ENV

The ENV division of DDBJ contains sequence data and other information on environmental samples. Though frequently confused, the term, ‘environmental samples’, does NOT mean “wild type”.
Environmental samples are identified sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism.

The ENV division contains (but is not limited to) the following types of data:

• sequences derived by direct molecular isolation from soil, sea water, etc.
• clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host
• mixed culture derived from an environmental sample

Environmental samples do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture).

Notes on environmental sample submission

• In many cases of environmental samples, we assign the lineage that as far as submitters could specify is used for the description of organism name with the header “uncultured”. See also Organism Qualifier 3. Environmental sample for further detail.
• The environmental_sample qualifier is required in source feature.
• The isolation_source qualifier is required in source feature to describe origin of the sample.
• Either clone or isolate qualifier is required as an identifier.
• Do not use strain qualifier.

Sample flat file

Aspects of environmental samples

• LOCUS line provides the division name, “ENV”.
• KEYWORDS line provides the keyword name, “ENV”.
• In may cases, ORGANISM line includes “environmental samples”. Please note there are some exceptions.

LOCUS       AB000000              450 bp    mRNA    linear   ENV 16-DEC-2012
DEFINITION  Uncultured Acetobacter sp. gene for 16S ribosomal RNA, partial
            sequence, clone: M12-34.
ACCESSION   AB000000
VERSION     AB000000.1
KEYWORDS    ENV.
SOURCE      uncultured Acetobacter sp.
  ORGANISM  uncultured Acetobacter sp.
            Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales;
            Acetobacteraceae; Acetobacter; environmental samples.
REFERENCE   1  (bases 1 to 450)
  AUTHORS   Mishima,H. and Shizuoka,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-DEC-2012) to the DDBJ/EMBL/GenBank databases.
            Contact:Hanako Mishima
            National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
            Mishima, Shizuoka 411-8540, Japan
REFERENCE   2
  AUTHORS   Mishima,H., Shizuoka,T. and Fuji,I.
  TITLE     Phylogenetic Profile of Sediment in Japan
  JOURNAL   Env Biol 12, 34-36 (2013)
COMMENT
FEATURES             Location/Qualifiers
     source          1..450
                     /clone="M12-34"
                     /collection_date="2007"
                     /db_xref="taxon:114714"
                     /environmental_sample
                     /geo_loc_name="Japan: Osaka"
                     /isolation_source="PCR-derived sequence from sediment"
                     /mol_type="genomic DNA"
                     /organism="uncultured Acetobacter sp."
     rRNA            <1..>450
                     /product="16S ribosomal RNA"
BASE COUNT          199 a          223 c          198 g           230 t
ORIGIN
        1 agtcgcacga aggtttcggc cttagtggcg gacgggtgag taacgcgtag gaatctatcc
        :
        -- The rest of nucleotide sequence is omitted --
        :
//