gsgs
Registered User
http://www.bbc.com/news/health-28440006
Scientists have discovered a previously unknown virus living in the human gut, according
to a study in Nature Communications.
CrAssphage virus.
bacteriophage
CrAssphage infects one of the most common types of bacteria in our guts.
[which ?]
DNA, some 100,000 letters long,
http://www.nature.com/ncomms/2014/140724/ncomms5498/full/ncomms5498.html
~97 kbp genome is six times more abundant in publicly available metagenomes than all other
known phages together; it comprises up to 90% and 22% of all reads in virus-like particle
(VLP)-derived metagenomes and total community metagenomes, respectively; and it totals
1.68% of all human faecal metagenomic sequencing reads in the public databases
Moreover, top similarity of the ORFs was identified across multiple bacterial phyla (Table 1) including
Bacteroidetes (twelve hits, two of which were Bacteroidetes-infecting phages),
Proteobacteria, (12 hits, 9 of which were Proteobacteria-infecting phages),
Firmicutes (10 hits, 1 of which was a Firmicutes-infecting phage),
Marinimicrobia (one hit),
Actinobacteria and
Cyanobacteria (each represented by one hit to a phage).
elephant in the room
GenBank/EMBL/DDBJ
JQ995537
KM000086
KM000121
http://www.ncbi.nlm.nih.gov/nuccore/JQ995537
http://www.ncbi.nlm.nih.gov/nuccore/KM000086 (not yet available)
http://www.ncbi.nlm.nih.gov/nuccore/KM000121 (not yet available)
http://www.ncbi.nlm.nih.gov/sra?term=SRA012183
Results: 6
Select item 34688
1.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
1 LS454 (454 GS FLX) run: 78,390 spots, 20.6M bases, 39.4Mb downloads
Accession: SRX028827
Select item 34687
2.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
2 LS454 (454 GS FLX) runs: 220,132 spots, 58.9M bases, 111.4Mb downloads
Accession: SRX028826
Select item 34686
3.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
2 LS454 (454 GS FLX) runs: 372,973 spots, 100.6M bases, 192.1Mb downloads
Accession: SRX028825
Select item 34685
4.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
2 LS454 (454 GS FLX) runs: 256,574 spots, 69.8M bases, 136Mb downloads
Accession: SRX028824
Select item 34684
5.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
1 LS454 (454 GS FLX) run: 286,146 spots, 78M bases, 177.7Mb downloads
Accession: SRX028823
Select item 25300
6.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
12 LS454 (454 GS FLX) runs: 104,033 spots, 27.9M bases, 49.7Mb downloads
Accession: SRX023429
----------------------------------------
DNA surveys suggest that humans have thousands of viral species in and on us.
-----------------------------------------------------
checking for amino-acid matches in my file of bacteria (genbank 199, ~May,2010) :
epifam6 crass1.p3 gbbct.ami 12 7
QLPSYVDDVLEY > CP001336 AAAW04000000 AAAW04000001 AAAW04000002 AAAW04000003,
Desulfitobacterium hafniense DCB-2
dismissed:
AAKKAAKKAPKK
GGGGSGGGGSGG
GGGGSGGGSGGG
RGGRGGRGGRRG
GGSGGGGSGGGG
GGRGGRGGRGGG
KAAKKAAKKAAK
KAAKKAAKKAAP
AKKAAKKAAPKK
GGGSGGGGSGGG
f1=243762 m=243762 f=243762 z=64884637 s=7 GLSEKEALKKA > CP000679 AALW01000000 AALW01000001-AALW01000136, Caldicellulosiruptor saccharolyticus DSM 8903
f1=244378 m=244378 f=244378 z=90248705 s=8 VPASQLPSYVD > CP001336 AAAW04000000 AAAW04000001 AAAW04000002 AAAW04000003, Desulfitobacterium hafniense DCB-2
f1=772806 m=772806 f=772806 z=195033712 s=7 KELAVKEEVTL > JQ271536, Bacillus amyloliquefaciens
17 amino-acids match with
http://www.ncbi.nlm.nih.gov/nuccore/cp001336
http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense
Desulfitobacterium hafniense DCB-2 isolated from sewage sludge
Scientists have discovered a previously unknown virus living in the human gut, according
to a study in Nature Communications.
CrAssphage virus.
bacteriophage
CrAssphage infects one of the most common types of bacteria in our guts.
[which ?]
DNA, some 100,000 letters long,
http://www.nature.com/ncomms/2014/140724/ncomms5498/full/ncomms5498.html
~97 kbp genome is six times more abundant in publicly available metagenomes than all other
known phages together; it comprises up to 90% and 22% of all reads in virus-like particle
(VLP)-derived metagenomes and total community metagenomes, respectively; and it totals
1.68% of all human faecal metagenomic sequencing reads in the public databases
Moreover, top similarity of the ORFs was identified across multiple bacterial phyla (Table 1) including
Bacteroidetes (twelve hits, two of which were Bacteroidetes-infecting phages),
Proteobacteria, (12 hits, 9 of which were Proteobacteria-infecting phages),
Firmicutes (10 hits, 1 of which was a Firmicutes-infecting phage),
Marinimicrobia (one hit),
Actinobacteria and
Cyanobacteria (each represented by one hit to a phage).
elephant in the room
GenBank/EMBL/DDBJ
JQ995537
KM000086
KM000121
http://www.ncbi.nlm.nih.gov/nuccore/JQ995537
http://www.ncbi.nlm.nih.gov/nuccore/KM000086 (not yet available)
http://www.ncbi.nlm.nih.gov/nuccore/KM000121 (not yet available)
http://www.ncbi.nlm.nih.gov/sra?term=SRA012183
Results: 6
Select item 34688
1.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
1 LS454 (454 GS FLX) run: 78,390 spots, 20.6M bases, 39.4Mb downloads
Accession: SRX028827
Select item 34687
2.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
2 LS454 (454 GS FLX) runs: 220,132 spots, 58.9M bases, 111.4Mb downloads
Accession: SRX028826
Select item 34686
3.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
2 LS454 (454 GS FLX) runs: 372,973 spots, 100.6M bases, 192.1Mb downloads
Accession: SRX028825
Select item 34685
4.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
2 LS454 (454 GS FLX) runs: 256,574 spots, 69.8M bases, 136Mb downloads
Accession: SRX028824
Select item 34684
5.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
1 LS454 (454 GS FLX) run: 286,146 spots, 78M bases, 177.7Mb downloads
Accession: SRX028823
Select item 25300
6.Metagenomic analysis of viruses in the fecal micorobiota of monozygotic twins and their mothers
12 LS454 (454 GS FLX) runs: 104,033 spots, 27.9M bases, 49.7Mb downloads
Accession: SRX023429
----------------------------------------
DNA surveys suggest that humans have thousands of viral species in and on us.
-----------------------------------------------------
checking for amino-acid matches in my file of bacteria (genbank 199, ~May,2010) :
epifam6 crass1.p3 gbbct.ami 12 7
QLPSYVDDVLEY > CP001336 AAAW04000000 AAAW04000001 AAAW04000002 AAAW04000003,
Desulfitobacterium hafniense DCB-2
dismissed:
AAKKAAKKAPKK
GGGGSGGGGSGG
GGGGSGGGSGGG
RGGRGGRGGRRG
GGSGGGGSGGGG
GGRGGRGGRGGG
KAAKKAAKKAAK
KAAKKAAKKAAP
AKKAAKKAAPKK
GGGSGGGGSGGG
f1=243762 m=243762 f=243762 z=64884637 s=7 GLSEKEALKKA > CP000679 AALW01000000 AALW01000001-AALW01000136, Caldicellulosiruptor saccharolyticus DSM 8903
f1=244378 m=244378 f=244378 z=90248705 s=8 VPASQLPSYVD > CP001336 AAAW04000000 AAAW04000001 AAAW04000002 AAAW04000003, Desulfitobacterium hafniense DCB-2
f1=772806 m=772806 f=772806 z=195033712 s=7 KELAVKEEVTL > JQ271536, Bacillus amyloliquefaciens
17 amino-acids match with
http://www.ncbi.nlm.nih.gov/nuccore/cp001336
Code:
...SGKVPASQLPSYVDDVLEY...
...DGKVPASQLPSYVDDVLEG...
nucleotides: (...GKVPASQLPSYVDDVLE...)
...GGCAAAGTGCCTGCATCGCAGTTGCCATCCTATGTAGACGATGTTTTAGAA...
...GGTAAAGTTCCAGCAAGTCAATTACCTAGTTATGTCGATGATGTTCTTGAA...
.....x.....x..x...xxx..x..x..xxxx.....x..x......x.x......http://en.wikipedia.org/wiki/Desulfitobacterium_hafniense
Desulfitobacterium hafniense DCB-2 isolated from sewage sludge