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Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis

Overview of attention for article published in Microbiome, September 2018
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (91st percentile)
  • Good Attention Score compared to outputs of the same age and source (69th percentile)

Mentioned by

blogs
1 blog
twitter
31 X users
wikipedia
1 Wikipedia page

Citations

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41 Dimensions

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74 Mendeley
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Title
Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis
Published in
Microbiome, September 2018
DOI 10.1186/s40168-018-0539-8
Pubmed ID
Authors

Jessica K. Jarett, Stephen Nayfach, Mircea Podar, William Inskeep, Natalia N. Ivanova, Jacob Munson-McGee, Frederik Schulz, Mark Young, Zackary J. Jay, Jacob P. Beam, Nikos C. Kyrpides, Rex R. Malmstrom, Ramunas Stepanauskas, Tanja Woyke

Abstract

Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habitats using 16S rRNA gene surveys, genome sequences have been available for only three Nanoarchaeota and their hosts. The host range and adaptation of Nanoarchaeota to a wide range of environmental conditions has thus largely remained elusive. Single-cell genomics is an ideal approach to address these questions as Nanoarchaeota can be isolated while still attached to putative hosts, enabling the exploration of cell-cell interactions and fine-scale genomic diversity. From 22 single amplified genomes (SAGs) from three hot springs in Yellowstone National Park, we derived a genome-based phylogeny of the phylum Nanoarchaeota, linking it to global 16S rRNA gene diversity. By exploiting sequencing of co-sorted tightly attached cells, we associated Nanoarchaeota with 6 novel putative hosts, 2 of which were found in multiple SAGs, and showed that the same host species may associate with multiple species of Nanoarchaeota. Comparison of single nucleotide polymorphisms (SNPs) within a population of Nanoarchaeota SAGs indicated that Nanoarchaeota attached to a single host cell in situ are likely clonal. In addition to an overall pattern of purifying selection, we found significantly higher densities of non-synonymous SNPs in hypothetical cell surface proteins, as compared to other functional categories. Genes implicated in interactions in other obligate microbe-microbe symbioses, including those encoding a cytochrome bd-I ubiquinol oxidase and a FlaJ/TadC homologue possibly involved in type IV pili production, also had relatively high densities of non-synonymous SNPs. This population genetics study of Nanoarchaeota greatly expands the known potential host range of the phylum and hints at what genes may be involved in adaptation to diverse environments or different hosts. We provide the first evidence that Nanoarchaeota cells attached to the same host cell are clonal and propose a hypothesis for how clonality may occur despite diverse symbiont populations.

X Demographics

X Demographics

The data shown below were collected from the profiles of 31 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 74 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 74 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 21 28%
Student > Ph. D. Student 16 22%
Student > Master 10 14%
Student > Bachelor 8 11%
Student > Doctoral Student 3 4%
Other 5 7%
Unknown 11 15%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 21 28%
Agricultural and Biological Sciences 17 23%
Environmental Science 10 14%
Earth and Planetary Sciences 5 7%
Immunology and Microbiology 4 5%
Other 2 3%
Unknown 15 20%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 28. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 08 April 2023.
All research outputs
#1,325,576
of 24,378,986 outputs
Outputs from Microbiome
#454
of 1,639 outputs
Outputs of similar age
#28,900
of 345,453 outputs
Outputs of similar age from Microbiome
#20
of 62 outputs
Altmetric has tracked 24,378,986 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 94th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,639 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 38.9. This one has gotten more attention than average, scoring higher than 72% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 345,453 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 91% of its contemporaries.
We're also able to compare this research output to 62 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 69% of its contemporaries.