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Schmidt N, Van Den Ham K, Bower L, Li S, Lorenzi H, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton P. Susceptibility to febrile malaria is associated with an inflammatory gut microbiome. RESEARCH SQUARE 2024:rs.3.rs-3974068. [PMID: 38645126 PMCID: PMC11030534 DOI: 10.21203/rs.3.rs-3974068/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Malaria is a major public health problem, but many of the factors underlying the pathogenesis of this disease are not well understood. Here, we demonstrate in Malian children that susceptibility to febrile malaria following infection with Plasmodium falciparum is associated with the composition of the gut microbiome prior to the malaria season. Gnotobiotic mice colonized with the fecal samples of malaria-susceptible children had a significantly higher parasite burden following Plasmodium infection compared to gnotobiotic mice colonized with the fecal samples of malaria-resistant children. The fecal microbiome of the susceptible children was enriched for bacteria associated with inflammation, mucin degradation, gut permeability and inflammatory bowel disorders (e.g., Ruminococcus gauvreauii, Ruminococcus torques, Dorea formicigenerans, Dorea longicatena, Lachnoclostridium phocaeense and Lachnoclostridium sp. YL32). However, the susceptible children also had a greater abundance of bacteria known to produce anti-inflammatory short-chain fatty acids and those associated with favorable prognosis and remission following dysbiotic intestinal events (e.g., Anaerobutyricum hallii, Blautia producta and Sellimonas intestinalis). Metabolomics analysis of the human fecal samples corroborated the existence of inflammatory and recovery-associated features within the gut microbiome of the susceptible children. There was an enrichment of nitric oxide-derived DNA adducts (deoxyinosine and deoxyuridine) and long-chain fatty acids, the absorption of which has been shown to be inhibited by inflamed intestinal epithelial cells, and a decrease in the abundance of mucus phospholipids. Nevertheless, there were also increased levels of pseudouridine and hypoxanthine, which have been shown to be regulated in response to cellular stress and to promote recovery following injury or hypoxia. Overall, these results indicate that the gut microbiome may contribute malaria pathogenesis and suggest that therapies targeting intestinal inflammation could decrease malaria susceptibility.
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2
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Maghini DG, Oduaran OH, Wirbel J, Olubayo LAI, Smyth N, Mathema T, Belger CW, Agongo G, Boua PR, Choma SSR, Gómez-Olivé FX, Kisiangani I, Mashaba GR, Micklesfield L, Mohamed SF, Nonterah EA, Norris S, Sorgho H, Tollman S, Wafawanaka F, Tluway F, Ramsay M, Bhatt AS, Hazelhurst S. Expanding the human gut microbiome atlas of Africa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584859. [PMID: 38559015 PMCID: PMC10980044 DOI: 10.1101/2024.03.13.584859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.
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Affiliation(s)
- Dylan G Maghini
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Jakob Wirbel
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Luicer A Ingasia Olubayo
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Natalie Smyth
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Theophilous Mathema
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Carl W Belger
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Solomon SR Choma
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Given R Mashaba
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - Lisa Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Shane Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Furahini Tluway
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ami S Bhatt
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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3
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Mir TUG, Manhas S, Khurshid Wani A, Akhtar N, Shukla S, Prakash A. Alterations in microbiome of COVID-19 patients and its impact on forensic investigations. Sci Justice 2024; 64:81-94. [PMID: 38182316 DOI: 10.1016/j.scijus.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 11/12/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
The human microbiome is vital for maintaining human health and has garnered substantial attention in recent years, particularly in the context of the coronavirus disease 2019 (COVID-19) outbreak. Studies have underscored significant alterations in the microbiome of COVID-19 patients across various body niches, including the gut, respiratory tract, oral cavity, skin, and vagina. These changes manifest as shifts in microbiota composition, characterized by an increase in opportunistic pathogens and a decrease in beneficial commensal bacteria. Such microbiome transformations may play a pivotal role in influencing the course and severity of COVID-19, potentially contributing to the inflammatory response. This ongoing relationship between COVID-19 and the human microbiome serves as a compelling subject of research, underscoring the necessity for further investigations into the underlying mechanisms and their implications for patient health. Additionally, these alterations in the microbiome may have significant ramifications for forensic investigations, given the microbiome's potential in establishing individual characteristics. Consequently, changes in the microbiome could introduce a level of complexity into forensic determinations. As research progresses, a more profound understanding of the human microbiome within the context of COVID-19 may offer valuable insights into disease prevention, treatment strategies, and its potential applications in forensic science. Consequently, this paper aims to provide an overarching review of microbiome alterations due to COVID-19 and the associated impact on forensic applications, bridging the gap between the altered microbiome of COVID-19 patients and the challenges forensic investigations may encounter when analyzing this microbiome as a forensic biomarker.
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Affiliation(s)
- Tahir Ul Gani Mir
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India; State Forensic Science Laboratory, Srinagar, Jammu and Kashmir 190001, India.
| | - Sakshi Manhas
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Saurabh Shukla
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India.
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
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Van Den Ham KM, Little MR, Bednarski OJ, Fusco EM, Mandal RK, Mitra R, Li S, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton PD, Schmidt NW. Creation of a non-Western humanized gnotobiotic mouse model through the transplantation of rural African fecal microbiota. Microbiol Spectr 2023; 11:e0155423. [PMID: 37819130 PMCID: PMC10714993 DOI: 10.1128/spectrum.01554-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE There is increasing evidence that microbes residing within the intestines (gut microbiota) play important roles in the well-being of humans. Yet, there are considerable challenges in determining the specific role of gut microbiota in human diseases owing to the complexity of diverse internal and environmental factors that can contribute to diseases. Mice devoid of all microorganisms (germ-free mice) can be colonized with human stool samples to examine the specific contribution of the gut microbiota to a disease. These approaches have been primarily focused on stool samples obtained from individuals in Western countries. Thus, there is limited understanding as to whether the same methods used to colonize germ-free mice with stool from Western individuals would apply to the colonization of germ-free mice with stool from non-Western individuals. Here, we report the results from colonizing germ-free mice with stool samples of Malian children.
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Affiliation(s)
- Kristin M. Van Den Ham
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Morgan R. Little
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Olivia J. Bednarski
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Elizabeth M. Fusco
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rabindra K. Mandal
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Riten Mitra
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, USA
| | - Shanping Li
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Safiatou Doumbo
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Didier Doumtabe
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Kassoum Kayentao
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Aissata Ongoiba
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Boubacar Traore
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Peter D. Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Nathan W. Schmidt
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
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5
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Shi H, Yu X, Cheng G. Impact of the microbiome on mosquito-borne diseases. Protein Cell 2023; 14:743-761. [PMID: 37186167 PMCID: PMC10599646 DOI: 10.1093/procel/pwad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Mosquito-borne diseases present a significant threat to human health, with the possibility of outbreaks of new mosquito-borne diseases always looming. Unfortunately, current measures to combat these diseases such as vaccines and drugs are often either unavailable or ineffective. However, recent studies on microbiomes may reveal promising strategies to fight these diseases. In this review, we examine recent advances in our understanding of the effects of both the mosquito and vertebrate microbiomes on mosquito-borne diseases. We argue that the mosquito microbiome can have direct and indirect impacts on the transmission of these diseases, with mosquito symbiotic microorganisms, particularly Wolbachia bacteria, showing potential for controlling mosquito-borne diseases. Moreover, the skin microbiome of vertebrates plays a significant role in mosquito preferences, while the gut microbiome has an impact on the progression of mosquito-borne diseases in humans. As researchers continue to explore the role of microbiomes in mosquito-borne diseases, we highlight some promising future directions for this field. Ultimately, a better understanding of the interplay between mosquitoes, their hosts, pathogens, and the microbiomes of mosquitoes and hosts may hold the key to preventing and controlling mosquito-borne diseases.
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Affiliation(s)
- Huicheng Shi
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xi Yu
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Gong Cheng
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Department of Parasitology, School of Basic Medical Sciences, Central South University, Changsha 410013, China
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6
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Mandal RK, Mandal A, Denny JE, Namazii R, John CC, Schmidt NW. Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria. Nat Commun 2023; 14:6465. [PMID: 37833304 PMCID: PMC10575898 DOI: 10.1038/s41467-023-42235-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Malaria is caused by Plasmodium species and remains a significant cause of morbidity and mortality globally. Gut bacteria can influence the severity of malaria, but the contribution of specific bacteria to the risk of severe malaria is unknown. Here, multiomics approaches demonstrate that specific species of Bacteroides are causally linked to the risk of severe malaria. Plasmodium yoelii hyperparasitemia-resistant mice gavaged with murine-isolated Bacteroides fragilis develop P. yoelii hyperparasitemia. Moreover, Bacteroides are significantly more abundant in Ugandan children with severe malarial anemia than with asymptomatic P. falciparum infection. Human isolates of Bacteroides caccae, Bacteroides uniformis, and Bacteroides ovatus were able to cause susceptibility to severe malaria in mice. While monocolonization of germ-free mice with Bacteroides alone is insufficient to cause susceptibility to hyperparasitemia, meta-analysis across multiple studies support a main role for Bacteroides in susceptibility to severe malaria. Approaches that target gut Bacteroides present an opportunity to prevent severe malaria and associated deaths.
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Affiliation(s)
- Rabindra K Mandal
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anita Mandal
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Joshua E Denny
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA
| | - Ruth Namazii
- Department of Paediatrics and Child Health, Makerere University, Kampala, Uganda
| | - Chandy C John
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nathan W Schmidt
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA.
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7
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Mandal RK, Schmidt NW. Mechanistic insights into the interaction between the host gut microbiome and malaria. PLoS Pathog 2023; 19:e1011665. [PMID: 37824458 PMCID: PMC10569623 DOI: 10.1371/journal.ppat.1011665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Malaria is a devastating infectious disease and significant global health burden caused by the bite of a Plasmodium-infected female Anopheles mosquito. Gut microbiota was recently discovered as a risk factor of severe malaria. This review entails the recent advances on the impact of gut microbiota composition on malaria severity and consequence of malaria infection on gut microbiota in mammalian hosts. Additionally, this review provides mechanistic insight into interactions that might occur between gut microbiota and host immunity which in turn can modulate malaria severity. Finally, approaches to modulate gut microbiota composition are discussed. We anticipate this review will facilitate novel hypotheses to move the malaria-gut microbiome field forward.
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Affiliation(s)
- Rabindra K. Mandal
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indiana, United States of America
| | - Nathan W. Schmidt
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indiana, United States of America
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8
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Pheeha SM, Tamuzi JL, Chale-Matsau B, Manda S, Nyasulu PS. A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa. Microorganisms 2023; 11:2118. [PMID: 37630678 PMCID: PMC10458939 DOI: 10.3390/microorganisms11082118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The gut microbiota has emerged as a key human health and disease determinant. However, there is a significant knowledge gap regarding the composition, diversity, and function of the gut microbiota, specifically in the African population. This scoping review aims to examine the existing literature on gut microbiota research conducted in Africa, providing an overview of the current knowledge and identifying research gaps. A comprehensive search strategy was employed to identify relevant studies. Databases including MEDLINE (PubMed), African Index Medicus (AIM), CINAHL (EBSCOhost), Science Citation index (Web of Science), Embase (Ovid), Scopus (Elsevier), WHO International Clinical Trials Registry Platform (ICTRP), and Google Scholar were searched for relevant articles. Studies investigating the gut microbiota in African populations of all age groups were included. The initial screening included a total of 2136 articles, of which 154 were included in this scoping review. The current scoping review revealed a limited number of studies investigating diseases of public health significance in relation to the gut microbiota. Among these studies, HIV (14.3%), colorectal cancer (5.2%), and diabetes mellitus (3.9%) received the most attention. The top five countries that contributed to gut microbiota research were South Africa (16.2%), Malawi (10.4%), Egypt (9.7%), Kenya (7.1%), and Nigeria (6.5%). The high number (n = 66) of studies that did not study any specific disease in relation to the gut microbiota remains a gap that needs to be filled. This scoping review brings attention to the prevalent utilization of observational study types (38.3%) in the studies analysed and emphasizes the importance of conducting more experimental studies. Furthermore, the findings reflect the need for more disease-focused, comprehensive, and population-specific gut microbiota studies across diverse African regions and ethnic groups to better understand the factors shaping gut microbiota composition and its implications for health and disease. Such knowledge has the potential to inform targeted interventions and personalized approaches for improving health outcomes in African populations.
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Affiliation(s)
- Sara M. Pheeha
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
- Department of Chemical Pathology, Faculty of Medicine and Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa
- National Health Laboratory Service, Dr George Mukhari Academic Hospital, Pretoria 0208, South Africa
| | - Jacques L. Tamuzi
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
| | - Bettina Chale-Matsau
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria, Pretoria 0028, South Africa
- National Health Laboratory Service, Steve Biko Academic Hospital, Pretoria 0002, South Africa
| | - Samuel Manda
- Department of Statistics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0028, South Africa
| | - Peter S. Nyasulu
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
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Su X, Stadler RV, Xu F, Wu J. Malaria Genomics, Vaccine Development, and Microbiome. Pathogens 2023; 12:1061. [PMID: 37624021 PMCID: PMC10459703 DOI: 10.3390/pathogens12081061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Recent advances in malaria genetics and genomics have transformed many aspects of malaria research in areas of molecular evolution, epidemiology, transmission, host-parasite interaction, drug resistance, pathogenicity, and vaccine development. Here, in addition to introducing some background information on malaria parasite biology, parasite genetics/genomics, and genotyping methods, we discuss some applications of genetic and genomic approaches in vaccine development and in studying interactions with microbiota. Genetic and genomic data can be used to search for novel vaccine targets, design an effective vaccine strategy, identify protective antigens in a whole-organism vaccine, and evaluate the efficacy of a vaccine. Microbiota has been shown to influence disease outcomes and vaccine efficacy; studying the effects of microbiota in pathogenicity and immunity may provide information for disease control. Malaria genetics and genomics will continue to contribute greatly to many fields of malaria research.
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Affiliation(s)
- Xinzhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (R.V.S.); (F.X.); (J.W.)
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10
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Beyhan YE, Yıldız MR. Microbiota and parasite relationship. Diagn Microbiol Infect Dis 2023; 106:115954. [PMID: 37267741 DOI: 10.1016/j.diagmicrobio.2023.115954] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 06/04/2023]
Abstract
The diversity of microbiota is different in each person. Many health problems such as autoimmune diseases, diabetes, cardiovascular diseases, and depression can be caused by microbiota imbalance. Since the parasite needs a host to survive, it interacts closely with the microbiota elements. Blastocystis acts on the inflammatory state of the intestine and may cause various gastrointestinal symptoms, on the contrary, it is more important for gut health because it causes bacterial diversity and richness. Blastocystis is associated with changes in gut microbiota composition, the ultimate indicator of which is the Firmicutes/Bacteroidetes ratio. The Bifidobacterium genus was significantly reduced in IBS patients and Blastocystis, and there is a significant decrease in Faecalibacterium prausnitzii, which has anti-inflammatory properties in Blastocystis infection without IBS. Lactobacillus species reduce the presence of Giardia, and the produced bacteriocins prevent parasite adhesion. The presence of helminths has been strongly associated with the transition from Bacteroidetes to Firmicutes and Clostridia. Contrary to Ascaris, alpha diversity in the intestinal microbiota decreases in chronic Trichuris muris infection, and growth and nutrient metabolism efficiency can be suppressed. Helminth infections indirectly affect mood and behavior in children through their effects on microbiota change. The main and focus of this review is to address the relationship of parasites with microbiota elements and to review the data about what changes they cause. Microbiota studies have gained importance recently and it is thought that it will contribute to the treatment of many diseases as well as in the fight against parasitic diseases in the future.
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Affiliation(s)
- Yunus E Beyhan
- Department of Parasitology, Van Yüzüncü Yil University Faculty of Medicine, Van, Turkey.
| | - Muhammed R Yıldız
- Department of Parasitology, Van Yüzüncü Yil University Faculty of Medicine, Van, Turkey
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11
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Farinella DN, Kaur S, Tran V, Cabrera-Mora M, Joyner CJ, Lapp SA, Pakala SB, Nural MV, DeBarry JD, Kissinger JC, Jones DP, Moreno A, Galinski MR, Cordy RJ. Malaria disrupts the rhesus macaque gut microbiome. Front Cell Infect Microbiol 2023; 12:1058926. [PMID: 36710962 PMCID: PMC9880479 DOI: 10.3389/fcimb.2022.1058926] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/12/2022] [Indexed: 01/14/2023] Open
Abstract
Previous studies have suggested that a relationship exists between severity and transmissibility of malaria and variations in the gut microbiome, yet only limited information exists on the temporal dynamics of the gut microbial community during a malarial infection. Here, using a rhesus macaque model of relapsing malaria, we investigate how malaria affects the gut microbiome. In this study, we performed 16S sequencing on DNA isolated from rectal swabs of rhesus macaques over the course of an experimental malarial infection with Plasmodium cynomolgi and analyzed gut bacterial taxa abundance across primary and relapsing infections. We also performed metabolomics on blood plasma from the animals at the same timepoints and investigated changes in metabolic pathways over time. Members of Proteobacteria (family Helicobacteraceae) increased dramatically in relative abundance in the animal's gut microbiome during peak infection while Firmicutes (family Lactobacillaceae and Ruminococcaceae), Bacteroidetes (family Prevotellaceae) and Spirochaetes amongst others decreased compared to baseline levels. Alpha diversity metrics indicated decreased microbiome diversity at the peak of parasitemia, followed by restoration of diversity post-treatment. Comparison with healthy subjects suggested that the rectal microbiome during acute malaria is enriched with commensal bacteria typically found in the healthy animal's mucosa. Significant changes in the tryptophan-kynurenine immunomodulatory pathway were detected at peak infection with P. cynomolgi, a finding that has been described previously in the context of P. vivax infections in humans. During relapses, which have been shown to be associated with less inflammation and clinical severity, we observed minimal disruption to the gut microbiome, despite parasites being present. Altogether, these data suggest that the metabolic shift occurring during acute infection is associated with a concomitant shift in the gut microbiome, which is reversed post-treatment.
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Affiliation(s)
| | - Sukhpreet Kaur
- Department of Biology, Wake Forest University, Winston-Salem, NC, United States
| | - ViLinh Tran
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Monica Cabrera-Mora
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Chester J. Joyner
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States,Department of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Stacey A. Lapp
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Suman B. Pakala
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Mustafa V. Nural
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Jeremy D. DeBarry
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States,Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Jessica C. Kissinger
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States,Department of Genetics, University of Georgia, Athens, GA, United States
| | - Dean P. Jones
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Alberto Moreno
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Mary R. Galinski
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Regina Joice Cordy
- Department of Biology, Wake Forest University, Winston-Salem, NC, United States,Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States,*Correspondence: Regina Joice Cordy,
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12
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Piazzesi A, Pane S, Putignani L. How Modulations of the Gut Microbiota May Help in Preventing or Treating Parasitic Diseases. CURRENT TROPICAL MEDICINE REPORTS 2022. [DOI: 10.1007/s40475-022-00275-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Olatunde AC, Cornwall DH, Roedel M, Lamb TJ. Mouse Models for Unravelling Immunology of Blood Stage Malaria. Vaccines (Basel) 2022; 10:1525. [PMID: 36146602 PMCID: PMC9501382 DOI: 10.3390/vaccines10091525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Malaria comprises a spectrum of disease syndromes and the immune system is a major participant in malarial disease. This is particularly true in relation to the immune responses elicited against blood stages of Plasmodium-parasites that are responsible for the pathogenesis of infection. Mouse models of malaria are commonly used to dissect the immune mechanisms underlying disease. While no single mouse model of Plasmodium infection completely recapitulates all the features of malaria in humans, collectively the existing models are invaluable for defining the events that lead to the immunopathogenesis of malaria. Here we review the different mouse models of Plasmodium infection that are available, and highlight some of the main contributions these models have made with regards to identifying immune mechanisms of parasite control and the immunopathogenesis of malaria.
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Affiliation(s)
| | | | | | - Tracey J. Lamb
- Department of Pathology, University of Utah, Emma Eccles Jones Medical Research Building, 15 N Medical Drive E, Room 1420A, Salt Lake City, UT 84112, USA
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14
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Mukherjee D, Chora ÂF, Lone JC, Ramiro RS, Blankenhaus B, Serre K, Ramirez M, Gordo I, Veldhoen M, Varga-Weisz P, Mota MM. Host lung microbiota promotes malaria-associated acute respiratory distress syndrome. Nat Commun 2022; 13:3747. [PMID: 35768411 PMCID: PMC9243033 DOI: 10.1038/s41467-022-31301-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/13/2022] [Indexed: 11/14/2022] Open
Abstract
Severe malaria can manifest itself with a variety of well-recognized clinical phenotypes that are highly predictive of death - severe anaemia, coma (cerebral malaria), multiple organ failure, and respiratory distress. The reasons why an infected individual develops one pathology rather than another remain poorly understood. Here we use distinct rodent models of infection to show that the host microbiota is a contributing factor for the development of respiratory distress syndrome and host mortality in the context of malaria infections (malaria-associated acute respiratory distress syndrome, MA-ARDS). We show that parasite sequestration in the lung results in sustained immune activation. Subsequent production of the anti-inflammatory cytokine IL-10 by T cells compromises microbial control, leading to severe lung disease. Notably, bacterial clearance with linezolid, an antibiotic commonly used in the clinical setting to control lung-associated bacterial infections, prevents MA-ARDS-associated lethality. Thus, we propose that the host's anti-inflammatory response to limit tissue damage can result in loss of microbial control, which promotes MA-ARDS. This must be considered when intervening against life-threatening respiratory complications.
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Affiliation(s)
- Debanjan Mukherjee
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Ângelo Ferreira Chora
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Jean-Christophe Lone
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
- School of Life Sciences, University of Essex, Colchester, UK
| | | | - Birte Blankenhaus
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Karine Serre
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Mário Ramirez
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Marc Veldhoen
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Patrick Varga-Weisz
- School of Life Sciences, University of Essex, Colchester, UK
- São Paulo Excellence Chair, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Maria M Mota
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028, Lisboa, Portugal.
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15
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Cao D, Pang M, Wu D, Chen G, Peng X, Xu K, Fan H. Alterations in the Gut Microbiota of Tibetan Patients With Echinococcosis. Front Microbiol 2022; 13:860909. [PMID: 35615499 PMCID: PMC9126193 DOI: 10.3389/fmicb.2022.860909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/30/2022] [Indexed: 01/30/2023] Open
Abstract
There are two main types of echinococcosis, namely alveolar echinococcosis (AE) and cystic echinococcosis (CE). They are zoonotic parasitic diseases caused by the metacestodes of Echinococcus multilocularis and Echinococcus granulosus. In order to explore the gut microbiome composition of patients with echinococcosis, we analyzed fecal samples of seven patients with AE, six patients with CE, and 13 healthy individuals from the Qinghai-Tibetan Plateau, China. Using metagenomic next-generation sequencing, we identified fecal bacteria in the patients with AE and CE. The gut microbiota was analyzed by next-generation metagenomic sequencing (mNGS) to compare patients with either AE or CE against healthy individuals. We found there were some differences between them in abundant bacteria. Our results led to five findings: (1) Between patients with echinococcosis and healthy individuals, the differential bacteria were from four phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria. (2) Rothia mucilaginosa, Veillonella dispar, Veillonella atypica, Streptococcus parasanguinis, Streptococcus salivarius, and Alistipes finegoldii were abundant in the feces of patients with AE. (3) Bacteroides dorei, Parabacteroides distasonis, Escherichia sp_E4742, and Methanobrevibacter smithii were abundant in the feces of the patients with CE. (4) At the phylum and class level, compared to the AE group, the healthy group was characterized by higher numbers of Actinobacteria. (5) At the family level, Lachnospiraceae and Eubacteriaceae were more abundant in the feces of healthy individuals than in AE patients. The genera Coprococcus, Eubacterium, and Bilophia were more abundant in the healthy group, while the genus Rothia was more abundant in the AE group. The results of this study enrich our understanding of the gut microbiome composition of patients with AE and CE in the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Deping Cao
- The Department of Human Parasitology, Basic Medical College of Guilin Medical University, Guilin, China
| | - Mingquan Pang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Qinghai University, Xining, China.,The Key Echinococcosis Laboratory, Affiliated Hospital of Qinghai University, Xining, China
| | - Defang Wu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Qinghai University, Xining, China.,The Key Echinococcosis Laboratory, Affiliated Hospital of Qinghai University, Xining, China
| | - Gen Chen
- The Department of Human Parasitology, Basic Medical College of Guilin Medical University, Guilin, China
| | - Xiaohong Peng
- The Department of Human Parasitology, Basic Medical College of Guilin Medical University, Guilin, China
| | - Kai Xu
- The Key Echinococcosis Laboratory, Affiliated Hospital of Qinghai University, Xining, China
| | - Haining Fan
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Qinghai University, Xining, China.,The Key Echinococcosis Laboratory, Affiliated Hospital of Qinghai University, Xining, China
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16
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Guan W, Song X, Yang S, Zhu H, Li F, Li J. Observation of the Gut Microbiota Profile in BALB/c Mice Induced by Plasmodium yoelii 17XL Infection. Front Microbiol 2022; 13:858897. [PMID: 35432291 PMCID: PMC9009211 DOI: 10.3389/fmicb.2022.858897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/22/2022] [Indexed: 02/01/2023] Open
Abstract
Rodent malaria caused by Plasmodium yoelii 17XL (Py 17XL) is an ideal animal model for human malaria studies. Although the gut microbiota plays an important role in the occurrence and development of infectious diseases, the gut microbiota associated with Py 17XL infection remains unclear. In the current study, the gut microbiota composition of infected BALB/c mice was surveyed. Mouse fecal samples were collected at 0, 2, 5 days post-infection (dpi), and the gut microbiota was characterized by 16S rRNA sequencing. Operational taxonomic units (OTUs) were 634 ± 26 on average. Firmicutes and Bacteroidetes were typically predominant in the gut microbiota composition at the phylum level. Compared with the Ctrl, Firmicutes was significantly decreased after infection, while Bacteroidetes was notably increased. The most dominant family was Lactobacillaceae in all samples. The alpha diversity index showed that compared with that of the Ctrl, the observed OTU number was decreased at 2 dpi and then slightly increased at 5 dpi. LEfSe analysis revealed several bacterial taxa were notably related to Py-infected mice at the phylogenetic level. Several bacterial genera, such as Lactobacillus, were overrepresented in the Py-infected fecal microbiota at 2 dpi, while Muribaculaceae was overrepresented at 5 dpi. Moreover, Alistipes and Helicobacter were overrepresented at 5 dpi compared with 2 dpi. The results indicated Py infection could alter the gut microbiota composition of mice. Besides, biomarkers could serve as direct targets to elucidate their roles in the progression and pathogenesis of malaria and provide insights into studies of antimalarial drugs and malaria vaccines.
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Affiliation(s)
- Wei Guan
- Department of Human Parasitology, School of Basic Medicine Science, Hubei University of Medicine, Shiyan, China
| | - Xiaonan Song
- Department of Human Parasitology, School of Basic Medicine Science, Hubei University of Medicine, Shiyan, China
| | - Shuguo Yang
- Department of Human Parasitology, School of Basic Medicine Science, Hubei University of Medicine, Shiyan, China
| | - Huiyin Zhu
- Department of Human Parasitology, School of Basic Medicine Science, Hubei University of Medicine, Shiyan, China
| | - Fang Li
- Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Fang Li,
| | - Jian Li
- Department of Human Parasitology, School of Basic Medicine Science, Hubei University of Medicine, Shiyan, China
- Jian Li,
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17
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Possible Interactions between Malaria, Helminthiases and the Gut Microbiota: A Short Review. Microorganisms 2022; 10:microorganisms10040721. [PMID: 35456772 PMCID: PMC9025727 DOI: 10.3390/microorganisms10040721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 02/01/2023] Open
Abstract
Malaria, caused by the Plasmodium species, is an infectious disease responsible for more than 600 thousand deaths and more than 200 million morbidity cases annually. With above 90% of those deaths and cases, sub-Saharan Africa is affected disproportionately. Malaria clinical manifestations range from asymptomatic to simple, mild, and severe disease. External factors such as the gut microbiota and helminthiases have been shown to affect malaria clinical manifestations. However, little is known about whether the gut microbiota has the potential to influence malaria clinical manifestations in humans. Similarly, many previous studies have shown divergent results on the effects of helminths on malaria clinical manifestations. To date, a few studies, mainly murine, have shown the gut microbiota’s capacity to modulate malaria’s prospective risk of infection, transmission, and severity. This short review seeks to summarize recent literature about possible interactions between malaria, helminthiases, and the gut microbiota. The knowledge from this exercise will inform innovation possibilities for future tools, technologies, approaches, and policies around the prevention and management of malaria in endemic countries.
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18
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Ulusan Bagci O, Caner A. The interaction of gut microbiota with parasitic protozoa. J Parasit Dis 2022; 46:8-11. [PMID: 35299914 PMCID: PMC8901934 DOI: 10.1007/s12639-021-01443-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022] Open
Abstract
The human intestinal microbiota is composed of a complex combination of microorganisms including bacteria, virus, and eukaryotes. The microbiota plays a critical role in homeostasis through creating a mucosal barrier, providing protective responses to pathogens, and affecting the immune system and metabolism of the host. Molecules secreted by parasites can alter composition of microbiota both by acting directly on the microbial community and indirectly by affecting the host physiology. On the other hand, the microbiota composition can affect the survival, physiology, and virulence of many parasitic protozoa. Explanation of possible interactions between the microbiota, immune response, and protozoa may further clarify the underlying mechanisms of infectivity, clinical variations, and life-cycle of protozoa.
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Affiliation(s)
- Ozlem Ulusan Bagci
- grid.8302.90000 0001 1092 2592Department of Parasitology, Faculty of Medicine, Ege University Medical School, 35100 Bornova, Izmir, Turkey
| | - Ayse Caner
- grid.8302.90000 0001 1092 2592Department of Parasitology, Faculty of Medicine, Ege University Medical School, 35100 Bornova, Izmir, Turkey ,grid.8302.90000 0001 1092 2592Cancer Research Center, Ege University, Izmir, Turkey ,grid.240145.60000 0001 2291 4776Departments of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
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19
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Palinauskas V, Mateos-Hernandez L, Wu-Chuang A, de la Fuente J, Aželytė J, Obregon D, Cabezas-Cruz A. Exploring the Ecological Implications of Microbiota Diversity in Birds: Natural Barriers Against Avian Malaria. Front Immunol 2022; 13:807682. [PMID: 35250978 PMCID: PMC8891477 DOI: 10.3389/fimmu.2022.807682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
Natural antibodies (Abs), produced in response to bacterial gut microbiota, drive resistance to infection in vertebrates. In natural systems, gut microbiota diversity is expected to shape the spectrum of natural Abs and resistance to parasites. This hypothesis has not been empirically tested. In this 'Hypothesis and Theory' paper, we propose that enteric microbiota diversity shapes the immune response to the carbohydrate α-Gal and resistance to avian malaria. We further propose that anti-α-Gal Abs are transmitted from mother to eggs for early malaria protection in chicks. Microbiota modulation by anti-α-Gal Abs is also proposed as a mechanism favoring the early colonization of bacterial taxa with α1,3-galactosyltransferase (α1,3GT) activity in the bird gut. Our preliminary data shows that bacterial α1,3GT genes are widely distributed in the gut microbiome of wild and domestic birds. We also showed that experimental infection with the avian malaria parasite P. relictum induces anti-α-Gal Abs in bird sera. The bird-malaria-microbiota system allows combining field studies with infection and transmission experiments in laboratory animals to test the association between microbiota composition, anti-α-Gal Abs, and malaria infection in natural populations of wild birds. Understanding how the gut microbiome influences resistance to malaria can bring insights on how these mechanisms influence the prevalence of malaria parasites in juvenile birds and shape the host population dynamics.
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Affiliation(s)
| | - Lourdes Mateos-Hernandez
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - Alejandra Wu-Chuang
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Justė Aželytė
- Nature Research Centre, Akademijos 2, Vilnius, Lithuania
| | - Dasiel Obregon
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, France
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20
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Yawen Z, Xiangyun C, Binyou L, Xingchen Y, Taiping L, Xuedong Z, Jiyao L, Lei C, Wenyue X, Biao R. The dynamic landscape of parasitemia dependent intestinal microbiota shifting and the correlated gut transcriptome during Plasmodium yoelii infection. Microbiol Res 2022; 258:126994. [DOI: 10.1016/j.micres.2022.126994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023]
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21
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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] [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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22
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Haarkötter C, Saiz M, Gálvez X, Medina-Lozano MI, Álvarez JC, Lorente JA. Usefulness of Microbiome for Forensic Geolocation: A Review. Life (Basel) 2021; 11:life11121322. [PMID: 34947853 PMCID: PMC8707258 DOI: 10.3390/life11121322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
Forensic microbiomics is a promising tool for crime investigation. Geolocation, which connects an individual to a certain place or location by microbiota, has been fairly well studied in the literature, and several applications have been found. The aim of this review is to highlight the main findings in this field, including the current sample storage, DNA extraction, sequencing and data analysis techniques that are being used, and its potential applications in human trafficking and ancient DNA studies. Second, the challenges and limitations of forensic microbiomics and geolocation are emphasised, providing recommendations for the establishment of this tool in the forensic science community.
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Guan W, Yang S, Zhao Y, Cheng W, Song X, Yao Y, Xie Y, Du W, Li J. Observation of the Gut Microbiota Profile in C57BL/6 Mice Induced by Plasmodium berghei ANKA Infection. Front Cell Infect Microbiol 2021; 11:680383. [PMID: 34778098 PMCID: PMC8581563 DOI: 10.3389/fcimb.2021.680383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/14/2021] [Indexed: 12/24/2022] Open
Abstract
The genus of Plasmodium parasites can cause malaria, which is a prevalent infectious disease worldwide, especially in tropical and subtropical regions. C57BL/6 mice infected with P. berghei ANKA (PbA) will suffer from experimental cerebral malaria (ECM). However, the gut microbiota in C57BL/6 mice has rarely been investigated, especially regarding changes in the intestinal environment caused by infectious parasites. P. berghei ANKA-infected (PbA group) and uninfected C57BL/6 (Ctrl group) mice were used in this study. C57BL/6 mice were infected with PbA via intraperitoneal injection of 1 × 106 infected red blood cells. Fecal samples of two groups were collected. The microbiota of feces obtained from both uninfected and infected mice was characterized by targeting the V4 region of the 16S rRNA through the Illumina MiSeq platform. The variations in the total gut microbiota composition were determined based on alpha and beta diversity analyses of 16S rRNA sequencing. The raw sequences from all samples were generated and clustered using ≥ 97% sequence identity into many microbial operational taxonomic units (OTUs). The typical microbiota composition in the gut was dominated by Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia at the phylum level. Bacteroidetes and Verrucomicrobia were considerably decreased after PbA infection compared with the control group (Ctrl), while Firmicutes and Proteobacteria were increased substantially after PbA infection compared with Ctrl. The alpha diversity index showed that the observed OTU number was increased in the PbA group compared with the Ctrl group. Moreover, the discreteness of the beta diversity revealed that the PbA group samples had a higher number of OTUs than the Ctrl group. LEfSe analysis revealed that several potential bacterial biomarkers were clearly related to the PbA-infected mice at the phylogenetic level. Several bacterial genera, such as Acinetobacter, Lactobacillus, and Lachnospiraceae_NK4A136_group, were overrepresented in the PbA-infected fecal microbiota. Meanwhile, a method similar to gene coexpression network construction was used to generate the OTU co-abundance units. These results indicated that P. berghei ANKA infection could alter the gut microbiota composition of C57BL/6 mice. In addition, potential biomarkers should offer insight into malaria pathogenesis and antimalarial drug and malaria vaccine studies.
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Affiliation(s)
- Wei Guan
- Department of Human Parasitology, School of Basic Medicine, Hubei University of Medicine, Shiyan, China
| | - Shuguo Yang
- Department of Human Parasitology, School of Basic Medicine, Hubei University of Medicine, Shiyan, China
| | - Yanqing Zhao
- Department of Human Parasitology, School of Basic Medicine, Hubei University of Medicine, Shiyan, China
| | - Weijia Cheng
- Department of Human Parasitology, School of Basic Medicine, Hubei University of Medicine, Shiyan, China
| | - Xiaonan Song
- Department of Human Parasitology, School of Basic Medicine, Hubei University of Medicine, Shiyan, China
| | - Yi Yao
- Department of Human Parasitology, School of Basic Medicine, Hubei University of Medicine, Shiyan, China
| | - Yiting Xie
- Department of Human Parasitology, School of Basic Medicine, Hubei University of Medicine, Shiyan, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Jian Li
- Department of Human Parasitology, School of Basic Medicine, Hubei University of Medicine, Shiyan, China.,Department of Infectious Diseases, Renmin Hospital, Hubei University of Medicine, Shiyan, China
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24
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Shen C, Xu Y, Ji J, Wei J, Jiang Y, Yang Y, Yang M, Huang H, Zou R, Fang C, Zeng F, Yang F, Wang X, Yuan J, Li J, Wang X, Yang H, Gong S, Wang H, Xia H, Ma J, Liu Y. Intestinal microbiota has important effect on severity of hand foot and mouth disease in children. BMC Infect Dis 2021; 21:1062. [PMID: 34645414 PMCID: PMC8513321 DOI: 10.1186/s12879-021-06748-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 09/29/2021] [Indexed: 11/12/2022] Open
Abstract
Background The incidence of hand foot and mouth disease (HFMD) has increased in recent years, making it a very common childhood illness worldwide. The relationship between different enterovirus genotypes and disease severity is not clearly understood. Given that enteroviruses are transmitted through the gastrointestinal tract, we hypothesized that variation in intestinal microorganisms of the host might play a role in the prognosis of HFMD. Methods We carried out a meta-transcriptomic-wide association study of fecal samples obtained from a cohort of children (254 patients, 227 tested positive for enterovirus, including 16 patients co-infectied with 2 kinds of enterovirus) with mild and severe HFMD and healthy controls. Results We found there was no significant difference in the amount of each virus type between the mild and severe cases. Genes of enterovirus 71 (EV71) and coxsackievirus A (CV-A) from the severe and mild cases did not show significant clustering. Clostridium sp. L2-50 and Bacteroides stercoris ATCC 43183 were enriched in the guts of children with severe HFMD and KEGG enrichment was found between mild and severe cases. Conclusions Intestinal microorganisms appear to interact with enterovirus to determine the progression of HFMD. Genes of Bacteroides and Clostridium may be used as predictive markers for a more efficient prognosis and intervention. The enrichment of intestinal bacteria genes with functions may facilitate the development of severe symptoms for HFMD patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06748-7.
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Affiliation(s)
- Chenguang Shen
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China. .,School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| | - Yi Xu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510120, China
| | - Jingkai Ji
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jinli Wei
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Yujin Jiang
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Yang Yang
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Minghui Yang
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Huaxin Huang
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Rongrong Zou
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Chunxiao Fang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510120, China
| | - Fansen Zeng
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510120, China
| | - Fengxia Yang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510120, China
| | - Xinfa Wang
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Jing Yuan
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Jianmin Li
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Xianfeng Wang
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Science, Hangzhou, 310058, China
| | - Sitang Gong
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510120, China
| | - Hui Wang
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China.,BGI-Shenzhen, Shenzhen, 518083, China.,Department of Engineering Science, University of Oxford, Oxford, OX3 7DQ, UK
| | - Huimin Xia
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510120, China.
| | - Jinmin Ma
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Yingxia Liu
- Graduate Collaborative Training Base of the Third People's Hospital of Shenzhen, Hengyang Medical School, University of South China, Hunan, 421001, China.
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25
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Linking microbiota composition with antimalarial antibody response. Trends Parasitol 2021; 37:853-855. [PMID: 34391664 DOI: 10.1016/j.pt.2021.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022]
Abstract
Microbiota composition recently arose as a factor correlating with malaria infection. Mandal et al. showed, via cecal transplant and antibacterial treatment, that the mouse microbiota modulates parasitemia by affecting spleen germinal centers where B cells are matured. They further identified correlations between microbiota composition and malaria severity in Ugandan children.
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26
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Ward H, Kim K. Editorial overview. Curr Opin Microbiol 2021; 58:vi-ix. [PMID: 33328088 DOI: 10.1016/j.mib.2020.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Honorine Ward
- Departments of Medicine and Public Health and Community Medicine, Tufts University School of Medicine, United States; Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, United States
| | - Kami Kim
- Division of Infectious Diseases and International Medicine at the Morsani College of Medicine, University of South Florida, United States
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27
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Mandal RK, Denny JE, Namazzi R, Opoka RO, Datta D, John CC, Schmidt NW. Dynamic modulation of spleen germinal center reactions by gut bacteria during Plasmodium infection. Cell Rep 2021; 35:109094. [PMID: 33979614 PMCID: PMC8141963 DOI: 10.1016/j.celrep.2021.109094] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/08/2021] [Accepted: 04/15/2021] [Indexed: 12/16/2022] Open
Abstract
Gut microbiota educate the local and distal immune system in early life to imprint long-term immunological outcomes while maintaining the capacity to dynamically modulate the local mucosal immune system throughout life. It is unknown whether gut microbiota provide signals that dynamically regulate distal immune responses following an extra-gastrointestinal infection. We show here that gut bacteria composition correlated with the severity of malaria in children. Using the murine model of malaria, we demonstrate that parasite burden and spleen germinal center reactions are malleable to dynamic cues provided by gut bacteria. Whereas antibiotic-induced changes in gut bacteria have been associated with immunopathology or impairment of immunity, the data demonstrate that antibiotic-induced changes in gut bacteria can enhance immunity to Plasmodium. This effect is not universal but depends on baseline gut bacteria composition. These data demonstrate the dynamic communications that exist among gut bacteria, the gut-distal immune system, and control of Plasmodium infection.
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Affiliation(s)
- Rabindra K Mandal
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA; Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Joshua E Denny
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA
| | - Ruth Namazzi
- Department of Paediatrics and Child Health, Makerere University, Kampala, Uganda
| | - Robert O Opoka
- Department of Paediatrics and Child Health, Makerere University, Kampala, Uganda
| | - Dibyadyuti Datta
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chandy C John
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nathan W Schmidt
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA; Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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28
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Bamgbose T, Anvikar AR, Alberdi P, Abdullahi IO, Inabo HI, Bello M, Cabezas-Cruz A, de la Fuente J. Functional Food for the Stimulation of the Immune System Against Malaria. Probiotics Antimicrob Proteins 2021; 13:1254-1266. [PMID: 33791994 PMCID: PMC8012070 DOI: 10.1007/s12602-021-09780-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2021] [Indexed: 12/20/2022]
Abstract
Drug resistance has become a threat to global health, and new interventions are needed to control major infectious diseases. The composition of gut microbiota has been linked to human health and has been associated with severity of malaria. Fermented foods contribute to the community of healthy gut bacteria. Despite the studies connecting gut microbiota to the prevention of malaria transmission and severity, research on developing functional foods for the purpose of manipulating the gut microbiota for malaria control is limited. This review summarizes recent knowledge on the role of the gut microbiota in malaria prevention and treatment. This information should encourage the search for lactic acid bacteria expressing α-Gal and those that exhibit the desired immune stimulating properties for the development of functional food and probiotics for malaria control.
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Affiliation(s)
- Timothy Bamgbose
- ICMR, -National Institute of Malaria Research, Sector 8, Dwarka, New Delhi, India
- Department of Microbiology, Ahmadu Bello University, Samaru Zaria, Kaduna, Nigeria
| | - Anupkumar R Anvikar
- ICMR, -National Institute of Malaria Research, Sector 8, Dwarka, New Delhi, India
| | - Pilar Alberdi
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005, Ciudad Real, Spain
| | - Isa O Abdullahi
- Department of Microbiology, Ahmadu Bello University, Samaru Zaria, Kaduna, Nigeria
| | - Helen I Inabo
- Department of Microbiology, Ahmadu Bello University, Samaru Zaria, Kaduna, Nigeria
| | - Mohammed Bello
- Department of Veterinary Public Health and Preventive Medicine, Ahmadu Bello University, Samaru Zaria, Kaduna, Nigeria
| | - Alejandro Cabezas-Cruz
- UMR BIPAR, INRAE, ANSES, Ecole Nationale Vétérinaire D'Alfort, Université Paris-Est, 94700, Maisons-Alfort, France
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005, Ciudad Real, Spain.
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
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29
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Sainz T, Delgado J, Mendez‐Echevarría A, Santiago B, Lopez‐Varela E, Aguilera‐Alonso D, Saavedra‐Lozano J, Rodríguez‐Fernández R, Holguín Á, Navarro ML, Muñoz‐Fernández MÁ, Rivero‐Calle I, Solana MJ, López‐Herce J, Calvo C. The clinical relevance of the microbiome when managing paediatric infectious diseases-Narrative review. Acta Paediatr 2021; 110:441-449. [PMID: 32961592 DOI: 10.1111/apa.15578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/18/2020] [Accepted: 09/15/2020] [Indexed: 11/28/2022]
Abstract
In recent years, the field of infectious diseases has been hit by the overwhelming amount of information generated while the human microbiome is being disentangled. Based on the interaction between the microbiota and the immune system, the implications regarding infectious diseases are probably major and remain a challenge. AIMS This review was conceived as a comprehensive tool to provide an overview of the available evidence regarding the influence of the microbiome on infectious diseases in children. METHODS We present the main findings aroused from microbiome research in prevention, diagnosis and treatment of infectious disease under a paediatric perspective, to inform clinicians of the potential relevance of microbiome-related knowledge for translation to clinical practice. RESULTS AND CONCLUSION The evidence shown in this review highlights the numerous research gaps ahead and supports the need to move forward to integrating the so-called microbiome thinking into our routine clinical practice.
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Affiliation(s)
- Talía Sainz
- Hospital La Paz and La Paz Research Intitute (IdiPAZ) Madrid Spain
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
| | - Jaime Delgado
- Hospital La Paz and La Paz Research Intitute (IdiPAZ) Madrid Spain
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
| | - Ana Mendez‐Echevarría
- Hospital La Paz and La Paz Research Intitute (IdiPAZ) Madrid Spain
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
| | - Begoña Santiago
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
- Hospital General Universitario Gregorio Marañón and Research Institute IISGM Madrid Spain
| | - Elisa Lopez‐Varela
- ISGlobal, Barcelona Centre for International Health ResearchHospital Clinic ‐ Universitat de Barcelona Barcelona Spain
| | - David Aguilera‐Alonso
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
- Hospital General Universitario Gregorio Marañón and Research Institute IISGM Madrid Spain
| | - Jesús Saavedra‐Lozano
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
- Hospital General Universitario Gregorio Marañón and Research Institute IISGM Madrid Spain
| | - Rosa Rodríguez‐Fernández
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
- Hospital General Universitario Gregorio Marañón and Research Institute IISGM Madrid Spain
| | - África Holguín
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
- Ramón y Cajal Research Institute (IRyCIS)‐CIBERESP in Hospital Ramón y Cajal Madrid Spain
| | - Marisa L. Navarro
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
- Hospital General Universitario Gregorio Marañón and Research Institute IISGM Madrid Spain
| | - María Ángeles Muñoz‐Fernández
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
- Hospital General Universitario Gregorio Marañón and Research Institute IISGM Madrid Spain
| | - Irene Rivero‐Calle
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
- Hospital Clínico Universitario de Santiago‐CHUS and Health Research Institute of Santiago de Compostela (IDIS) Santiago de Compostela Spain
| | - María José Solana
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
- Hospital General Universitario Gregorio Marañón and Research Institute IISGM Madrid Spain
| | - Jesús López‐Herce
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
- Hospital General Universitario Gregorio Marañón and Research Institute IISGM Madrid Spain
| | - Cristina Calvo
- Hospital La Paz and La Paz Research Intitute (IdiPAZ) Madrid Spain
- The Traslational Research Network of Pediatric Infectious Diseases (RITIP) Madrid Spain
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30
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Eukaryotic and Prokaryotic Microbiota Interactions. Microorganisms 2020; 8:microorganisms8122018. [PMID: 33348551 PMCID: PMC7767281 DOI: 10.3390/microorganisms8122018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 12/12/2022] Open
Abstract
The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies were analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.
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Waide ML, Polidoro R, Powell WL, Denny JE, Kos J, Tieri DA, Watson CT, Schmidt NW. Gut Microbiota Composition Modulates the Magnitude and Quality of Germinal Centers during Plasmodium Infections. Cell Rep 2020; 33:108503. [PMID: 33326773 PMCID: PMC7772993 DOI: 10.1016/j.celrep.2020.108503] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/09/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023] Open
Abstract
Gut microbiota composition is associated with human and rodent Plasmodium infections, yet the mechanism by which gut microbiota affects the severity of malaria remains unknown. Humoral immunity is critical in mediating the clearance of Plasmodium blood stage infections, prompting the hypothesis that mice with gut microbiota-dependent decreases in parasite burden exhibit better germinal center (GC) responses. In support of this hypothesis, mice with a low parasite burden exhibit increases in GC B cell numbers and parasite-specific antibody titers, as well as better maintenance of GC structures and a more targeted, qualitatively different antibody response. This enhanced humoral immunity affects memory, as mice with a low parasite burden exhibit robust protection against challenge with a heterologous, lethal Plasmodium species. These results demonstrate that gut microbiota composition influences the biology of spleen GCs as well as the titer and repertoire of parasite-specific antibodies, identifying potential approaches to develop optimal treatments for malaria. Research has shown that gut microbiota composition influences malaria severity, but the mechanism has remained unclear. Waide et al. show that microbiota composition drives differences in the humoral immune response, including differences in germinal center cell numbers and parasite-specific antibodies, ultimately affecting the memory response to subsequent infection.
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Affiliation(s)
- Morgan L Waide
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA; Ryan White Center for Pediatric Infectious Diseases and Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rafael Polidoro
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Whitney L Powell
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA
| | - Joshua E Denny
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA
| | - Justin Kos
- Department of Biochemistry, University of Louisville, Louisville, KY, USA
| | - David A Tieri
- Department of Biochemistry, University of Louisville, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry, University of Louisville, Louisville, KY, USA
| | - Nathan W Schmidt
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA; Ryan White Center for Pediatric Infectious Diseases and Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
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Immune Response and Microbiota Profiles during Coinfection with Plasmodium vivax and Soil-Transmitted Helminths. mBio 2020; 11:mBio.01705-20. [PMID: 33082257 PMCID: PMC7587435 DOI: 10.1128/mbio.01705-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Plasmodium (malaria) and helminth parasite coinfections are frequent, and both infections can be affected by the host gut microbiota. However, the relationship between coinfection and the gut microbiota is unclear. By performing comprehensive analyses on blood/stool samples from 130 individuals in Colombia, we found that the gut microbiota may have a stronger relationship with the number of P. vivax (malaria) parasites than with the number of helminth parasites infecting a host. Microbiota analysis identified more predictors of the P. vivax parasite burden, whereas analysis of blood samples identified predictors of the helminth parasite burden. These results were unexpected, because we expected each parasite to be associated with greater differences in its biological niche (blood for P. vivax and the intestine for helminths). Instead, we find that bacterial taxa were the strongest predictors of P. vivax parasitemia levels, while circulating TGF-β levels were the strongest predictor of helminth parasite burdens. The role of the gut microbiota during coinfection with soil-transmitted helminths (STH) and Plasmodium spp. is poorly understood. We examined peripheral blood and fecal samples from 130 individuals who were either infected with Plasmodium vivax only, coinfected with P. vivax and STH, infected with STH alone, or not infected with either P. vivax or STH. In addition to a complete blood count (CBC) with differential, transcriptional profiling of peripheral blood samples was performed by transcriptome sequencing (RNA-Seq), fecal microbial communities were determined by 16S rRNA gene sequencing, and circulating cytokine levels were measured by bead-based immunoassays. Differences in blood cell counts, including an increased percentage of neutrophils, associated with a transcriptional signature of neutrophil activation, were driven primarily by P. vivax infection. P. vivax infection was also associated with increased levels of interleukin 6 (IL-6), IL-8, and IL-10; these cytokine levels were not affected by STH coinfection. Surprisingly, P. vivax infection was more strongly associated with differences in the microbiota than STH infection. Children infected with only P. vivax exhibited elevated Bacteroides and reduced Prevotella and Clostridiaceae levels, but these differences were not observed in individuals coinfected with STH. We also observed that P. vivax parasitemia was higher in the STH-infected population. When we used machine learning to identify the most important predictors of the P. vivax parasite burden (among P. vivax-infected individuals), bacterial taxa were the strongest predictors of parasitemia. In contrast, circulating transforming growth factor β (TGF-β) was the strongest predictor of the Trichuris trichiura egg burden. This study provides unexpected evidence that the gut microbiota may have a stronger link with P. vivax than with STH infection.
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33
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Waide ML, Schmidt NW. The gut microbiome, immunity, and Plasmodium severity. Curr Opin Microbiol 2020; 58:56-61. [PMID: 33007644 DOI: 10.1016/j.mib.2020.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/24/2020] [Indexed: 12/21/2022]
Abstract
Malaria continues to pose a severe threat to over half of the world's population each year. With no long-term, effective vaccine available and a growing resistance to antimalarials, there is a need for innovative methods of Plasmodium treatment. Recent evidence has pointed to a role of the composition of the gut microbiota in the severity of Plasmodium infection in both animal models and human studies. Further evidence has shown that the gut microbiota influences the adaptive immune response of the host, the arm of the immune system necessary for Plasmodium clearance, sustained Plasmodium immunity, and vaccine efficacy. Together, this illustrates the future potential of gut microbiota modulation as a novel method of preventing severe malaria.
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Affiliation(s)
- Morgan L Waide
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA; Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, and Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nathan W Schmidt
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, and Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
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Kappler K, Hennet T. Emergence and significance of carbohydrate-specific antibodies. Genes Immun 2020; 21:224-239. [PMID: 32753697 PMCID: PMC7449879 DOI: 10.1038/s41435-020-0105-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/14/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022]
Abstract
Carbohydrate-specific antibodies are widespread among all classes of immunoglobulins. Despite their broad occurrence, little is known about their formation and biological significance. Carbohydrate-specific antibodies are often classified as natural antibodies under the assumption that they arise without prior exposure to exogenous antigens. On the other hand, various carbohydrate-specific antibodies, including antibodies to ABO blood group antigens, emerge after the contact of immune cells with the intestinal microbiota, which expresses a vast diversity of carbohydrate antigens. Here we explore the development of carbohydrate-specific antibodies in humans, addressing the definition of natural antibodies and the production of carbohydrate-specific antibodies upon antigen stimulation. We focus on the significance of the intestinal microbiota in shaping carbohydrate-specific antibodies not just in the gut, but also in the blood circulation. The structural similarity between bacterial carbohydrate antigens and surface glycoconjugates of protists, fungi and animals leads to the production of carbohydrate-specific antibodies protective against a broad range of pathogens. Mimicry between bacterial and human glycoconjugates, however, can also lead to the generation of carbohydrate-specific antibodies that cross-react with human antigens, thereby contributing to the development of autoimmune disorders.
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Affiliation(s)
| | - Thierry Hennet
- Institute of Physiology, University of Zurich, Zurich, Switzerland.
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35
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Ashour DS, Othman AA. Parasite-bacteria interrelationship. Parasitol Res 2020; 119:3145-3164. [PMID: 32748037 DOI: 10.1007/s00436-020-06804-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/06/2020] [Indexed: 12/18/2022]
Abstract
Parasites and bacteria have co-evolved with humankind, and they interact all the time in a myriad of ways. For example, some bacterial infections result from parasite-dwelling bacteria as in the case of Salmonella infection during schistosomiasis. Other bacteria synergize with parasites in the evolution of human disease as in the case of the interplay between Wolbachia endosymbiont bacteria and filarial nematodes as well as the interaction between Gram-negative bacteria and Schistosoma haematobium in the pathogenesis of urinary bladder cancer. Moreover, secondary bacterial infections may complicate several parasitic diseases such as visceral leishmaniasis and malaria, due to immunosuppression of the host during parasitic infections. Also, bacteria may colonize the parasitic lesions; for example, hydatid cysts and skin lesions of ectoparasites. Remarkably, some parasitic helminths and arthropods exhibit antibacterial activity usually by the release of specific antimicrobial products. Lastly, some parasite-bacteria interactions are induced as when using probiotic bacteria to modulate the outcome of a variety of parasitic infections. In sum, parasite-bacteria interactions involve intricate processes that never cease to intrigue the researchers. However, understanding and exploiting these interactions could have prophylactic and curative potential for infections by both types of pathogens.
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Affiliation(s)
- Dalia S Ashour
- Medical Parasitology Department, Faculty of Medicine, Tanta University, Tanta, 31527, Egypt.
| | - Ahmad A Othman
- Medical Parasitology Department, Faculty of Medicine, Tanta University, Tanta, 31527, Egypt
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36
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Cassotta M, Forbes-Hernández TY, Calderón Iglesias R, Ruiz R, Elexpuru Zabaleta M, Giampieri F, Battino M. Links between Nutrition, Infectious Diseases, and Microbiota: Emerging Technologies and Opportunities for Human-Focused Research. Nutrients 2020; 12:E1827. [PMID: 32575399 PMCID: PMC7353391 DOI: 10.3390/nu12061827] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 02/06/2023] Open
Abstract
The interaction between nutrition and human infectious diseases has always been recognized. With the emergence of molecular tools and post-genomics, high-resolution sequencing technologies, the gut microbiota has been emerging as a key moderator in the complex interplay between nutrients, human body, and infections. Much of the host-microbial and nutrition research is currently based on animals or simplistic in vitro models. Although traditional in vivo and in vitro models have helped to develop mechanistic hypotheses and assess the causality of the host-microbiota interactions, they often fail to faithfully recapitulate the complexity of the human nutrient-microbiome axis in gastrointestinal homeostasis and infections. Over the last decade, remarkable progress in tissue engineering, stem cell biology, microfluidics, sequencing technologies, and computing power has taken place, which has produced a new generation of human-focused, relevant, and predictive tools. These tools, which include patient-derived organoids, organs-on-a-chip, computational analyses, and models, together with multi-omics readouts, represent novel and exciting equipment to advance the research into microbiota, infectious diseases, and nutrition from a human-biology-based perspective. After considering some limitations of the conventional in vivo and in vitro approaches, in this review, we present the main novel available and emerging tools that are suitable for designing human-oriented research.
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Affiliation(s)
- Manuela Cassotta
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), 39001 Santander, Spain; (M.C.); (R.C.I.); (R.R.)
| | - Tamara Yuliett Forbes-Hernández
- Department of Analytical and Food Chemistry, Nutrition and Food Science Group, CITACA, CACTI, University of Vigo, 36310 Vigo, Spain;
| | - Ruben Calderón Iglesias
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), 39001 Santander, Spain; (M.C.); (R.C.I.); (R.R.)
| | - Roberto Ruiz
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), 39001 Santander, Spain; (M.C.); (R.C.I.); (R.R.)
| | - Maria Elexpuru Zabaleta
- Dipartimento di Scienze Cliniche e Molecolari, Facoltà di Medicina, Università Politecnica delle Marche, 60131 Ancona, Italy;
| | - Francesca Giampieri
- Department of Analytical and Food Chemistry, Nutrition and Food Science Group, CITACA, CACTI, University of Vigo, 36310 Vigo, Spain;
- Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, 60131 Ancona, Italy
- College of Food Science and Technology, Northwest University, Xi’an 710069, China
| | - Maurizio Battino
- Department of Analytical and Food Chemistry, Nutrition and Food Science Group, CITACA, CACTI, University of Vigo, 36310 Vigo, Spain;
- Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, 60131 Ancona, Italy
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
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Mandal RK, Crane RJ, Berkley JA, Gumbi W, Wambua J, Ngoi JM, Ndungu FM, Schmidt NW. Longitudinal Analysis of Infant Stool Bacteria Communities Before and After Acute Febrile Malaria and Artemether-Lumefantrine Treatment. J Infect Dis 2020; 220:687-698. [PMID: 30590681 PMCID: PMC6639600 DOI: 10.1093/infdis/jiy740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/22/2018] [Indexed: 12/24/2022] Open
Abstract
Background Gut microbiota were recently shown to impact malaria disease progression and outcome, and prior studies have shown that Plasmodium infections increase the likelihood of enteric bacteria causing systemic infections. Currently, it is not known whether Plasmodium infection impacts human gut microbiota as a prelude to bacteremia or whether antimalarials affect gut microbiota. Our goal was to determine to what degree Plasmodium infections and antimalarial treatment affect human gut microbiota. Methods One hundred Kenyan infants underwent active surveillance for malaria from birth to 10 months of age. Each malaria episode was treated with artemether-lumefantrine (AL). Any other treatments, including antibiotics, were recorded. Stool samples were collected on an approximately biweekly basis. Ten children were selected on the basis of stool samples having been collected before (n = 27) or after (n = 17) a malaria episode and without antibiotics having been administered between collections. These samples were subjected to 16S ribosomal ribonucleic acid gene (V3–V4 region) sequencing. Results Bacterial community network analysis revealed no obvious differences in the before and after malaria/AL samples, which was consistent with no difference in alpha and beta diversity and taxonomic analysis at the family and genus level with one exception. At the sequence variant (SV) level, akin to bacterial species, only 1 of the top 100 SVs was significantly different. In addition, predicted metagenome analysis revealed no significant difference in metagenomic capacity between before and after malaria/AL samples. The number of malaria episodes, 1 versus 2, explained significant variation in gut microbiota composition of the infants. Conclusions In-depth bioinformatics analysis of stool bacteria has revealed for the first time that human malaria episode/AL treatment have minimal effects on gut microbiota in Kenyan infants.
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Affiliation(s)
- Rabindra K Mandal
- Department of Microbiology and Immunology, University of Louisville, Kentucky
| | - Rosie J Crane
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, United Kingdom
| | - James A Berkley
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, United Kingdom
| | - Wilson Gumbi
- KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | - Nathan W Schmidt
- Department of Microbiology and Immunology, University of Louisville, Kentucky
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Rajagopala SV, Singh H, Yu Y, Zabokrtsky KB, Torralba MG, Moncera KJ, Frank B, Pieper R, Sender L, Nelson KE. Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy. MICROBIAL ECOLOGY 2020; 79:1034-1043. [PMID: 31754744 DOI: 10.1007/s00248-019-01448-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Prophylactic or therapeutic antibiotic use along with chemotherapy treatment potentially has a long-standing adverse effect on the resident gut microbiota. We have established a case-control cohort of 32 pediatric and adolescent acute lymphoblastic leukemia (ALL) patients and 25 healthy siblings (sibling controls) to assess the effect of chemotherapy as well as antibiotic prophylaxis on the gut microbiota. We observe that the microbiota diversity and richness of the ALL group is significantly lower than that of the control group at diagnosis and during chemotherapy. The microbiota diversity is even lower in antibiotics-exposed ALL patients. Although the gut microbial diversity tends to stabilize after 1-year post-chemotherapy, their abundances were altered because of chemotherapy and prophylactic antibiotic treatments. Specifically, the abundances of mucolytic gram-positive anaerobic bacteria, including Ruminococcus gnavus and Ruminococcus torques, tended to increase during the chemotherapy regimen and continued to be elevated 1 year beyond the initiation of chemotherapy. This dysbiosis may contribute to the development of gastrointestinal complications in ALL children following chemotherapy. These findings set the stage to further understand the role of the gut microbiome dynamics in ALL patients and their potential role in alleviating some of the adverse side effects of chemotherapy and antibiotics use in immunocompromised children.
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Affiliation(s)
- Seesandra V Rajagopala
- J. Craig Venter Institute (JCVI), Rockville, MD, USA
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Yanbao Yu
- J. Craig Venter Institute (JCVI), Rockville, MD, USA
| | - Keri B Zabokrtsky
- Hyundai Cancer Genomics Center, Children's Hospital Orange County (CHOC Children's), Orange, CA, USA
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of California-Irvine, Orange, CA, USA
| | | | | | - Bryan Frank
- J. Craig Venter Institute (JCVI), Rockville, MD, USA
| | | | - Leonard Sender
- Hyundai Cancer Genomics Center, Children's Hospital Orange County (CHOC Children's), Orange, CA, USA
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of California-Irvine, Orange, CA, USA
- Division of Oncology, Hyundai Cancer Institute, CHOC Children's, Orange, CA, USA
- Department of Pediatrics, School of Medicine, University of California-Irvine, Orange, CA, USA
| | - Karen E Nelson
- J. Craig Venter Institute (JCVI), Rockville, MD, USA
- J. Craig Venter Institute (JCVI), La Jolla, CA, USA
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39
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Ordiz MI, Janssen S, Humphrey G, Ackermann G, Stephenson K, Agapova S, Divala O, Kaimila Y, Maleta K, Zhong C, Knight R, Trehan I, Tarr PI, Rusconi B, Manary MJ. The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months. Am J Clin Nutr 2020; 111:884-892. [PMID: 32047925 PMCID: PMC8287943 DOI: 10.1093/ajcn/nqaa011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Common bean and cowpea contain about 25% protein and 25% fiber, and are recommended as complementary foods in sub-Saharan Africa. OBJECTIVE The objective of this study was to determine if a daily legume supplement given to Malawian infants aged 6 to 12 mo alters the 16S configuration of the fecal microbiota as read out by amplicon sequence variants (ASVs). METHODS This study was conducted within the context of a randomized, double-blind, controlled clinical trial to assess whether cowpea or common bean supplementation reduced intestinal permeability or increased linear growth. There were 2 village clusters in which the study was conducted. Fresh stool collections were flash frozen from 236 infants at ≤6 time points. The stools were sequenced using Earth Microbiome project protocols and data were processed using Qiime and Qiita, open-source, validated software packages. α-diversity was measured using the Faith's test. The 16S configuration was characterized by determining the weighted UniFrac distances of the ASVs and comparing them using permutational multivariate ANOVA. RESULTS Among the 1249 samples analyzed, the α-diversity of the fecal microbiome was unchanged among subjects after initiation of legume supplementation. Neither cowpea nor common bean altered the overall 16S configuration at any age. The 16S configuration differed between children with adequate and poor linear growth aged from 6 to 9 mo, but no specific ASVs differed in relative abundance. The 16S configuration differed between children with normal and abnormal intestinal permeability at 9 mo, but no specific ASVs differed in relative abundance. Among categorical characteristics of the population associated with different 16S configurations, village cluster was most pronounced. CONCLUSION Legume supplementation in breastfed, rural African infants did not affect the structure of the gut microbial communities until the children were aged 9 mo. This trial was registered at clinicaltrials.gov as NCT02472262.
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Affiliation(s)
- M Isabel Ordiz
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
| | - Kevin Stephenson
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Sophia Agapova
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Oscar Divala
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
| | - Yankho Kaimila
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
| | - Ken Maleta
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
| | - Caroline Zhong
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La
Jolla, CA, USA
- Department of Computer Science and Engineering, University of
California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego,
La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San
Diego, La Jolla, CA, USA
| | - Indi Trehan
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
- Department of Paediatrics and Child Health, University of Malawi,
Blantyre, Malawi
| | - Phillip I Tarr
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Brigida Rusconi
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
| | - Mark J Manary
- Department of Pediatrics, Washington University at St. Louis, St.
Louis, MO, USA
- Department of Community Health, College of Medicine, University of
Malawi, Malawi
- USDA/Agricultural Research Service Children's Nutrition Research
Center, Houston, TX, USA
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40
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Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen GL. Emerging Priorities for Microbiome Research. Front Microbiol 2020; 11:136. [PMID: 32140140 PMCID: PMC7042322 DOI: 10.3389/fmicb.2020.00136] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external environment as part of an ecological community. Understanding the role of microbiota, including their dynamic interactions with their hosts and other microbes, can enable the engineering of new diagnostic techniques and interventional strategies that can be used in a diverse spectrum of fields, spanning from ecology and agriculture to medicine and from forensics to exobiology. From June 19-23 in 2017, the NIH and NSF jointly held an Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome. This review is inspired by some of the topics that arose as priority areas from this unique, interactive workshop. The goal of this review is to summarize the Innovation Lab's findings by introducing the reader to emerging challenges, exciting potential, and current directions in microbiome research. The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe interactions, (3) analytical and mathematical methods currently used in microbiome research, (4) leveraging knowledge of microbial composition and interactions to develop engineering solutions, and (5) interventional approaches and engineered microbiota that may be enabled by selectively altering microbial composition. As such, this review seeks to arm the reader with a broad understanding of the priorities and challenges in microbiome research today and provide inspiration for future investigation and multi-disciplinary collaboration.
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Affiliation(s)
- Chad M. Cullen
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
| | | | - Sinem Beyhan
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, United States
| | - Clara E. Cho
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, Logan, UT, United States
| | - Stephen Woloszynek
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
- College of Medicine, Drexel University, Philadelphia, PA, United States
| | - Matteo Convertino
- Nexus Group, Faculty of Information Science and Technology, Gi-CoRE Station for Big Data & Cybersecurity, Hokkaido University, Sapporo, Japan
| | - Sophie J. McCoy
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Yanyan Zhang
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Matthew Z. Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | | | - Ekaterina Smirnova
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, United States
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ananya Sen Gupta
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA, United States
| | - Kevin Cheung
- Department of Dermatology, The University of Iowa, Iowa City, IA, United States
| | | | - Zhengqiao Zhao
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
| | - Gail L. Rosen
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
- Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States
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Huwe T, Prusty BK, Ray A, Lee S, Ravindran B, Michael E. Interactions between Parasitic Infections and the Human Gut Microbiome in Odisha, India. Am J Trop Med Hyg 2020; 100:1486-1489. [PMID: 30963988 DOI: 10.4269/ajtmh.18-0968] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Soil-transmitted helminth (STH) infections and malaria are parasitic diseases with enormous global health burdens. Research has demonstrated a relationship between each of these parasites and the gut microbiome, suggesting that the gut microbiota may be implicated in governing host susceptibility to diverse pathogens, and perhaps even coinfection by different pathogens, through similar microbiome-influenced pathways. Here, we have derived a first microbiome community profile associated with STH infections in Odisha, India, and tested the hypothesis that the gut microbiome can modulate host susceptibility to multiple parasite infections through the same pathways. This study revealed several bacterial taxa negatively associated with specific STH infections, including Lactobacillus and Lachnospiracaea. Our results also suggest that relative abundance of Lactobacillus is driven by the STH infection status more so than by the Plasmodium infection status. This study contributes to efforts to understand the effects of the microbiome on host susceptibility to parasitic infections in endemic communities.
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Affiliation(s)
- Tiffany Huwe
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | | | - Aisurya Ray
- Institute of Life Sciences, Bhubaneswar, India
| | - Shaun Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | | | - Edwin Michael
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
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42
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Lee MK, Binns C. Breastfeeding and the Risk of Infant Illness in Asia: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 17:E186. [PMID: 31888064 PMCID: PMC6981475 DOI: 10.3390/ijerph17010186] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022]
Abstract
Infancy remains the most vulnerable period of human life for death, illness, and establishing a lifetime trajectory of growth and health. It is estimated that there are 5.3 million deaths under five years of age worldwide and approximately 800,000 lives could be saved by improving breastfeeding rates and duration. In Asia, an estimated 300,000-350,000 child deaths could be prevented with optimal breastfeeding and the majority would be under 12 months of age. We present a systematic review of studies of infection and breastfeeding in infants in Asia and further review interactions of selected infectious diseases and breastfeeding. Initially, 2459 records of possible interest were identified, 153 full text papers were reviewed in detail, and 13 papers describing diarrhoeal disease and/or acute respiratory tract infection were selected for inclusion in the review. Additional papers were selected to discuss specific diseases and their relationship to breastfeeding. The review found that a variety of methods were used with differing definitions of breastfeeding and diseases. Overall, breastfeeding when compared to the use of infant formula, is associated with significantly lower rates of diarrhoeal disease and lower respiratory tract infection, with a reduction of 50% or more to be expected, especially in infants under six months of age. The relationship between breastfeeding and specific diseases including measles and HTLV1 were reviewed. Breastfeeding reduces some disease rates, but there remain a few conditions where breastfeeding may be contra-indicated.
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Affiliation(s)
- Mi Kyung Lee
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Colin Binns
- School of Public Health, Curtin University, Bentley, WA 6102, Australia
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43
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Fan ZG, Li X, Fu HY, Zhou LM, Gong FL, Fang M. Gut Microbiota Reconstruction Following Host Infection with Blood-stage Plasmodium berghei ANKA Strain in a Murine Model. Curr Med Sci 2019; 39:883-889. [PMID: 31845218 DOI: 10.1007/s11596-019-2119-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/27/2019] [Indexed: 12/27/2022]
Abstract
Malaria remains a global health problem. The relationship between Plasmodium spp. and the gut microbiota as well as the impact of Plasmodium spp. on the gut microbiota in vertebrate hosts is unclear. The aim of the current study was to evaluate the effect of blood-stage Plasmodium parasites on the gut microbiota of mice. The gut microbiota was analyzed by 16S rRNA sequencing and bioinformatic analyses at three stages. The gut microbiota changed during the three phases: the healthy stage, the infection stage, and the cure stage (on the 9th day after malarial elimination). Moreover, the gut microbiota of these infected animals did not recover after malaria infection. There were 254 operational taxonomic units (OTUs) across all three stages, and there were unique strains or OTUs at each stage of the experiment. The percentages of community abundance of 8 OTUs changed significantly (P<0.05). The dominant OTU in both the healthy mice and the mice with malaria was OTU265, while that in the cured mice was OTU234. In addition, the changes in OTU147 were the most noteworthy. Its percentage of community abundance varied greatly, with higher values during malaria than before malaria infection and after malaria elimination. These results indicated that the external environment influenced the gut microbiota after host C57BL/6 mice were infected with blood-stage P. berghei ANKA and that the same was true during and after elimination of blood-stage P. berghei ANKA. In addition, we could not isolate OTU147 for further study. This study identified gut microbiota components that were reconstructed after infection by and elimination of blood-stage P. berghei ANKA in host C57BL/6 mice, and this process was affected by P. berghei ANKA and the external environment of the host.
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Affiliation(s)
- Zhi-Gang Fan
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Pathogenic Biology, Hainan Medical University, Haikou, 571199, China
| | - Xiao Li
- Department of Pathogenic Biology, Hainan Medical University, Haikou, 571199, China
| | - Hai-Yi Fu
- Department of Pathogenic Biology, Hainan Medical University, Haikou, 571199, China
| | - Li-Min Zhou
- Department of Pathogenic Biology, Hainan Medical University, Haikou, 571199, China
| | - Fei-Li Gong
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Min Fang
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Mukherjee D, Chora ÂF, Mota MM. Microbiota, a Third Player in the Host-Plasmodium Affair. Trends Parasitol 2019; 36:11-18. [PMID: 31787522 DOI: 10.1016/j.pt.2019.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022]
Abstract
Plasmodium, the causative agent of malaria, is responsible for more than 200 million new infections and 400 000 deaths yearly. While in recent years the influence of the microbiota in homeostasis and a wide variety of disorders has taken center stage, its contribution during malaria infections has only now started to emerge. The few published studies suggest two distinct but complementary directions. Plasmodium infections can cause significant alterations in host (at least gut) microbiota, and host gut microbiota can influence the clinical outcome of malaria infections. In this opinion article, we highlight the most fundamental unanswered questions in the field that will, hopefully, point future research directions towards unveiling key mechanistic insights of the Plasmodium-host-microbiota axis.
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Affiliation(s)
- Debanjan Mukherjee
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | - Ângelo Ferreira Chora
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Maria M Mota
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal.
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45
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Tran TM, Crompton PD. Decoding the complexities of human malaria through systems immunology. Immunol Rev 2019; 293:144-162. [PMID: 31680289 DOI: 10.1111/imr.12817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022]
Abstract
The complexity of the Plasmodium parasite and its life cycle poses a challenge to our understanding of the host immune response against malaria. Studying human immune responses during natural and experimental Plasmodium infections can enhance our understanding of malaria-protective immunity and inform the design of disease-modifying adjunctive therapies and next-generation malaria vaccines. Systems immunology can complement conventional approaches to facilitate our understanding of the complex immune response to the highly dynamic malaria parasite. In this review, recent studies that used systems-based approaches to evaluate human immune responses during natural and experimental Plasmodium falciparum and Plasmodium vivax infections as well as during immunization with candidate malaria vaccines are summarized and related to each other. The potential for next-generation technologies to address the current limitations of systems-based studies of human malaria are discussed.
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Affiliation(s)
- Tuan M Tran
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.,Ryan White Center for Pediatric Infectious Disease and Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
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Harris EV, de Roode JC, Gerardo NM. Diet-microbiome-disease: Investigating diet's influence on infectious disease resistance through alteration of the gut microbiome. PLoS Pathog 2019; 15:e1007891. [PMID: 31671152 PMCID: PMC6822718 DOI: 10.1371/journal.ppat.1007891] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Abiotic and biotic factors can affect host resistance to parasites. Host diet and host gut microbiomes are two increasingly recognized factors influencing disease resistance. In particular, recent studies demonstrate that (1) particular diets can reduce parasitism; (2) diets can alter the gut microbiome; and (3) the gut microbiome can decrease parasitism. These three separate relationships suggest the existence of indirect links through which diets reduce parasitism through an alteration of the gut microbiome. However, such links are rarely considered and even more rarely experimentally validated. This is surprising because there is increasing discussion of the therapeutic potential of diets and gut microbiomes to control infectious disease. To elucidate these potential indirect links, we review and examine studies on a wide range of animal systems commonly used in diet, microbiome, and disease research. We also examine the relative benefits and disadvantages of particular systems for the study of these indirect links and conclude that mice and insects are currently the best animal systems to test for the effect of diet-altered protective gut microbiomes on infectious disease. Focusing on these systems, we provide experimental guidelines and highlight challenges that must be overcome. Although previous studies have recommended these systems for microbiome research, here we specifically recommend these systems because of their proven relationships between diet and parasitism, between diet and the microbiome, and between the microbiome and parasite resistance. Thus, they provide a sound foundation to explore the three-way interaction between diet, the microbiome, and infectious disease.
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Affiliation(s)
- Erica V. Harris
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
| | - Jacobus C. de Roode
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Nicole M. Gerardo
- Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, Georgia, United States of America
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Loiseau C, Cooper MM, Doolan DL. Deciphering host immunity to malaria using systems immunology. Immunol Rev 2019; 293:115-143. [PMID: 31608461 DOI: 10.1111/imr.12814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022]
Abstract
A century of conceptual and technological advances in infectious disease research has changed the face of medicine. However, there remains a lack of effective interventions and a poor understanding of host immunity to the most significant and complex pathogens, including malaria. The development of successful interventions against such intractable diseases requires a comprehensive understanding of host-pathogen immune responses. A major advance of the past decade has been a paradigm switch in thinking from the contemporary reductionist (gene-by-gene or protein-by-protein) view to a more holistic (whole organism) view. Also, a recognition that host-pathogen immunity is composed of complex, dynamic interactions of cellular and molecular components and networks that cannot be represented by any individual component in isolation. Systems immunology integrates the field of immunology with omics technologies and computational sciences to comprehensively interrogate the immune response at a systems level. Herein, we describe the system immunology toolkit and report recent studies deploying systems-level approaches in the context of natural exposure to malaria or controlled human malaria infection. We contribute our perspective on the potential of systems immunity for the rational design and development of effective interventions to improve global public health.
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Affiliation(s)
- Claire Loiseau
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Martha M Cooper
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
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Abstract
OBJECTIVES The determinants of gut microbiota composition and its effects on common childhood illnesses are only partly understood, especially in low-income settings. The aim of the present study was to investigate whether morbidity predicts gut microbiota composition in Malawian children and whether microbiota predicts subsequent morbidity. We tested the hypothesis that common infectious disease symptoms would be predictive of lower microbiota maturity and diversity. METHODS We used data from 631 participants in a randomized-controlled nutrition intervention trial, in which a small-quantity lipid-based nutrient supplement was provided to pregnant and lactating mothers and their children at 6 to 18 months of age. Fecal samples were collected from the children at 6, 12, 18, and 30 months of age and analyzed using 16S rRNA sequencing. Microbiota variables consisted of measures of microbiota diversity (Shannon Index), microbiota maturity (microbiota-for-age z score), and the relative abundances of taxa. Morbidity variables included gastrointestinal and respiratory symptoms and fever. RESULTS Diarrhea and respiratory symptoms from 11 to 12 months were predictive of lower microbiota-for-age z score and higher Shannon Index, respectively (P = 0.035 and P = 0.023). Morbidity preceding sample collection was predictive of the relative abundances of several bacterial taxa at all time points. Higher microbiota maturity and diversity at 6 months were predictive of a lower incidence rate of fever in the subsequent 6 months (P = 0.007 and P = 0.031). CONCLUSIONS Our findings generally do not support the hypothesis that morbidity prevalence predicts a subsequent decrease in gut microbiota maturity or diversity in rural Malawian children. Certain morbidity symptoms may be predictive of microbiota maturity and diversity and relative abundances of several bacterial taxa. Furthermore, microbiota diversity and maturity may be associated with the subsequent incidence of fever.
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Abstract
MOTIVATION The interactions among the constituent members of a microbial community play a major role in determining the overall behavior of the community and the abundance levels of its members. These interactions can be modeled using a network whose nodes represent microbial taxa and edges represent pairwise interactions. A microbial network is typically constructed from a sample-taxa count matrix that is obtained by sequencing multiple biological samples and identifying taxa counts. From large-scale microbiome studies, it is evident that microbial community compositions and interactions are impacted by environmental and/or host factors. Thus, it is not unreasonable to expect that a sample-taxa matrix generated as part of a large study involving multiple environmental or clinical parameters can be associated with more than one microbial network. However, to our knowledge, microbial network inference methods proposed thus far assume that the sample-taxa matrix is associated with a single network. RESULTS We present a mixture model framework to address the scenario when the sample-taxa matrix is associated with K microbial networks. This count matrix is modeled using a mixture of K Multivariate Poisson Log-Normal distributions and parameters are estimated using a maximum likelihood framework. Our parameter estimation algorithm is based on the minorization-maximization principle combined with gradient ascent and block updates. Synthetic datasets were generated to assess the performance of our approach on absolute count data, compositional data and normalized data. We also addressed the recovery of sparse networks based on an l1-penalty model. AVAILABILITY AND IMPLEMENTATION MixMPLN is implemented in R and is freely available at https://github.com/sahatava/MixMPLN. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sahar Tavakoli
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, USA
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Brewster R, Tamburini FB, Asiimwe E, Oduaran O, Hazelhurst S, Bhatt AS. Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation. Trends Microbiol 2019; 27:824-835. [PMID: 31178123 DOI: 10.1016/j.tim.2019.05.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/09/2019] [Accepted: 05/15/2019] [Indexed: 12/16/2022]
Abstract
Descriptive and translational investigations into the human gut microbiome (GM) are rapidly expanding; however, studies are largely restricted to industrialized populations in the USA and Europe. Little is known about microbial variability and its implications for health and disease in other parts of the world. Populations in Africa are particularly underrepresented. What limited research has been performed has focused on a few subject domains, including the impact of long-term lifestyle and dietary factors on GM ecology, its maturation during infancy, and the interrelationships between the microbiome, infectious disease, and undernutrition. Recently, international consortia have laid the groundwork for large-scale genomics and microbiome studies on the continent, with a particular interest in the epidemiologic transition to noncommunicable disease. Here, we survey the current landscape of GM scholarship in Africa and propose actionable recommendations to improve research capacity and output.
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Affiliation(s)
- Ryan Brewster
- School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Edgar Asiimwe
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Ovokeraye Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa; School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.
| | - Ami S Bhatt
- School of Medicine, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine (Hematology), Stanford University, Stanford, CA, USA.
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