Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes

Gil, Joshua C; Hird, Sarah M.

doi:10.1128/spectrum.02384-22

Cited by 8 publications

(5 citation statements)

References 75 publications

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“…Due to a paucity of data within the family Narnaviridae , and the divergent nature of Ao, we re-queried Serratus for Ao-like RdRp palmprints. We retrieved and assembled 166 matching runs from 46 BioProjects with 32 species-like operational taxonomic units (sOTUs) (186 distinct virus-run observations, Supplementary Table S3) (Chen et al, 2022; Zhou et al, 2021; Gil and Hird, 2022; Gao et al, 2021; He et al, 2021; Chen et al, 2021b; Rhie et al, 2021; Bittner et al, 2022; Chen et al, 2021a; Xie et al, 2021; Cui et al, 2022; Wen et al, 2022; Zhou et al, 2022b; Sun et al, 2022; Wu et al, 2021). We recovered relevant Narnavirus RdRp contigs for all 32/32 (100%) sOTU, of which 22/32 (75%) contained a sufficiently long RdRp sequence ( ≈ 390 amino acids, motif F-E (Venkataraman et al, 2018) and thumb) for robust phylogenetic reconstruction.…”

Section: Resultsmentioning

confidence: 99%

A Parasite Odyssey: An RNA virus concealed inToxoplasma gondii

Gupta,

Hiller,

Chowdhury

et al. 2023

Preprint

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We are in the midst of the "Platinum Age of Virus Discovery", an era characterized by the exponential growth in the discovery of virus biodiversity. In humans (or any animal) there are more viruses than simply those directly infecting the animal cells. Viruses infect all species constituting the microbiome: including bacteria, fungi, and unicellular parasites. Thus the complexity of possible interactions between host, microbe, and viruses is unfathomable. To understand this network we must employ computationally assisted virology as a means of analyzing and interpreting the millions of available samples to decipher the myriad of ways in which viruses may intersect human health. From a global screen for human neuron-associated viruses, we identify a novel narnavirus Achaeavirus odysseus (Ao) which likely infects the neurotropic parasite Toxoplasma gondii. Previously, several parasitic protozoan viruses (PPVs) have been mechanistically established as triggers of host innate responses, and here we present in silico evidence that Ao is a plausible pro-inflammatory factor in mouse and human cells infected by T. gondii. T. gondii infects billions of people worldwide, yet the prognosis of toxoplasmosis disease is highly variable, and PPVs like Ao could function as a hitherto undescribed hypervirulence factor. More broadly, we explore phylogenetically proximal viruses to Ao and discover 18 new species of Achaeavirus, all found in vertebrate transcriptome and metatranscriptomes. While the Narnavirus samples making up this genus-like clade are derived from sheep, goat, bat, rabbit, chicken, and pigeon, the presence of virus is strongly predictive of parasitic (Apicomplexa) nucleic acid co-occurrence, supporting that these are a clade of parasite-infecting viruses. This is a computational proof-of-concept study in which we rapidly analyze millions of datasets from which we distill a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict this highly diverged Ao RNA virus is biologically a T. gondii infection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.

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Section: Resultsmentioning

confidence: 99%

A Parasite Odyssey: An RNA virus concealed inToxoplasma gondii

Gupta,

Hiller,

Chowdhury

et al. 2023

Preprint

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“…Firstly, this may reflect the reduced sensitivity of current mcrA gene HMM models to detect highly divergent mcrA sequences from the Bathyarchaeia, as existing models are constructed largely from sequences from classical methanogens. Secondly, this discrepancy may arise due to overprediction by PICRUST2 due to the limited number of reference genomes in its database 60 . Nonetheless, the detection of mcrA genes belonging to the Bathyarchaeia in our sequenced metagenomes confirms their presence in burnt peat and suggests their potential role in methane emissions post-fire.…”

Section: Discussionmentioning

confidence: 99%

Elevated methane flux in a tropical peatland post-fire is linked to depth-dependent changes in peat microbiome assembly

Bandla,

Akhtar,

Lupascu

et al. 2024

npj Biofilms Microbiomes

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Fires in tropical peatlands extend to depth, transforming them from carbon sinks into methane sources and severely limit forest recovery. Peat microbiomes influence carbon transformations and forest recovery, yet our understanding of microbiome shifts post-fire is currently limited. Our previous study highlighted altered relationships between the peat surface, water table, aboveground vegetation, and methane flux after fire in a tropical peatland. Here, we link these changes to post-fire shifts in peat microbiome composition and assembly processes across depth. We report kingdom-specific and depth-dependent shifts in alpha diversity post-fire, with large differences at deeper depths. Conversely, we found shifts in microbiome composition across all depths. Compositional shifts extended to functional groups involved in methane turnover, with methanogens enriched and methanotrophs depleted at mid and deeper depths. Finally, we show that community shifts at deeper depths result from homogeneous selection associated with post-fire changes in hydrology and aboveground vegetation. Collectively, our findings provide a biological basis for previously reported methane fluxes after fire and offer new insights into depth-dependent shifts in microbiome assembly processes, which ultimately underlie ecosystem function predictability and ecosystem recovery.

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“…frequently found in wild birds [ 10 , 46 ]. These findings may imply a lack of significant crossover between MG1, MG1 avian vectors, and human/human-related waste, as AMR prevalence is associated with the propensity for microbial hosts to reside within and feed upon human waste [ 47 ], although we cannot be certain of the causitive nature of AMR absence in MG1. It is also important to consider that these findings are all based on in silico genome exploration and gene orthology detection.…”

Section: Discussionmentioning

confidence: 99%

Genomic Characterization and Wetland Occurrence of a Novel Campylobacter Isolate from Canada Geese

et al. 2023

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Populations of resident, non-migratory Canada geese are rapidly increasing. Canada geese are known to transmit viral and bacterial diseases, posing a possible threat to human health. The most prevalent pathogens vectored by geese are Campylobacter species, yet the current understanding of the identity and virulence of these pathogens is limited. In our previous study, we observed a high prevalence of Campylobacter spp. in the Banklick Creek wetland—a constructed treatment wetland (CTW) located in northern KY (USA) used to understand sources of fecal contamination originating from humans and waterfowl frequenting the area. To identify the types of Campylobacter spp. found contaminating the CTW, we performed genetic analyses of Campylobacter 16s ribosomal RNA amplified from CTW water samples and collected fecal material from birds frequenting those areas. Our results showed a high occurrence of a Campylobacter canadensis-like clade from the sampling sites. Whole-genome sequence analyses of an isolate from Canada goose fecal material, called MG1, were used to confirm the identity of the CTW isolates. Further, we examined the phylogenomic position, virulence gene content, and antimicrobial resistance gene profile of MG1. Lastly, we developed an MG1-specific real-time PCR assay and confirmed the presence of MG1 in Canada goose fecal samples surrounding the CTW. Our findings reveal that the Canada goose-vectored Campylobacter sp. MG1 is a novel isolate compared to C. canadensis that possesses possible zoonotic potential, which may be of human health concern.

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Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes

Abstract: The taxonomic composition of a microbiome is predominately identified using amplicon sequencing of 16S rRNA genes, but as a single marker, it cannot identify functions (genes). Metagenome and metatranscriptome sequencing can determine microbiome function but can be cost prohibitive.

Cited by 8 publications

References 75 publications

A Parasite Odyssey: An RNA virus concealed inToxoplasma gondii

A Parasite Odyssey: An RNA virus concealed inToxoplasma gondii

Elevated methane flux in a tropical peatland post-fire is linked to depth-dependent changes in peat microbiome assembly

Genomic Characterization and Wetland Occurrence of a Novel Campylobacter Isolate from Canada Geese

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