Longitudinal Analysis of Infant Stool Bacteria Communities Before and After Acute Febrile Malaria and Artemether-Lumefantrine Treatment

Gut microbiota composition differences are associated with geographic location and age in malaria-endemic regions of Rwanda

Evidence suggests that a significant interplay exists between the host gut microbiota and both the transmission and severity of malaria. Therefore, we explored the association between malaria and the gut microbiota across various geographic regions, considering host's nutritional habits, helminth coinfections and age. This observational study was conducted in 3 malaria-endemic provinces of Rwanda: West, South and East. Demographic data, blood and fecal samples were collected from 169 participants (85 females and 84 males) aged between 2-78 years. We used questionnaire-derived qualitative data based on geographic regions, age, and nutrition. Malaria and soil-transmitted helminth diagnosis was assessed by microscopy. The gut microbial composition was analyzed based on bacterial 16S rRNA gene amplicon sequencing. We observed that preschool children had a significantly lower microbiota diversity compared to both school children (q = 0.027, K-Wallis) and adults (q = 0.011, K-Wallis). Unlike age, infection status (uninfected, malaria alone, soil-transmitted helminth alone or coinfection) was not significantly associated with the gut microbiota. However, using Bray-Curtis distances, we found a significantly differential gut microbial beta-diversity with a convergent distribution in the Western province compared to the other provinces (q = 0.0045, pairwise PERMANOVA). This geographic difference was not explained by any change in energy intake, protein, lipids, or carbohydrates consumption but was likely due to lower dietary fibre intake in the West compared to the South (q < 0.0001, ANOVA) and the East (q = 0.07, ANOVA). In conclusion, we have not found significant links between infection and gut microbiota. However, we showed a significant difference in the gut microbiota composition of people living in different geographic locations in Rwanda, possibly due to their nutritional habits.

Gut microbiota influences Plasmodium falciparum malaria susceptibility

Background

The gut microbiota has recently been associated with malaria susceptibility/resistance in animal models and humans. This study aimed to assess its influence on malaria attack and Plasmodium parasitemia in children living in a malaria-endemic area of Mali.

Methods

Healthy children were enrolled in a 16-month cohort study in Bandiagara. Their gut bacteria and fungi community structures were characterized via 16S and ITS metabarcoding at enrolment. Clinicians monitored malaria attacks. Asymptomatic Plasmodium carriage was assessed by real-time polymerase chain reaction.

Results

Of the 300 children, 107 (36 %) had at least one malaria attack, and 82 (27 %) had at least one episode of asymptomatic Plasmodium parasitemia. The gut bacterial community structure, but not the fungal community, was associated with susceptibility/resistance to both malaria attacks and asymptomatic P. falciparum parasitemia. Higher gut bacteria richness was independently associated with susceptibility to both asymptomatic parasitemia episodes and malaria attacks. 17 bacteria, and 7 fungi were associated with susceptibility to malaria attacks, and 8 bacteria, and 3 fungi were associated with resistance. 15 bacteria and 13 fungi were associated with susceptibility to asymptomatic Plasmodium parasitemia episodes, and 19 bacteria and 3 fungi were associated with resistance.

Conclusion

Further studies are needed to confirm these findings, which point the way to strategies aimed at reducing the risk of malaria by modulating gut microbiota components in at-risk populations.

Applicability of Redirecting Artemisinins for New Targets

Employing new therapeutic indications for drugs that are already approved for human use has obvious advantages, including reduced costs and timelines, because some routine steps of drug development and regulation are not required. This work concentrates on the redirection of artemisinins (ARTS) that already are approved for clinical use, or investigated, for malaria treatment. Several mechanisms of action are suggested for ARTS, among which only a few have been successfully examined in vivo, mainly the induction of oxidant stress and anti-inflammatory effects. Despite these seemingly contradictory effects, ARTS are proposed for repurposing in treatment of inflammatory disorders and diverse types of diseases caused by viral, bacterial, fungal, and parasitic infections. When pathogens are treated the expected outcome is diminution of the causative agents and/or their inflammatory damage. In general, repurposing ARTS is successful in only a very few cases, specifically when a valid mechanism can be targeted using an additional therapeutic agent and appropriate drug delivery. Investigation of repurposing should include optimization of drug combinations followed by examination in relevant cell lines, organoids, and animal models, before moving to clinical trials.

Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria

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.

A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa

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.

Mouse Models for Unravelling Immunology of Blood Stage Malaria

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.

Possible Interactions between Malaria, Helminthiases and the Gut Microbiota: A Short Review

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.

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research

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.

Dynamic modulation of spleen germinal center reactions by gut bacteria during Plasmodium infection

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.

Gut Microbiota Composition Modulates the Magnitude and Quality of Germinal Centers during Plasmodium Infections

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.

Immune Response and Microbiota Profiles during Coinfection with Plasmodium vivax and Soil-Transmitted Helminths

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.

The gut microbiome, immunity, and Plasmodium severity

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.

Oral Administration of Clinically Relevant Antimalarial Drugs Does Not Modify the Murine Gut Microbiota

Malaria is an infectious disease responsible for the death of around 450,000 people annually. As an effective vaccine against the parasite that causes malaria is not available, antimalarial drug treatments are critical in fighting the disease. Previous data has shown that the gut microbiota is important in modulating the severity of malaria. Although it is well appreciated that antibiotics substantially alter the gut microbiota, it is largely unknown how antimalarial drugs impact the gut microbiota. We show here that the two commonly used artemisinin combination therapies of artesunate plus amodiaquine and artemether plus lumefantrine do not change the gut microbiota. The overall relative species abundance and alpha diversity remained stable after treatment, while beta diversity analysis showed minimal changes due to drug treatment, which were transient and quickly returned to baseline. Additionally, treatment with antimalarial drugs did not change the kinetics of later Plasmodium infection. Taken together, antimalarial drug administration does not affect the gut microbiota.