic diversity and species richness did not differ significantly between diarrhea and recovery stools. However, of children who had a bacterial enteropathogen detected in any diarrhea stool, none experienced an increase in phylogenetic diversity in recovery, whereas of those in whom no bacterial enteropathogens were detected in their diarrhea stool(s), 59% experienced an increase in phylogenetic diversity in recovery (P = 0.008). This preliminary study suggests that recovery of the gut microbiota after a diarrhea episode may take longer time than previously thought and may be pathogen specific.
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Affiliation(s)
- Sylvia Becker-Dreps
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Imane Allali
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Andrea Monteagudo
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Samuel Vilchez
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Michael G Hudgens
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Elizabeth T Rogawski
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Ian M Carroll
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Luis Enrique Zambrana
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Felix Espinoza
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - M Andrea Azcarate-Peril
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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Abstract
This is a summary of the activities and scientific content of the first International Society for Computational Biology Student Council symposium in Africa. This meeting organized by the students for the students took place 8th of March 2015 in Dar Es Salaam, Tanzania.
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Affiliation(s)
- Yassine Souilmi
- Department of Biology, Mohamed Vth University, Rabat, 110 066, Morocco
- Department of Biomedical Informatics, Harvard University, Cambridge, MA, 02138, USA
| | - Imane Allali
- Department of Biology, Mohamed Vth University, Rabat, 110 066, Morocco
| | - Oussama Badad
- Department of Biology, Mohamed Vth University, Rabat, 110 066, Morocco
| | - Chinmay Kumar Dwibedi
- Department of Clinical Microbiology, Umea University, Umea, 901 87, Sweden
- Swedish Defence Research Agency, Umea, 164 90, Sweden
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Allali I, Delgado S, Marron PI, Astudillo A, Yeh JJ, Ghazal H, Amzazi S, Keku T, Azcarate-Peril MA. Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain. Gut Microbes 2015; 6:161-72. [PMID: 25875428 PMCID: PMC4615176 DOI: 10.1080/19490976.2015.1039223] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer in the world and the second leading cause of cancer deaths in the US and Spain. The molecular mechanisms involved in the etiology of CRC are not yet elucidated due in part to the complexity of the human gut microbiota. In this study, we compared the microbiome composition of 90 tumor and matching adjacent tissue (adjacent) from cohorts from the US and Spain by 16S rRNA amplicon sequencing in order to determine the impact of the geographic origin on the CRC microbiome. Data showed a significantly (P < 0.05) higher Phylogenetic Diversity (PD) for the US (PD Adjacent = 26.3 ± 5.3, PD Tumor = 23.3 ± 6.2) compared to the Spanish cohort (PD Adjacent = 18.9 ± 5.9, PD Tumor = 18.7 ± 6.6) while no significant differences in bacterial diversity were observed between tumor and adjacent tissues for individuals from the same country. Adjacent tissues from the Spanish cohort were enriched in Firmicutes (SP = 43.9% and US = 22.2%, P = 0.0001) and Actinobacteria (SP = 1.6% and US = 0.5%, P = 0.0018) compared to US adjacent tissues, while adjacent tissues from the US had significantly higher abundances of Fusobacteria (US = 8.1% and SP = 1.5%, P = 0.0023) and Sinergistetes (US = 0.3% and SP = 0.1%, P = 0.0097). Comparisons between tumor and adjacent tissues in each cohort identified the genus Eikenella significantly over represented in US tumors (T = 0.024% and A = 0%, P = 0.03), and the genera Fusobacterium (T = 10.4% and A = 1.5%, P = <0.0001), Bulleida (T = 0.36% and A = 0.09%, P = 0.02), Gemella (T = 1.46% and A = 0.19%, P = 0.03), Parvimonas (T = 3.14% and A = 0.86%, P = 0.03), Campylobacter (T = 0.15% and A = 0.008%, P = 0.047), and Streptococcus (T = 2.84% and A = 2.19%, P = 0.05) significantly over represented in Spanish tumors. Predicted metagenome functional content from 16S rRNA surveys showed that bacterial motility proteins and proteins involved in flagellar assembly were over represented in adjacent tissues of both cohorts, while pathways involved in fatty acid biosynthesis, the MAPK signaling pathway, and bacterial toxins were over represented in tumors. Our study suggests that microbiome compositional and functional dissimilarities by geographic location should be taken in consideration when approaching CRC therapeutic options.
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Affiliation(s)
- Imane Allali
- Department of Cell Biology and Physiology, and Microbiome Core Facility; University of North Carolina School of Medicine; Chapel Hill, NC, USA,Laboratory of Biochemistry & Immunology; Faculty of Sciences; University Mohammed V; Rabat, Morocco,Laboratory of Genetics and Biotechnology; Faculty of Sciences of Oujda; University Mohammed Premier; Oujda, Morocco
| | - Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products; Instituto de Productos Lácteos de Asturias (IPLA-CSIC); Villaviciosa-Asturias, Spain
| | - Pablo Isidro Marron
- Instituto Universitario de Oncología del Principado de Asturias; Hospital Universitario Central de Asturias; Universidad de Oviedo; Asturias, Spain
| | - Aurora Astudillo
- Instituto Universitario de Oncología del Principado de Asturias; Hospital Universitario Central de Asturias; Universidad de Oviedo; Asturias, Spain
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center; Departments of Surgery and Pharmacology; University of North Carolina School of Medicine; Chapel Hill, NC, USA
| | - Hassan Ghazal
- Laboratory of Genetics and Biotechnology; Faculty of Sciences of Oujda; University Mohammed Premier; Oujda, Morocco,Polydisciplinary Faculty of Nador; University Mohammed Premier; Nador, Morocco
| | - Saaïd Amzazi
- Laboratory of Biochemistry & Immunology; Faculty of Sciences; University Mohammed V; Rabat, Morocco
| | - Temitope Keku
- Division of Gastroenterology & Hepatology; Department of Medicine; University of North Carolina School of Medicine; Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Cell Biology and Physiology, and Microbiome Core Facility; University of North Carolina School of Medicine; Chapel Hill, NC, USA,Correspondence to: M Andrea Azcarate-Peril
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Frank R, Phan-Thuc H, Blanc P, Allali I, Goutte R, Vedel J, Fontaine G, Grosgogeat Y. [Attenuated nodal response. Apropos of 30 cases]. Arch Mal Coeur Vaiss 1980; 73:1007-17. [PMID: 6776922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In a population of 600 consecutive patients undergoing endocavitary electrophysiological study to assess nodal conduction, 40 had an atriohisian Wenckenbach point of over 200/mn. In 30 cases, vagal stimulation with ATP (10 to 40 mg IV) provoked an increase in atrioventricular conduction, with lengthening the AH interval by over 100 p. 100 or transient atrioventricular block. This increase allowed elimination of an accessory atriohisian pathway which could give similar high Wenckenbach points, but which do not show decremental conduction. In all our cases, the conduction passed through the artrioventricular node (AVN) whose response to rapid atrial stimulation was attenuated compared to normal. The parameter of this attenuated nodal response varied from case to case, but in general, the intervals were shorter than normal. The AH interval was less than 50 ms in 22 cases (N = 70 +/- 20 ms). The effective nodal refractory period was shorter than the functional atrial refractory period in 20 cases. The shortest atrial cycles transmitted 1/1 to the ventricles ranged from 230 to 300 ms (274 +/- 33 ms) (N = 375 +/- 40 ms). The functional structure of the AVN was studied by the lengthening of the AH interval with heart rate : 5 types were distinguished : 10 patients had progressive lengthening of AH interval greater than 100 ms (Type I) as in a normal AVN; 5 had progressive lengthening of AH interval of less than 50 ms (Type II), 5 had progressive lengthening of AH which then remained stable for a number of heart rates before lengthening again (Type III); 3 had an initial moderate lengthening of the AH interval which then became more rapid (Type IV) and 7 had no change in AH until 120/mn and then a progressive lengthening was observed (Type V). Two functional groups could also be identified depending on whether the lengthening was progressive, suggesting a single nodal pathway (Types I and II) or on whether differing increases were observed related to the atrial rate, suggesting two (Types IV and V) or even three (Type III) atrionodal or intranodal pathways with different refractory periods. Of these 30 patients, only 14 had documented supraventricular tachycardia, 13 being atrial fibrillation and the other a junctional tachycardia. Attenuated nodal behavior does not seem to be a direct cause of supraventricular arrhythmias but these arrhythmias were not tolerated as well because of the special properties of the atrioventricular node.
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