Heme-Peroxidase 2, a Peroxinectin-Like Gene, Regulates Bacterial Homeostasis in Anopheles stephensi Midgut

Kakani, Parik; Gupta, Lalita; Kumar, Sanjeev

doi:10.3389/fphys.2020.572340

Cited by 8 publications

(4 citation statements)

References 70 publications

(143 reference statements)

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“…Mosquito-associated bacteria are acquired primarily through horizontal transmission from water to larvae, where they colonise multiple organs, primarily the midgut, with some microbiome members persisting until adulthood (21,79). Within the mosquito, bacteria must withstand a fluctuating environment, including spatial permutations during metamorphosis (93), changes in nutrition (105,106), temperature (107), pH (108), oxidative stress (109), and competition with other members of the microbiota (23,84). The mechanism of adaptation to both an aquatic lifestyle and colonisation in the mosquito remains poorly understood.…”

Section: Discussionmentioning

confidence: 99%

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

Foo,

Brettell,

Nichols

et al. 2023

Preprint

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Mosquitoes transmit medically important human pathogens, including viruses like dengue virus and parasites such asPlasmodiumspp., the causative agent of malaria. Mosquito microbiomes are critically important for the ability of mosquitoes to transmit disease-causing agents. However, while large collections of bacterial isolates and genomic data exist for vertebrate microbiomes, the vast majority of work in mosquitoes to date is based on 16S rRNA gene amplicon data that provides limited taxonomic resolution and no functional information. To address this gap and facilitate future studies using experimental microbiome manipulations, we generated a bacterialMosquito-Associated IsolateCollection (MosAIC) consisting of 392 bacterial isolates with extensive metadata and high-quality draft genome assemblies that are publicly available for use by the scientific community. MosAIC encompasses 142 species spanning 29 bacterial families, with members of theEnterobacteriaceaecomprising 40% of the collection. Phylogenomic analysis of three genera,Enterobacter, Serratia, andElizabethkingia, reveal lineages of mosquito-associated bacteria isolated from different mosquito species in multiple laboratories. Investigation into species’ pangenomes further reveals clusters of genes specific to these lineages, which are of interest for future work to identify functions underlying mosquito host association. Altogether, we describe the generation of a physical collection of mosquito-associated bacterial isolates, their genomic data, and analyses of selected groups in context of genome data from closely related isolates, providing a unique, highly valuable resource to investigate factors for bacterial colonisation and adaptation within mosquito hosts. Future efforts will expand the collection to include broader geographic and host species representation, especially from individuals collected from field populations, as well as other mosquito-associated microbes, including fungi, archaea, and protozoa.

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Section: Discussionmentioning

confidence: 99%

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

Foo,

Brettell,

Nichols

et al. 2023

Preprint

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“…Mosquito microbiomes are highly variable, dependent on multiple deterministic processes such as the environment 8 – 12 , season 13 , host factors 14 , 15 , microbial interactions 16 – 18 and mosquito-microbe interactions 19 – 23 . These findings from mosquito microbiome studies are largely driven by amplicon-based 16S rRNA sequencing approaches 18 , 24 , 25 .…”

Section: Introductionmentioning

confidence: 99%

Recovery of metagenomic data from the Aedes aegypti microbiome using a reproducible snakemake pipeline: MINUUR

Foo¹,

Cerdeira²,

Hughes³

et al. 2023

Wellcome Open Res

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Background: Ongoing research of the mosquito microbiome aims to uncover novel strategies to reduce pathogen transmission. Sequencing costs, especially for metagenomics, are however still significant. A resource that is increasingly used to gain insights into host-associated microbiomes is the large amount of publicly available genomic data based on whole organisms like mosquitoes, which includes sequencing reads of the host-associated microbes and provides the opportunity to gain additional value from these initially host-focused sequencing projects. Methods: To analyse non-host reads from existing genomic data, we developed a snakemake workflow called MINUUR (Microbial INsights Using Unmapped Reads). Within MINUUR, reads derived from the host-associated microbiome were extracted and characterised using taxonomic classifications and metagenome assembly followed by binning and quality assessment. We applied this pipeline to five publicly available Aedes aegypti genomic datasets, consisting of 62 samples with a broad range of sequencing depths. Results: We demonstrate that MINUUR recovers previously identified phyla and genera and is able to extract bacterial metagenome assembled genomes (MAGs) associated to the microbiome. Of these MAGS, 42 are high-quality representatives with >90% completeness and <5% contamination. These MAGs improve the genomic representation of the mosquito microbiome and can be used to facilitate genomic investigation of key genes of interest. Furthermore, we show that samples with a high number of KRAKEN2 assigned reads produce more MAGs. Conclusions: Our metagenomics workflow, MINUUR, was applied to a range of Aedes aegypti genomic samples to characterise microbiome-associated reads. We confirm the presence of key mosquito-associated symbionts that have previously been identified in other studies and recovered high-quality bacterial MAGs. In addition, MINUUR and its associated documentation are freely available on GitHub and provide researchers with a convenient workflow to investigate microbiome data included in the sequencing data for any applicable host genome of interest.

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“…Studies show the mosquito microbiome influences vectorial capacity (13), blood feeding propensity (14) and life history traits (15)(16)(17). Mosquito microbiomes are understood to be highly variable, dependent on a suite of deterministic processes such as the environment (18)(19)(20)(21), host factors (22,23), microbial interactions (14,24,25) and mosquito-microbe interactions (26,27). These important findings have been aided by amplicon based 16S rRNA sequencing approaches to characterize the microbiome.…”

Section: Introductionmentioning

confidence: 99%

“…Mosquito microbiomes are highly variable, dependent on multiple deterministic processes such as the environment (8)(9)(10)(11)(12), season (13), host factors (14,15), microbial interactions (16)(17)(18) and mosquito-microbe interactions (19)(20)(21)(22)(23). These findings from mosquito microbiome studies are largely driven by amplicon based 16S rRNA sequencing approaches (18,24,25).…”

Section: Introductionmentioning

confidence: 99%

Recovery of Metagenomic Data from theAedes aegyptiMicrobiome using a Reproducible Snakemake Pipeline: MINUUR

Foo

Cerdeira

Hughes

et al. 2022

Preprint

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The microbiome is a collection of microbes that exist in symbiosis with a host. Whole genome sequencing produces off-target, non-specific reads, to the host in question, which can be used for metagenomic inference of a microbiome. This data is advantageous over barcoding methods since higher taxonomic resolution and functional predictions of microbes are possible. With the growing number of genomic sequencing data publicly available, comes opportunity to elucidate reads pertaining to the microbiome. However, characterization of these reads can be complex, with many steps required to perform a robust analysis. To address this, we developed MINUUR (Microbial INsights Using Unmapped Reads); a snakemake pipeline to characterize non-host reads from existing genomic data. We apply this pipeline to ten, publicly available, high coverage Aedes aegypti (Ae. aegypti) genomic samples. Using MINUUR, we describe species level microbial classifications; predict microbe associated genes and pathways and find bacterial metagenome assembled genomes (MAGs) associated to the Ae. aegypti microbiome. Of these MAGS, 19 are high-quality representatives with over 90% completeness and under 5% contamination. In summary, we present an in-depth analysis of non-host reads from Ae. aegypti whole genome sequencing data within a reproducible and open-access pipeline.

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Heme-Peroxidase 2, a Peroxinectin-Like Gene, Regulates Bacterial Homeostasis in Anopheles stephensi Midgut

Cited by 8 publications

References 70 publications

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

Recovery of metagenomic data from the Aedes aegypti microbiome using a reproducible snakemake pipeline: MINUUR

Recovery of Metagenomic Data from theAedes aegyptiMicrobiome using a Reproducible Snakemake Pipeline: MINUUR

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