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Williams LM, Cao S. Harnessing and delivering microbial metabolites as therapeutics via advanced pharmaceutical approaches. Pharmacol Ther 2024; 256:108605. [PMID: 38367866 PMCID: PMC10985132 DOI: 10.1016/j.pharmthera.2024.108605] [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: 10/31/2023] [Revised: 01/05/2024] [Accepted: 02/08/2024] [Indexed: 02/19/2024]
Abstract
Microbial metabolites have emerged as key players in the interplay between diet, the gut microbiome, and host health. Two major classes, short-chain fatty acids (SCFAs) and tryptophan (Trp) metabolites, are recognized to regulate inflammatory, immune, and metabolic responses within the host. Given that many human diseases are associated with dysbiosis of the gut microbiome and consequent reductions in microbial metabolite production, the administration of these metabolites represents a direct, multi-targeted treatment. While a multitude of preclinical studies showcase the therapeutic potential of both SCFAs and Trp metabolites, they often rely on high doses and frequent dosing regimens to achieve systemic effects, thereby constraining their clinical applicability. To address these limitations, a variety of pharmaceutical formulations approaches that enable targeted, delayed, and/or sustained microbial metabolite delivery have been developed. These approaches, including enteric encapsulations, esterification to dietary fiber, prodrugs, and nanoformulations, pave the way for the next generation of microbial metabolite-based therapeutics. In this review, we first provide an overview of the roles of microbial metabolites in maintaining host homeostasis and outline how compromised metabolite production contributes to the pathogenesis of inflammatory, metabolic, autoimmune, allergic, infectious, and cancerous diseases. Additionally, we explore the therapeutic potential of metabolites in these disease contexts. Then, we provide a comprehensive and up-to-date review of the pharmaceutical strategies that have been employed to enhance the therapeutic efficacy of microbial metabolites, with a focus on SCFAs and Trp metabolites.
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Affiliation(s)
- Lindsey M Williams
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA 98195, United States
| | - Shijie Cao
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA 98195, United States.
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Maradana MR, Marzook NB, Diaz OE, Mkandawire T, Diny NL, Li Y, Liebert A, Shah K, Tolaini M, Kváč M, Stockinger B, Sateriale A. Dietary environmental factors shape the immune defense against Cryptosporidium infection. Cell Host Microbe 2023; 31:2038-2050.e4. [PMID: 38052207 DOI: 10.1016/j.chom.2023.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/05/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023]
Abstract
Cryptosporidium is a leading cause of diarrheal-related deaths in children, especially in resource-poor settings. It also targets the immunocompromised, chronically infecting people living with HIV and primary immunodeficiencies. There is no vaccine or effective treatment. Although it is known from human cases and animal models that CD4+ T cells play a role in curbing Cryptosporidium, the role of CD8+ T cells remains to be defined. Using a Cryptosporidium tyzzeri mouse model, we show that gut-resident CD8+ intraepithelial lymphocytes (IELs) confer resistance to parasite growth. CD8+ IELs express and depend on the ligand-dependent transcription factor aryl hydrocarbon receptor (AHR). AHR deficiency reduces CD8+ IELs, decreases their cytotoxicity, and worsens infection. Transfer of CD8+ IELs rescues severely immunodeficient mice from death following Cryptosporidium challenge. Finally, dietary supplementation of the AHR pro-ligand indole-3-carbinol in newborn mice promotes resistance to infection. Therefore, common dietary metabolites augment the host immune response to cryptosporidiosis, protecting against disease.
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Affiliation(s)
| | | | - Oscar E Diaz
- AhR Immunity Lab, The Francis Crick Institute, London, UK
| | | | | | - Ying Li
- AhR Immunity Lab, The Francis Crick Institute, London, UK
| | - Anke Liebert
- AhR Immunity Lab, The Francis Crick Institute, London, UK
| | - Kathleen Shah
- AhR Immunity Lab, The Francis Crick Institute, London, UK
| | - Mauro Tolaini
- AhR Immunity Lab, The Francis Crick Institute, London, UK
| | - Martin Kváč
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Adam Sateriale
- Cryptosporidiosis Lab, The Francis Crick Institute, London, UK.
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Piazzesi A, Pane S, Russo A, Del Chierico F, Francalanci P, Cotugno N, Rossi P, Locatelli F, Palma P, Putignani L. Case Report: The impact of severe cryptosporidiosis on the gut microbiota of a pediatric patient with CD40L immunodeficiency. Front Cell Infect Microbiol 2023; 13:1281440. [PMID: 37965266 PMCID: PMC10641285 DOI: 10.3389/fcimb.2023.1281440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/15/2023] [Indexed: 11/16/2023] Open
Abstract
Cryptosporidium parvum is a protozoan parasite and one of the leading causes of gastroenteritis in the world, primarily affecting very young children and immunocompromised patients. While infection is usually self-limiting, it can become chronic and even lethal in these vulnerable populations, in whom Cryptosporidium treatments are generally ineffective, due to their acting in concert with a functioning immune system. Here, we describe a case of chronic cryptosporidiosis in a European child with severe CD40L immunodeficiency infected with Cryptosporidium parvum of the IIa20G1 subgenotype, a lineage which has thus far only ever been described in the Middle East. After years of on-off treatment with conventional and non-conventional anti-parasitic drugs failed to clear parasitosis, we performed targeted metagenomics to observe the bacterial composition of the patient's gut microbiota (GM), and to evaluate fecal microbiota transplantation (FMT) as a potential treatment option. We found that C. parvum infection led to significant shifts in GM bacterial composition in our patient, with consequent shifts in predicted intestinal functional signatures consistent with a state of persistent inflammation. This, combined with the patient's poor prognosis and increasing parasitic burden despite many rounds of anti-parasitic drug treatments, made the patient a potential candidate for an experimental FMT procedure. Unfortunately, given the many comorbidities that were precipitated by the patient's immunodeficiency and chronic C. parvum infection, FMT was postponed in favor of more urgently necessary liver and bone marrow transplants. Tragically, after the first liver transplant failed, the patient lost his life before undergoing FMT and a second liver transplant. With this case report, we present the first description of how cryptosporidiosis can shape the gut microbiota of a pediatric patient with severe immunodeficiency. Finally, we discuss how both our results and the current scientific literature suggest that GM modulations, either by probiotics or FMT, can become novel treatment options for chronic Cryptosporidium infection and its consequent complications, especially in those patients who do not respond to the currently available anti-parasitic therapies.
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Affiliation(s)
- Antonia Piazzesi
- Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Stefania Pane
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Alessandra Russo
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | | | - Paola Francalanci
- Department of Pathology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Nicola Cotugno
- Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Systems Medicine, Chair of Pediatrics, University of Rome “Tor Vergata”, Rome, Italy
| | - Paolo Rossi
- Department of Systems Medicine, Chair of Pediatrics, University of Rome “Tor Vergata”, Rome, Italy
- Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Franco Locatelli
- Department of Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - Paolo Palma
- Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Systems Medicine, Chair of Pediatrics, University of Rome “Tor Vergata”, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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Hares MF, Griffiths BE, Johnson F, Nelson C, Haldenby S, Stewart CJ, Duncan JS, Oikonomou G, Coombes JL. Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis. Anim Microbiome 2023; 5:43. [PMID: 37700351 PMCID: PMC10496319 DOI: 10.1186/s42523-023-00265-5] [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: 04/21/2023] [Accepted: 09/03/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Cryptosporidium parvum is the main cause of calf scour worldwide. With limited therapeutic options and research compared to other Apicomplexa, it is important to understand the parasites' biology and interactions with the host and microbiome in order to develop novel strategies against this infection. The age-dependent nature of symptomatic cryptosporidiosis suggests a link to the undeveloped immune response, the immature intestinal epithelium, and its associated microbiota. This led us to hypothesise that specific features of the early life microbiome could predict calf susceptibility to C. parvum infection. RESULTS In this study, a single faecal swab sample was collected from each calf within the first week of life in a cohort of 346 animals. All 346 calves were subsequently monitored for clinical signs of cryptosporidiosis, and calves that developed diarrhoea were tested for Rotavirus, Coronavirus, E. coli F5 (K99) and C. parvum by lateral flow test (LFT). A retrospective case-control approach was taken whereby a subset of healthy calves (Control group; n = 33) and calves that went on to develop clinical signs of infectious diarrhoea and test positive for C. parvum infection via LFT (Cryptosporidium-positive group; n = 32) were selected from this cohort, five of which were excluded due to low DNA quality. A metagenomic analysis was conducted on the faecal microbiomes of the control group (n = 30) and the Cryptosporidium-positive group (n = 30) prior to infection, to determine features predictive of cryptosporidiosis. Taxonomic analysis showed no significant differences in alpha diversity, beta diversity, and taxa relative abundance between controls and Cryptosporidium-positive groups. Analysis of functional potential showed pathways related to isoprenoid precursor, haem and purine biosynthesis were significantly higher in abundance in calves that later tested positive for C. parvum (q ≤ 0.25). These pathways are either absent or streamlined in the C. parvum parasites. Though the de novo production of isoprenoid precursors, haem and purines are absent, C. parvum has been shown to encode enzymes that catalyse the downstream reactions of these pathway metabolites, indicating that C. parvum may scavenge those products from an external source. CONCLUSIONS The host has previously been put forward as the source of essential metabolites, but our study suggests that C. parvum may also be able to harness specific metabolic pathways of the microbiota in order to survive and replicate. This finding is important as components of these microbial pathways could be exploited as potential therapeutic targets for the prevention or mitigation of cryptosporidiosis in bovine neonates.
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Affiliation(s)
- M F Hares
- Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, iC2 Liverpool Science Park, Liverpool, L3 5RF, UK.
| | - B E Griffiths
- Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, Wirral, CH64 7TE, UK
| | - F Johnson
- Centre of Genomic Research, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - C Nelson
- Centre of Genomic Research, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - S Haldenby
- Centre of Genomic Research, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - C J Stewart
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, NE2 4HH, UK
| | - J S Duncan
- Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, Wirral, CH64 7TE, UK
| | - G Oikonomou
- Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, Wirral, CH64 7TE, UK
| | - J L Coombes
- School of Pharmacy and Life Sciences, Robert Gordon University, Garthdee Road, Aberdeen, AB10 7GJ, UK.
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Mead JR. Indole metabolites generated by microbiota inhibit Cryptosporidium growth. Trends Parasitol 2023; 39:716-717. [PMID: 37500333 DOI: 10.1016/j.pt.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Funkhouser-Jones et al. recently identified gut metabolites that affected Cryptosporidium growth. A key focus, indole, was shown to inhibit the parasite in vivo and in vitro by decreasing the host mitochondria function and the membrane potential of parasite mitosomes. These findings help clarify the role microflora and metabolites play in host resistance.
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Affiliation(s)
- Jan R Mead
- Department of Pediatrics, Emory University and Children's Healthcare Organization of Atlanta, Atlanta, GA 30322, USA; Atlanta VA Medical Center, Decatur, GA 30033, USA.
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