Gut microbiome of helminth-infected indigenous Malaysians is context dependent

Tee, Mian Zi; Er, Yi Xian; Easton, Alice V.; Yap, Nan Jiun; Lee, Ii Li; Devlin, Joseph C.; Chen, Ze; Ng, Kee Seong; Subramanian, Poorani; Angelova, Angelina; Oyesola, Oyebola O.; Sargsian, Shushan; Ngui, Romano; Beiting, Daniel P.; Boey, Christopher Chiong Meng; Chua, Kek Heng; Cadwell, Ken; Lim, Yvonne Ai Lian; Loke, P’ng; Lee, Soo Ching

doi:10.1186/s40168-022-01385-x

Cited by 9 publications

(9 citation statements)

References 62 publications

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“…In addition to making our software simple to install through pip and easily parametrized, we integrated CORRAL into the automated data loading workflow for our open-science platform, MicrobiomeDB.org. As of Release 30 (9 Nov 2022), the site contains 6337 samples from 8 published metagenomic studies [ 22 - 29 ]. Automated analysis of these samples by CORRAL occurs at the time a study is loaded for public release onto the database website, and microbial eukaryote data becomes readily available to users through a sophisticated web toolkit (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Since curated sample metadata is loaded together with microbiome data for each study represented on MicrobiomeDB.org, we can explore the relationship between diagnostic assay results and metagenomic results. For example, the Malaysia Helminth metagenomic [ 29 ] study currently available on MicrobiomeDB.org specifically addresses the impact of helminth infection on the microbiome and thus includes sample metadata for different helminth species detected in 650 stool samples from over 400 participants. Nearly half of all samples tested positive by microscopy for either Ascaris , hookworms, or Trichuris , yet none of these organisms were detected in any samples by either EukDetect or CORRAL (data not shown; MicrobiomeDB.org).…”

Section: Discussionmentioning

confidence: 99%

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Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes

et al. 2023

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Background Eukaryotes such as fungi and protists frequently accompany bacteria and archaea in microbial communities. Unfortunately, their presence is difficult to study with “shotgun” metagenomic sequencing since prokaryotic signals dominate in most environments. Recent methods for eukaryotic detection use eukaryote-specific marker genes, but they do not incorporate strategies to handle the presence of eukaryotes that are not represented in the reference marker gene set, and they are not compatible with web-based tools for downstream analysis. Results Here, we present CORRAL (for Clustering Of Related Reference ALignments), a tool for the identification of eukaryotes in shotgun metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. Using a combination of simulated datasets, mock community standards, and large publicly available human microbiome studies, we demonstrate that our method is not only sensitive and accurate but is also capable of inferring the presence of eukaryotes not included in the marker gene reference, such as novel strains. Finally, we deploy CORRAL on our MicrobiomeDB.org resource, producing an atlas of eukaryotes present in various environments of the human body and linking their presence to study covariates. Conclusions CORRAL allows eukaryotic detection to be automated and carried out at scale. Implementation of CORRAL in MicrobiomeDB.org creates a running atlas of microbial eukaryotes in metagenomic studies. Since our approach is independent of the reference used, it may be applicable to other contexts where shotgun metagenomic reads are matched against redundant but non-exhaustive databases, such as the identification of bacterial virulence genes or taxonomic classification of viral reads.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes

et al. 2023

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“…In this regard, gut microbiota helps in metabolising albendazole and influence drug bioavailability and efficacy on infected individuals. 35,36 However, a huge diversity and functional capacity of human gut microbiome perform in various ways regarding the protection against pathogen overgrowth, inflammation, influence host-cell proliferation, biosynthesis of vitamins, and react differently to drugs and their metabolism. 37 Similarly, anthelmintic treatment could affect the gut microbiome through acting on intestinal protozoa, which have close interaction with gut microbiome, thus leading to improvement in the nutritional status of the children and to combat the multi-micronutrient deficiencies including zinc.…”

Section: Discussionmentioning

confidence: 99%

Zinc status or supplementation and its relation to soil‐transmitted helminthiasis in children: A systematic review

Iqbal,

Abid,

Akram

et al. 2023

Parasite Immunology

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Soil‐transmitted helminths (STHs) parasitic infection is known as one of the most common infections around the world affecting more than a quarter of the world's population. The relationship between STH infections and micronutrient deficiencies are closely related and often coexist among the affected population. The study, therefore, aimed to summarise the available literature focusing on the effect of zinc status/deficiency or supplementation on STH infection or reinfection in children. For this purpose, we adopted a systematic approach and searched the existing literature on PubMed, Scopus, and Cochrane Library databases. A search term was entered to retrieve the available data. A total of 12 articles were included in this review after applying the inclusion/exclusion criteria. Most of the included studies reported a lower zinc status in children affected with any parasitic infection. Regarding the effect of zinc status and supplementation on parasitic infection in children, we found only a few studies (n = 4) with inconsistent result findings. This review reported that children infected with STH have lower zinc levels; however, a limited number of studies showed the effect of zinc supplements on the risk of STH warrants the need for further studies in this regard.

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“…In addition to making our software simple to install through pip and easily parametrized, we integrated CORRAL into the automated data loading workflow for our open-science platform, MicrobiomeDB.org. As of Release 30 (9 Nov 2022), the site contains 6337 samples from 8 published metagenomic studies (22)(23)(24)(25)(26)(27)(28)(29). Automated analysis of these samples by CORRAL occurs at the time a study is loaded for public release onto the database website, and microbial eukaryote data becomes readily available to users through a sophisticated web toolkit (Figure S2).…”

Section: Automating Eukaryote Detection With Corralmentioning

confidence: 99%

“…We thank the authors of the metagenomic studies cited in this work (22)(23)(24)(25)(26)(27)(28)(29) for their assistance with loading and representing their data on MicrobiomeDB.org.…”

Section: Acknowledgementsmentioning

confidence: 99%

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes

Bażant

Blevins

Crouch

et al. 2022

Preprint

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Background Eukaryotes such as fungi and protists frequently accompany bacteria and archaea in microbial communities. Unfor- tunately, their presence is difficult to study with shotgun sequencing techniques, since prokaryotic signals dominate in most environments. Recent methods for eukaryotic detection use eukaryote-specific marker genes, but they do not yet incorporate strategies to handle presence of unknown eukaryotes. Results Here we present CORALE (for Clustering of Reference Alignments), a tool for identification of eukaryotes in shot- gun metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. Using a combination of simulated datasets and large publicly available human microbiome studies, we demonstrate that our method is not only sensitive and accurate, but is also capable of inferring the presence of eukaryotes not included in the marker gene reference, such as novel species and strains. We finally deploy CORALE on our MicrobiomeDB.org resource, demonstrating adequate reliability and throughput. Conclusion CORALE allows eukaryotic detection to be automated and carried out at scale. Since our approach is independent of the reference used, it is applicable to other contexts where shotgun metagenomic reads are matched against redundant but non-exhaustive databases, such as identification of novel bacterial strains or taxonomic classification of viral reads.

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Gut microbiome of helminth-infected indigenous Malaysians is context dependent

Cited by 9 publications

References 62 publications

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes

Zinc status or supplementation and its relation to soil‐transmitted helminthiasis in children: A systematic review

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes

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