Abstract
Cerebral malaria (CM) is the most severe form of malaria with the highest mortality rate and can result in life-long neurological deficits and ongoing comorbidities. Factors contributing to severity of infection and development of CM are not fully elucidated. Recent studies have indicated a key role of the gut microbiome in a range of health conditions that affect the brain, but limited microbiome research has been conducted in the context of malaria. To address this knowledge gap, the impact of CM on the gut microbiome was investigated in mice. C57BL/6J mice were infected with Plasmodium berghei ANKA (PbA) parasites and compared to non-infected controls. Microbial DNA from faecal pellets collected daily for 6-days post-infection were extracted, and microbiome comparisons conducted using 16S rRNA profiling. We identified significant differences in the composition of bacterial communities between the infected and the non-infected groups, including a higher abundance of the genera Akkermansia, Alistipes and Alloprevotella in PbA-infected mice. Furthermore, intestinal samples were collected post-cull for morphological analysis. We determined that the caecal weight was significantly lower, and the small intestine was significantly longer in PbA-infected mice than in the non-infected controls. We concluded that changes in microbial community composition were primarily driven by the infection protocol and, to a lesser extent, by the time of infection. Our findings pave the way for a new area of research and novel intervention strategies to modulate the severity of cerebral malaria disease.
Similar content being viewed by others
Data availability
Not applicable.
References
Adams JB, Johansen LJ, Powell LD, Quig D, Rubin RA (2011) Gastrointestinal flora and gastrointestinal status in children with autism-comparisons to typical children and correlation with autism severity. BMC Gastroenterol 11:22. https://doi.org/10.1186/1471-230x-11-22
Bangirana P, Opoka RO, Boivin MJ, Idro R, Hodges JS, Romero RA, Shapiro E, John CC (2014) Severe malarial anemia is associated with long-term neurocognitive impairment. Clin Infect Dis 59:336–344. https://doi.org/10.1093/cid/ciu293
Barthel M, Hapfelmeier S, Quintanilla-Martínez L, Kremer M, Rohde M, Hogardt M, Pfeffer K, Rüssmann H, Hardt W-D (2003) Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host. Infect Immun 71:2839–2858. https://doi.org/10.1128/IAI.71.5.2839-2858.2003
Belzer C, de Vos WM (2012) Microbes inside-from diversity to function: the case of Akkermansia. ISME J 6:1449. https://doi.org/10.1038/ismej.2012.6
Bollinger RR, Barbas AS, Bush EL, Lin SS, Parker W (2007) Biofilms in the large bowel suggest an apparent function of the human vermiform appendix. J Theor Biol 249:826–831. https://doi.org/10.1016/j.jtbi.2007.08.032
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y et al (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852–857. https://doi.org/10.1038/s41587-019-0209-9
Brown K, Abbott DW, Uwiera RRE, Inglis GD (2018) Removal of the cecum affects intestinal fermentation, enteric bacterial community structure, and acute colitis in mice. Gut Microbes 9:218–235. https://doi.org/10.1080/19490976.2017.1408763
Cai T-T, Ye X-L, Li R-R, Chen H, Wang Y-Y, Yong H-J, Pan M-L, Lu W, Tang Y, Miao H, Snijders AM et al (2020) Resveratrol modulates the gut microbiota and inflammation to protect against diabetic nephropathy in mice. Front Pharmacol 11:1249. https://doi.org/10.3389/fphar.2020.01249
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. https://doi.org/10.1038/nmeth.3869
Comeau AM, Douglas GM, Langille MGI (2017) Microbiome helper: a custom and streamlined workflow for microbiome research. mSystems 2:e00127-00116. https://doi.org/10.1128/mSystems.00127-16
de Souza JB, Hafalla JCR, Riley EM, Couper KN (2010) Cerebral malaria: why experimental murine models are required to understand the pathogenesis of disease. Parasitology 137:755–772. https://doi.org/10.1017/S0031182009991715
Denny JE, Powers JB, Castro HF, Zhang J, Joshi-Barve S, Campagna SR, Schmidt NW (2019) Differential sensitivity to Plasmodium yoelii infection in C57BL/6 mice impacts gut-liver axis homeostasis. Sci Rep 9:3472. https://doi.org/10.1038/s41598-019-40266-6
Derrien M, Collado MC, Ben-Amor K, Salminen S, de Vos WM (2008) The mucin degrader Akkermansia muciniphila is an abundant resident of the human intestinal tract. Appl Environ Microbiol 74:1646–1648. https://doi.org/10.1128/aem.01226-07
Dinan TG, Stilling RM, Stanton C, Cryan JF (2015) Collective unconscious: how gut microbes shape human behavior. J Psychiatr Res 63:1–9. https://doi.org/10.1016/j.jpsychires.2015.02.021
Dixon P (2003) Vegan, a package of R functions for community ecology. J Veg Sci 14:927–930. https://doi.org/10.1111/j.1654-1103.2003.tb02228.x
Frémont M, Coomans D, Massart S, De Meirleir K (2013) High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients. Anaerobe 22:50–56. https://doi.org/10.1016/j.anaerobe.2013.06.002
Ghaisas S, Maher J, Kanthasamy A (2016) Gut microbiome in health and disease: linking the microbiome–gut–brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases. Pharmacol Ther 158:52–62. https://doi.org/10.1016/j.pharmthera.2015.11.012
Hasan N, Yang H (2019) Factors affecting the composition of the gut microbiota, and its modulation. PeerJ 7:e7502. https://doi.org/10.7717/peerj.7502
Herrera S, Enuameh Y, Adjei G, Ae-Ngibise KA, Asante KP, Sankoh O, Owusu-Agyei S, Yé Y (2017) A systematic review and synthesis of the strengths and limitations of measuring malaria mortality through verbal autopsy. Malar J 16:421. https://doi.org/10.1186/s12936-017-2071-x
Hugenholtz F, de Vos WM (2018) Mouse models for human intestinal microbiota research: a critical evaluation. Cell Mol Life Sci 75:149–160. https://doi.org/10.1007/s00018-017-2693-8
Idro R, Marsh K, John CC, Newton CRJ (2010) Cerebral malaria: mechanisms of brain injury and strategies for improved neurocognitive outcome. Pediatr Res 68:267–274. https://doi.org/10.1203/PDR.0b013e3181eee738
Illumina (2013) 16S Metagenomic sequencing library preparation. https://sapac.support.illumina.com/documentation.html. Accessed 12 Dec 2018
Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D (2015) Role of the normal gut microbiota. World J Gastroenterol 21:8787–8803. https://doi.org/10.3748/wjg.v21.i29.8787
Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, Wang W, Tang W, Tan Z, Shi J, Li L et al (2015) Altered fecal microbiota composition in patients with major depressive disorder. Brain Behav Immun 48:186–194. https://doi.org/10.1016/j.bbi.2015.03.016
Katoh K, Standley D (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780. https://doi.org/10.1093/molbev/mst010
Kaur H, Das C, Mande SS (2017) In silico analysis of putrefaction pathways in bacteria and its implication in colorectal cancer. Front Microbiol 8:2166. https://doi.org/10.3389/fmicb.2017.02166
Kelly TN, Bazzano LA, Ajami NJ, He H, Zhao J, Petrosino JF, Correa A, He J (2016) Gut microbiome associates with lifetime cardiovascular disease risk profile among Bogalusa Heart Study participants. Circ Res 119:956–964. https://doi.org/10.1161/CIRCRESAHA.116.309219
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2012) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:e1–e1. https://doi.org/10.1093/nar/gks808
Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS et al (2014) An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 32:834–841. https://doi.org/10.1038/nbt.2942
Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235. https://doi.org/10.1128/AEM.71.12.8228-8235.2005
Martin, M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17 https://doi.org/10.14806/ej.17.1.200
Martinez Arbizu, P (2020) pairwiseAdonis: pairwise multilevel comparison using adonis. https://github.com/pmartinezarbizu/pairwiseAdonis. Accessed 07/04/2022
McMurdie PJ, Holmes S (2013) phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8:e61217. https://doi.org/10.1371/journal.pone.0061217
Neuwirth, E (2014) RColorBrewer: ColorBrewer Palettes. R package version 1.1–2. https://cran.r-project.org/package=RColorBrewer/. Accessed 07/04/2022
Oliveira-Lima OC, Almeida NL, Almeida-Leite CM, Carvalho-Tavares J (2019) Mice chronically fed a high-fat diet are resistant to malaria induced by Plasmodium berghei ANKA. Parasitol Res 118:2969–2977. https://doi.org/10.1007/s00436-019-06427-2
Palomo J, Quesniaux VFJ, Togbe D, Reverchon F, Ryffel B (2018) Unravelling the roles of innate lymphoid cells in cerebral malaria pathogenesis. Parasite Immunol 40:e12502. https://doi.org/10.1111/pim.12502
Paone P, Cani PD (2020) Mucus barrier, mucins and gut microbiota: the expected slimy partners? Gut 69:2232–2243. https://doi.org/10.1136/gutjnl-2020-322260
Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, Harmsen HJM, Faber KN, Hermoso MA (2019) Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol 10:277. https://doi.org/10.3389/fimmu.2019.00277
Parker BJ, Wearsch PA, Veloo ACM, Rodriguez-Palacios A (2020) The genus Alistipes: gut bacteria with emerging implications to inflammation, cancer, and mental health. Front Immunol 11:906. https://doi.org/10.3389/fimmu.2020.00906
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J et al (2011) Scikit-learn: machine learning in python. J Mach Learn Res 12:2825–2830
Price MN, Dehal PS, Arkin AP (2010) FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490. https://doi.org/10.1371/journal.pone.0009490
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590–D596. https://doi.org/10.1093/nar/gks1219
R Core Team (2017) R: a language and environment for statistical computing. https://www.R-project.org/. Accessed 07/04/2022
Rakislova N, Jordao D, Ismail MR, Mayor A, Cisteró P, Marimon L, Ferrando M, Hurtado JC, Lovane L, Carrilho C, Lorenzoni C et al (2021) Accuracy of verbal autopsy, clinical data and minimally invasive autopsy in the evaluation of malaria-specific mortality: an observational study. BMJ Glob Health 6:e005218. https://doi.org/10.1136/bmjgh-2021-005218
Sato S (2021) Plasmodium-a brief introduction to the parasites causing human malaria and their basic biology. J Physiol Anthropol 40:1. https://doi.org/10.1186/s40101-020-00251-9
Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF et al (2011) Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology 141:1782–1791. https://doi.org/10.1053/j.gastro.2011.06.072
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A et al (2016) Linking the human gut microbiome to inflammatory cytokine production capacity. Cell 167:1125-1136.e1128. https://doi.org/10.1016/j.cell.2016.10.020
Schneider C, O’Leary CE, von Moltke J, Liang H-E, Ang QY, Turnbaugh PJ, Radhakrishnan S, Pellizzon M, Ma A, Locksley RM (2018) A metabolite-triggered tuft cell-ILC2 circuit drives small intestinal remodeling. Cell 174:271-284.e214. https://doi.org/10.1016/j.cell.2018.05.014
Schofield L, Grau GE (2005) Immunological processes in malaria pathogenesis. Nat Rev Immunol 5:722–735. https://doi.org/10.1038/nri1686
Sey ICM, Ehimiyein AM, Bottomley C, Riley EM, Mooney JP (2020) Does malaria cause diarrhoea? A Systematic Review Front Med (lausanne) 7:589379. https://doi.org/10.3389/fmed.2020.589379
Shimada M, Hirose Y, Shimizu K, Yamamoto DS, Hayakawa EH, Matsuoka H (2019) Upper gastrointestinal pathophysiology due to mouse malaria Plasmodium berghei ANKA infection. Trop Med Health 47:18. https://doi.org/10.1186/s41182-019-0146-9
Sierro F, Grau GER (2019) The ins and outs of cerebral malaria pathogenesis: immunopathology, extracellular vesicles, immunometabolism, and trained immunity. Front Immunol 10:830. https://doi.org/10.3389/fimmu.2019.00830
Songhet P, Barthel M, Stecher B, Müller AJ, Kremer M, Hansson GC, Hardt W-D (2011) Stromal IFN-γR-signaling modulates goblet cell function during Salmonella Typhimurium infection. PLoS ONE 6:e22459. https://doi.org/10.1371/journal.pone.0022459
Sorboni SG, Moghaddam HS, Jafarzadeh-Esfehani R, Soleimanpour S (2022) A comprehensive review on the role of the gut microbiome in human neurological disorders. Clin Microbiol Rev 35:e00338-e320. https://doi.org/10.1128/CMR.00338-20
Spanogiannopoulos P, Bess EN, Carmody RN, Turnbaugh PJ (2016) The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat Rev Micro 14:273–287. https://doi.org/10.1038/nrmicro.2016.17
Sun Y, Chen Q, Lin P, Xu R, He D, Ji W, Bian Y, Shen Y, Li Q, Liu C, Dong K et al (2019) Characteristics of gut microbiota in patients with rheumatoid arthritis in Shanghai. China Front Cell Infect Microbiol 9:369. https://doi.org/10.3389/fcimb.2019.00369
Taniguchi T, Miyauchi E, Nakamura S, Hirai M, Suzue K, Imai T, Nomura T, Handa T, Okada H, Shimokawa C, Onishi R et al (2015) Plasmodium berghei ANKA causes intestinal malaria associated with dysbiosis. Sci Rep 5:15699. https://doi.org/10.1038/srep15699
The Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207–214. https://doi.org/10.1038/nature11234
Tian L, Wang X-W, Wu A-K, Fan Y, Friedman J, Dahlin A, Waldor MK, Weinstock GM, Weiss ST, Liu Y-Y (2020) Deciphering functional redundancy in the human microbiome. Nat Commun 11:6217. https://doi.org/10.1038/s41467-020-19940-1
Torre S, Langlais D, Gros P (2018) Genetic analysis of cerebral malaria in the mouse model infected with Plasmodium berghei. Mamm Genome 29:488–506. https://doi.org/10.1007/s00335-018-9752-9
Valdes AM, Walter J, Segal E, Spector TD (2018) Role of the gut microbiota in nutrition and health. BMJ 361:k2179. https://doi.org/10.1136/bmj.k2179
Villarino NF, LeCleir GR, Denny JE, Dearth SP, Harding CL, Sloan SS, Gribble JL, Campagna SR, Wilhelm SW, Schmidt NW (2016) Composition of the gut microbiota modulates the severity of malaria. Proc Natl Acad Sci USA 113:2235–2240. https://doi.org/10.1073/pnas.1504887113
Wickham, H, Sievert, C (2016) ggplot2: elegant graphics for data analysis, 2nd edn. Springer, Cham https://doi.org/10.1007/978-3-319-24277-4
World Health Organization (2021) World malaria report 2021. Geneva, Switzerland. https://www.who.int/publications/i/item/9789240040496. Accessed 07/04/2022
Xie H, Guo R, Zhong H, Feng Q, Lan Z, Qin B, Ward KJ, Jackson MA, Xia Y, Chen X, Chen B et al (2016) Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome. Cell Syst 3:572-584.e573. https://doi.org/10.1016/j.cels.2016.10.004
Yao CK, Muir JG, Gibson PR (2016) Review article: insights into colonic protein fermentation, its modulation and potential health implications. Aliment Pharmacol Ther 43:181–196. https://doi.org/10.1111/apt.13456
Zhang T, Ji X, Lu G, Zhang F (2021) The potential of Akkermansia muciniphila in inflammatory bowel disease. Appl Microbiol Biotechnol 105:5785–5794. https://doi.org/10.1007/s00253-021-11453-1
Funding
This work was supported by an Australian Postgraduate Award to SAK at La Trobe University. ELH-Y is the recipient of an NHMRC Ideas Grant (APP2003848). TdK-W is the recipient of an NHMRC Senior Research Fellowship (1136300). SAK has been supported by a Defence Science Institute’s Research Higher Degree Student Grant.
Author information
Authors and Affiliations
Contributions
Sarah A Knowler: data analysis, investigation, writing—original draft. Anya Shindler: supervision, writing—review and editing. Jennifer L Wood: supervision, writing—review and editing. Colleen J Thomas: supervision, writing—review and editing. Asha Lakkavaram: Animal husbandry, experimental infections and faecal collection. Ashley E Franks: conceptualisation, tissue collection, supervision, writing—review and editing. Tania F de Koning-Ward: conceptualisation, tissue collection, writing—review and editing. Elisa L Hill-Yardin: conceptualisation, tissue collection, writing—review and editing. Teresa G Carvalho: conceptualisation, tissue collection, writing—review and editing.
Corresponding author
Ethics declarations
Ethics approval
The experiment was performed in strict accordance with the recommendations of the National Health and Medical Research Council Australian ‘Code of practice for the care and use of animals for scientific purposes.’ The protocols were approved by the Deakin University Animal Welfare Committee (approval number G11-2017).
Consent to participate
Not applicable.
Consent for publication
Not applicable.
Competing interests
The authors declare no competing interests.
Additional information
Handling Editor: Una Ryan
Publisher's note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Teresa G Carvalho and Ashley E Franks have equal position.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Knowler, S.A., Shindler, A., Wood, J.L. et al. Altered gastrointestinal tract structure and microbiome following cerebral malaria infection. Parasitol Res 122, 789–799 (2023). https://doi.org/10.1007/s00436-022-07775-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00436-022-07775-2