Evidence map›Paper›PMID 27313837›Full record

ArticleStandards in genomic sciences2016

High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T).

Nisreen Tashkandy, Sari Sabban, Mohammad Fakieh, Jan P Meier-Kolthoff, Sixing Huang, Brian J Tindall, Manfred Rohde, Mohammed N Baeshen, Nabih A Baeshen, Alla Lapidus and 12 more

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In one paragraph

Article in Standards in genomic sciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors.

Nisreen TashkandyDepartment of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
Sari SabbanDepartment of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
Mohammad FakiehDepartment of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
Jan P Meier-KolthoffLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Sixing HuangLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Brian J TindallLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Manfred RohdeHZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.
Mohammed N BaeshenDepartment of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia ; Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia.
Nabih A BaeshenDepartment of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia ; Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia.
Alla LapidusCentre for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia.
Alex CopelandDepartment of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA.
Manoj PillayBiological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA.
T B K ReddyDepartment of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA.
Marcel HuntemannDepartment of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA.
Amrita PatiDepartment of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA.
Natalia IvanovaDepartment of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA.
Victor MarkowitzBiological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA.
Tanja WoykeDepartment of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA.
Markus GökerLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Hans-Peter KlenkSchool of Biology, Newcastle University, Newcastle upon Tyne, UK.
Nikos C KyrpidesDepartment of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia ; Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA.
Richard L HahnkeLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5(T) (DSM 17707(T)) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5(T) is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5(T) has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5(T). Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5(T) feeds rather on proteins than saccharides and lipids.

Indexed as

AerobicBacteroidetesCarbohydrate active enzymeFlavobacteriaceaeGEBAGGDCGliding motilityGreenhouse soilKMG-1Polysaccharide utilization lociTree of Life

Identifiers

PMID27313837
PMCPMC4910214

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.