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Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

Overview of attention for article published in BMC Genomics, July 2018
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  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (79th percentile)
  • High Attention Score compared to outputs of the same age and source (80th percentile)

Mentioned by

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1 blog
twitter
3 tweeters

Citations

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20 Dimensions

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53 Mendeley
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Title
Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures
Published in
BMC Genomics, July 2018
DOI 10.1186/s12864-018-4959-4
Pubmed ID
Authors

Matej Medvecky, Darina Cejkova, Ondrej Polansky, Daniela Karasova, Tereza Kubasova, Alois Cizek, Ivan Rychlik

Abstract

In order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial anaerobes from chicken caecum. Altogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Among 204 sequenced isolates we identified 133 different strains belonging to seven different phyla - Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes. Genome sizes ranged from 1.51 Mb in Elusimicrobium minutum to 6.70 Mb in Bacteroides ovatus. Clustering based on the presence of protein coding genes showed that isolates from phyla Proteobacteria, Verrucomicrobia, Elusimicrobia and Synergistetes did not cluster with the remaining isolates. Firmicutes split into families Lactobacillaceae, Enterococcaceae, Veillonellaceae and order Clostridiales from which the Clostridium perfringens isolates formed a distinct sub-cluster. All Bacteroidetes isolates formed a separate cluster showing similar genetic composition in all isolates but distinct from the rest of the gut anaerobes. The majority of Actinobacteria clustered closely together except for the representatives of genus Gordonibacter showing that the genome of this genus differs from the rest of Actinobacteria sequenced in this study. Representatives of Bacteroidetes commonly encoded proteins (collagenase, hemagglutinin, hemolysin, hyaluronidase, heparinases, chondroitinase, mucin-desulfating sulfatase or glutamate decarboxylase) that may enable them to interact with their host. Aerotolerance was recorded in Akkermansia and Cloacibacillus and was also common among representatives of Bacteroidetes. On the other hand, Elusimicrobium and the majority of Clostridiales were highly sensitive to air exposure despite their potential for spore formation. Major gut microbiota members utilise different strategies for gut colonisation. High oxygen sensitivity of Firmicutes may explain their commonly reported decrease after oxidative burst during gut inflammation.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 53 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 53 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 15 28%
Researcher 10 19%
Student > Master 9 17%
Student > Doctoral Student 4 8%
Student > Bachelor 2 4%
Other 7 13%
Unknown 6 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 18 34%
Biochemistry, Genetics and Molecular Biology 9 17%
Environmental Science 4 8%
Immunology and Microbiology 4 8%
Veterinary Science and Veterinary Medicine 2 4%
Other 9 17%
Unknown 7 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 9. 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 06 August 2018.
All research outputs
#2,026,441
of 14,263,224 outputs
Outputs from BMC Genomics
#985
of 8,371 outputs
Outputs of similar age
#57,404
of 275,033 outputs
Outputs of similar age from BMC Genomics
#3
of 15 outputs
Altmetric has tracked 14,263,224 research outputs across all sources so far. Compared to these this one has done well and is in the 85th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 8,371 research outputs from this source. They receive a mean Attention Score of 4.2. This one has done well, scoring higher than 88% 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 275,033 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 79% of its contemporaries.
We're also able to compare this research output to 15 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 80% of its contemporaries.