A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis
Abstract Background The mechanisms underlying the clinical outcome disparity during human infection with Giardia duodenalis are still unclear. In recent years, evidence has pointed to the roles of host factors as well as parasite’s genetic heterogeneity as major contributing factors in the developme...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-07-01
|
| Series: | Parasites & Vectors |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13071-023-05821-1 |
| _version_ | 1797774363823439872 |
|---|---|
| author | Brett A. McGregor Elham Razmjou Hossein Hooshyar Drew R. Seeger Svetlana A. Golovko Mikhail Y. Golovko Steven M. Singer Junguk Hur Shahram Solaymani-Mohammadi |
| author_facet | Brett A. McGregor Elham Razmjou Hossein Hooshyar Drew R. Seeger Svetlana A. Golovko Mikhail Y. Golovko Steven M. Singer Junguk Hur Shahram Solaymani-Mohammadi |
| author_sort | Brett A. McGregor |
| collection | DOAJ |
| description | Abstract Background The mechanisms underlying the clinical outcome disparity during human infection with Giardia duodenalis are still unclear. In recent years, evidence has pointed to the roles of host factors as well as parasite’s genetic heterogeneity as major contributing factors in the development of symptomatic human giardiasis. However, it remains contested as to how only a small fraction of individuals infected with G. duodenalis develop clinical gastrointestinal manifestations, whereas the majority of infected individuals remain asymptomatic. Here, we demonstrate that diversity in the fecal microbiome correlates with the clinical outcome of human giardiasis. Methods The genetic heterogeneity of G. duodenalis clinical isolates from human subjects with asymptomatic and symptomatic giardiasis was determined using a multilocus analysis approach. We also assessed the genetic proximity of G. duodenalis isolates by constructing phylogenetic trees using the maximum likelihood. Total genomic DNA (gDNA) from fecal specimens was utilized to construct DNA libraries, followed by performing paired-end sequencing using the HiSeq X platform. The Kraken2-generated, filtered FASTQ files were assigned to microbial metabolic pathways and functions using HUMAnN 3.04 and the UniRef90 diamond annotated full reference database (version 201901b). Results from HUMAnN for each sample were evaluated for differences among the biological groups using the Kruskal–Wallis non-parametric test with a post hoc Dunn test. Results We found that a total of 8/11 (72.73%) human subjects were infected with assemblage A (sub-assemblage AII) of G. duodenalis, whereas 3/11 (27.27%) human subjects in the current study were infected with assemblage B of the parasite. We also found that the parasite’s genetic diversity was not associated with the clinical outcome of the infection. Further phylogenetic analysis based on the tpi and gdh loci indicated that those clinical isolates belonging to assemblage A of G. duodenalis subjects clustered compactly together in a monophyletic clade despite being isolated from human subjects with asymptomatic and symptomatic human giardiasis. Using a metagenomic shotgun sequencing approach, we observed that infected individuals with asymptomatic and symptomatic giardiasis represented distinctive microbial diversity profiles, and that both were distinguishable from the profiles of healthy volunteers. Conclusions These findings identify a potential association between host microbiome disparity with the development of clinical disease during human giardiasis, and may provide insights into the mechanisms by which the parasite induces pathological changes in the gut. These observations may also lead to the development of novel selective therapeutic targets for preventing human enteric microbial infections. Graphical Abstract |
| first_indexed | 2024-03-12T22:19:57Z |
| format | Article |
| id | doaj.art-95b79fddc8524a69b6e268fa44451f35 |
| institution | Directory Open Access Journal |
| issn | 1756-3305 |
| language | English |
| last_indexed | 2024-03-12T22:19:57Z |
| publishDate | 2023-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Parasites & Vectors |
| spelling | doaj.art-95b79fddc8524a69b6e268fa44451f352023-07-23T11:08:02ZengBMCParasites & Vectors1756-33052023-07-0116111910.1186/s13071-023-05821-1A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalisBrett A. McGregor0Elham Razmjou1Hossein Hooshyar2Drew R. Seeger3Svetlana A. Golovko4Mikhail Y. Golovko5Steven M. Singer6Junguk Hur7Shahram Solaymani-Mohammadi8Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North DakotaDepartment of Parasitology and Mycology, School of Medicine, Iran University of Medical SciencesDepartment of Medical Parasitology and Mycology, School of Medicine, Kashan University of Medical SciencesDepartment of Biomedical Sciences, School of Medicine and Health Sciences, University of North DakotaDepartment of Biomedical Sciences, School of Medicine and Health Sciences, University of North DakotaDepartment of Biomedical Sciences, School of Medicine and Health Sciences, University of North DakotaDepartment of Biology, Georgetown UniversityDepartment of Biomedical Sciences, School of Medicine and Health Sciences, University of North DakotaDepartment of Biomedical Sciences, School of Medicine and Health Sciences, University of North DakotaAbstract Background The mechanisms underlying the clinical outcome disparity during human infection with Giardia duodenalis are still unclear. In recent years, evidence has pointed to the roles of host factors as well as parasite’s genetic heterogeneity as major contributing factors in the development of symptomatic human giardiasis. However, it remains contested as to how only a small fraction of individuals infected with G. duodenalis develop clinical gastrointestinal manifestations, whereas the majority of infected individuals remain asymptomatic. Here, we demonstrate that diversity in the fecal microbiome correlates with the clinical outcome of human giardiasis. Methods The genetic heterogeneity of G. duodenalis clinical isolates from human subjects with asymptomatic and symptomatic giardiasis was determined using a multilocus analysis approach. We also assessed the genetic proximity of G. duodenalis isolates by constructing phylogenetic trees using the maximum likelihood. Total genomic DNA (gDNA) from fecal specimens was utilized to construct DNA libraries, followed by performing paired-end sequencing using the HiSeq X platform. The Kraken2-generated, filtered FASTQ files were assigned to microbial metabolic pathways and functions using HUMAnN 3.04 and the UniRef90 diamond annotated full reference database (version 201901b). Results from HUMAnN for each sample were evaluated for differences among the biological groups using the Kruskal–Wallis non-parametric test with a post hoc Dunn test. Results We found that a total of 8/11 (72.73%) human subjects were infected with assemblage A (sub-assemblage AII) of G. duodenalis, whereas 3/11 (27.27%) human subjects in the current study were infected with assemblage B of the parasite. We also found that the parasite’s genetic diversity was not associated with the clinical outcome of the infection. Further phylogenetic analysis based on the tpi and gdh loci indicated that those clinical isolates belonging to assemblage A of G. duodenalis subjects clustered compactly together in a monophyletic clade despite being isolated from human subjects with asymptomatic and symptomatic human giardiasis. Using a metagenomic shotgun sequencing approach, we observed that infected individuals with asymptomatic and symptomatic giardiasis represented distinctive microbial diversity profiles, and that both were distinguishable from the profiles of healthy volunteers. Conclusions These findings identify a potential association between host microbiome disparity with the development of clinical disease during human giardiasis, and may provide insights into the mechanisms by which the parasite induces pathological changes in the gut. These observations may also lead to the development of novel selective therapeutic targets for preventing human enteric microbial infections. Graphical Abstracthttps://doi.org/10.1186/s13071-023-05821-1HumanGiardiasisGutMicrobiomeInfectionMucosal |
| spellingShingle | Brett A. McGregor Elham Razmjou Hossein Hooshyar Drew R. Seeger Svetlana A. Golovko Mikhail Y. Golovko Steven M. Singer Junguk Hur Shahram Solaymani-Mohammadi A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis Parasites & Vectors Human Giardiasis Gut Microbiome Infection Mucosal |
| title | A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis |
| title_full | A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis |
| title_fullStr | A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis |
| title_full_unstemmed | A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis |
| title_short | A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis |
| title_sort | shotgun metagenomic analysis of the fecal microbiome in humans infected with giardia duodenalis |
| topic | Human Giardiasis Gut Microbiome Infection Mucosal |
| url | https://doi.org/10.1186/s13071-023-05821-1 |
| work_keys_str_mv | AT brettamcgregor ashotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT elhamrazmjou ashotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT hosseinhooshyar ashotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT drewrseeger ashotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT svetlanaagolovko ashotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT mikhailygolovko ashotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT stevenmsinger ashotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT jungukhur ashotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT shahramsolaymanimohammadi ashotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT brettamcgregor shotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT elhamrazmjou shotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT hosseinhooshyar shotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT drewrseeger shotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT svetlanaagolovko shotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT mikhailygolovko shotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT stevenmsinger shotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT jungukhur shotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis AT shahramsolaymanimohammadi shotgunmetagenomicanalysisofthefecalmicrobiomeinhumansinfectedwithgiardiaduodenalis |