| Title |
Identification of low abundance microbiome in clinical samples using whole genome sequencing
|
|---|---|
| Published in |
Genome Biology, November 2015
|
| DOI | 10.1186/s13059-015-0821-z |
| Pubmed ID | |
| Authors |
Chao Zhang, Kyle Cleveland, Felice Schnoll-Sussman, Bridget McClure, Michelle Bigg, Prashant Thakkar, Nikolaus Schultz, Manish A. Shah, Doron Betel |
| Abstract |
Identifying the microbiome composition from primary tissues directly affords an opportunity to study the causative relationships between the host microbiome and disease. However, this is challenging due the low abundance of microbial DNA relative to the host. We present a systematic evaluation of microbiome profiling directly from endoscopic biopsies by whole genome sequencing. We compared our methods with other approaches on datasets with previously identified microbial composition. We applied this approach to identify the microbiome from 27 stomach biopsies, and validated the presence of Helicobacter pylori by quantitative PCR. Finally, we profiled the microbial composition in The Cancer Genome Atlas gastric adenocarcinoma cohort. |
X Demographics
The data shown below were collected from the profiles of 43 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 17 | 40% |
| United Kingdom | 3 | 7% |
| Germany | 3 | 7% |
| Canada | 2 | 5% |
| Poland | 1 | 2% |
| Chile | 1 | 2% |
| France | 1 | 2% |
| Spain | 1 | 2% |
| Switzerland | 1 | 2% |
| Other | 1 | 2% |
| Unknown | 12 | 28% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 26 | 60% |
| Members of the public | 16 | 37% |
| Science communicators (journalists, bloggers, editors) | 1 | 2% |
Mendeley readers
The data shown below were compiled from readership statistics for 201 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 4 | 2% |
| Germany | 2 | <1% |
| Czechia | 1 | <1% |
| United Kingdom | 1 | <1% |
| Ireland | 1 | <1% |
| Thailand | 1 | <1% |
| Estonia | 1 | <1% |
| Japan | 1 | <1% |
| Spain | 1 | <1% |
| Other | 0 | 0% |
| Unknown | 188 | 94% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 42 | 21% |
| Researcher | 42 | 21% |
| Student > Master | 23 | 11% |
| Student > Bachelor | 21 | 10% |
| Other | 12 | 6% |
| Other | 31 | 15% |
| Unknown | 30 | 15% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 56 | 28% |
| Agricultural and Biological Sciences | 50 | 25% |
| Medicine and Dentistry | 15 | 7% |
| Immunology and Microbiology | 12 | 6% |
| Computer Science | 9 | 4% |
| Other | 21 | 10% |
| Unknown | 38 | 19% |
Attention Score in Context
This research output has an Altmetric Attention Score of 30. 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 May 2019.
All research outputs
#1,325,776
of 25,658,139 outputs
Outputs from Genome Biology
#1,016
of 4,498 outputs
Outputs of similar age
#21,702
of 396,027 outputs
Outputs of similar age from Genome Biology
#32
of 74 outputs
Altmetric has tracked 25,658,139 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 4,498 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.5. This one has done well, scoring higher than 77% 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 396,027 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 94% of its contemporaries.
We're also able to compare this research output to 74 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 56% of its contemporaries.