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--- four_bacillus_strains_2016 [2016/03/15 17:14] – [antiSMASH 3.0 results] hyjeong
+++ four_bacillus_strains_2016 [2021/03/17 13:09] (current) – external edit 127.0.0.1
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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 Kyung Sook Bae (2005, unpublished result), had been listed as a type strain of "//Bacillus nitroreducens//" from the KCTC web site until recently.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 |}}