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four_bacillus_strains_2016 [2016/03/15 17:19]
hyjeong [antiSMASH 3.0 results]
four_bacillus_strains_2016 [2017/03/20 15:03] (current)
hyjeong [Four Bacillus strains (2016)]
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 +====== Four Bacillus strains (2016) ======
 +  * Title: Draft genome sequences of four plant probiotic //​Bacillus//​ strains. [[http://​doi.org/​10.1128/​genomeA.00358-16|Genome Announcements (2016) 4 e00358-16.]]
 +===== antiSMASH 3.0 results =====
 +Genome sequences and annotations are also available from the NCBI web site.
 +  * //Bacillus endophyticus // KCTC 13922T {{:​kctc_13922.zip|Zipped GenBank file (PGAP)}} {{:​antismash_kctc_13922.zip|Zipped antiSMASH results}}
 +  * "//"​Bacillus gaemokensis//"​ KCTC 13318T {{:​kctc_13318.zip|Zipped GenBank file (PGAP)}} {{:​antismash_kctc_13318.zip|Zipped antiSMASH results}}
 +  * //Bacillus trypoxylicola//​ KCTC 13244T {{:​kctc_13244.zip|Zipped GenBank file (PGAP)}} {{:​antismash_kctc_13244.zip|Zipped antiSMASH results}} ​
 +  * //​Bacillus//​ sp. KCTC 13219 {{:​kctc_13219.zip|Zipped GenBank file (PAGP)}} {{:​antismash_kctc_13219.zip|Zipped antiSMASH results}}
 +===== Comments on Bacillus sp. KCTC 13219 =====
 +[[http://​kctc.kribb.re.kr/​jsearch/​j_sview.aspx?​sn=13219|KCTC 13219]] (=b04i-3), isolated from Pu'er tea by Dr. Kyung Sook Bae (2005, unpublished result), had been listed as a type strain of "//​Bacillus nitroreducens//"​ from the KCTC web site until recently. However, the original submitter did not propose it eventually as s novel species. There were two records in the NCBI for this strain before the genome sequencing of KCTC 13219: ​
 +  - 16S ribosomal gene sequence ([[http://​www.ncbi.nlm.nih.gov/​nuccore/​170716975|EU391158.1]]) ​
 +  - Information in the taxonomy browser ([[http://​www.ncbi.nlm.nih.gov/​Taxonomy/​Browser/​wwwtax.cgi?​id=512421|512421]])
  
 +The authors used to designate it just as b04i-3**T** or B04I-3**T** without KCTC number from the web site, probably because the information was registered to NCBI before the strain got an official KCTC number. A peroxide-degrading //​Bacillus//​ isolate (strain PLC9 =KACC 91464P) was named after it based on 100% 16S rRNA sequence similarity to KCTC 13219 (New bacteria //Bacillus nitroreducens//​ PLC9 with hydrogen peroxide-degrading activity with high survival rate in hydrogen peroxide. Appl Biochem Biotechnol 2013, 169:​701-711. PMID: [[http://​www.ncbi.nlm.nih.gov/​pubmed/​23271626|23271626]]).
 +
 +There is no relationship between KCTC 13219 (=b04i-3) and [[http://​togodb.biosciencedbc.jp/​togodb/​show/​diam_microbe_patent/​155498|Bacillus sp. B04I-3T]], a patented microorganism in Japan. It would be inappropriate that the Japanese patent information web site refers to the same NCBI taxonomy page ([[http://​www.ncbi.nlm.nih.gov/​Taxonomy/​Browser/​wwwtax.cgi?​id=512421|link]]) as KCTC 13219 does.
 +
 +The following neighbor-joining phylogenetic tree, based on 16S rRNA gene sequences, suggests that KCTC 13219 should be classified into the genus //​Lysinibacillus//​.
 +{{ :​nj_tree.png?​480 |}}
four_bacillus_strains_2016.txt ยท Last modified: 2017/03/20 15:03 by hyjeong