Human DNA in bacterial genomes? Yes? No? Maybe?

Astronomer Carl Sagan once said that “extraordinary claims require extraordinary evidence” and that basis I was primed for scepticism when I first glanced at this paper in mBio, which reports apparently human DNA sequences (specifically from the Line 1 retrotransposon) within a bacterial genome (that of the obligate human pathogen, Neisseria gonorrhoeae). But the most exciting scientific reports are those that overturn one’s assumptions and force one to realise that “there are more things in heaven and Earth than were ever dreamt of in your philosophy”. Examples for me include the discovery of reverse transcriptase in bacteria, group II introns in bacteria, the non-essentiality of the ATPase in flagellar protein export and evidence of Neanderthal admixture in non-African human genomes. After careful reading of the paper, I cannot find any obvious flaws, so I have to accept that human DNA does sometimes get incorporated into bacterial genomes.

But as a professional sceptic, I wanted to check whether these authors had not told the whole story, so I had a look for myself at the evidence for Line 1-like sequences in bacteria. The easiest place to start is to look for homology at the protein level. There are two CDSs within Line 1. Let’s start with ORF1. A BlastP search of the NR database does indeed find the gonococcal sequences:

 
 
>ref|ZP_04721371.1|  hypothetical protein NgonD_07408 [Neisseria gonorrhoeae DGI18]
 ref|ZP_04723444.1|  hypothetical protein NgonFA_07006 [Neisseria gonorrhoeae FA6140]
 ref|ZP_04733942.1|  hypothetical protein NgonPI_04276 [Neisseria gonorrhoeae PID24-1]
Length=147
 
 Score =  259 bits (661),  Expect = 5e-67
 Identities = 128/130 (99%), Positives = 128/130 (99%), Gaps = 0/130 (0%)
 
Query  35   MENDFDELREEGFRRSNYSELREDIQTKGKEVENFEKNLEECITRITNTEKCLKELMELK  94
            MENDFDELREEGFRRSNYSELREDIQTKGKEVENFEKNLEECITRITNTEKCLKELMELK
Sbjct  1    MENDFDELREEGFRRSNYSELREDIQTKGKEVENFEKNLEECITRITNTEKCLKELMELK  60
 
Query  95   TKARELREECRSLRSRCDQLEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVK  154
            TKAREL EECRSLRSRCD LEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVK
Sbjct  61   TKARELHEECRSLRSRCDPLEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVK  120
 
Query  155  RPNLRLIGVP  164
            RPNLRLIGVP
Sbjct  121  RPNLRLIGVP  130
 
 

But when the search results are limited to bacterial sequences, one also finds these

 
>ref|ZP_02004867.1|  hypothetical protein BGP_6678 [Beggiatoa sp. PS]
Length=100
 
 Score =  179 bits (453),  Expect = 6e-43
 Identities = 88/97 (91%), Positives = 92/97 (95%), Gaps = 0/97 (0%)
 
Query  114  LEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDVENGTK  173
            +EERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESD ENGTK
Sbjct  1    MEERVSAMEDEMNEMKREGKFREKRIKRNEQSLQEIWDYVKRPNLRLIGVPESDGENGTK  60
 
Query  174  LENTLQDIIQENFPNLARQANVQIQEIQRTPQRYSSR  210
            LENTLQDIIQENFPNLARQAN+QIQEIQR PQ  + +
Sbjct  61   LENTLQDIIQENFPNLARQANIQIQEIQRMPQEKAGK  97
 
 
>ref|ZP_02871253.1|  hypothetical protein cdivTM_13371 [candidate division TM7 single-cell
isolate TM7a]
Length=109
 
 Score =  175 bits (444),  Expect = 7e-42
 Identities = 92/109 (85%), Positives = 95/109 (88%), Gaps = 0/109 (0%)
 
Query  230  MLRAAREKGRVTLKGKPIRLTADLSAETLQARREWGPIFNILKEKNFQPRISFPAKLSFI  289
            MLRAARE G+VT KGKPIRLTADL AETLQARREWGPIFNILKEKNFQ  IS PAKLSFI
Sbjct  1    MLRAARETGQVTHKGKPIRLTADLLAETLQARREWGPIFNILKEKNFQLIISCPAKLSFI  60
 
Query  290  SEGERKYFTDKQMLRDFVTTRPTLKELLKEALNMERNNRYQPLQNHAKM  338
            SEG+ K  TDKQMLRD VT RP LKELLKEALNMERNN YQPLQ HAK+
Sbjct  61   SEGKIKSSTDKQMLRDSVTARPALKELLKEALNMERNNWYQPLQKHAKL  109
 
 
>ref|ZP_02871255.1|  hypothetical protein cdivTM_13381 [candidate division TM7 single-cell
isolate TM7a]
Length=68
 
 Score = 80.1 bits (196),  Expect = 4e-13
 Identities = 41/67 (62%), Positives = 48/67 (72%), Gaps = 2/67 (2%)
 
Query  1   MGKKQNRKTGNSKTQSASPPPKERSSSPATEQSWMENDFDELREEGFRRS--NYSELRED  58
           MG+ Q RK  NSK QSAS PPK+ SSSPA +QSWME  F +L E GFRRS  N+SEL+E
Sbjct  1   MGRNQGRKVENSKNQSASSPPKDHSSSPAVDQSWMEKGFQKLIEVGFRRSVINFSELKEH  60
 
Query  59  IQTKGKE  65
           + T  KE
Sbjct  61  VLTHCKE  67
 

Which at first glance provides additional evidence that Line-1-like sequences have found their way into other bacterial genome sequences. However, given that Beggiatoa is not intimately associated with humans and the sequence sits in its own little contig, one has to assume that contamination of the sequencing library is the most likely explanation. Ditto for the TM7 sequences.

What if we try similar searches with the second Line 1 CDS, the one that encodes reverse transcriptase. Well, here we turn up a dozen or more hits to bacterial proteins:

 
 
>ref|ZP_02544188.1|  hypothetical protein cdiviTM7_00470 [candidate division TM7 single-cell
isolate TM7c]
Length=316
 
 Score =  610 bits (1574),  Expect = 4e-172
 Identities = 308/316 (98%), Positives = 312/316 (99%), Gaps = 0/316 (0%)
 
Query  570  MQGWFNIRKSINVIQHINRAKDKNHMIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKI  629
            MQGWFNIRKSINVIQHINRAKDKNHMIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKI
Sbjct  1    MQGWFNIRKSINVIQHINRAKDKNHMIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKI  60
 
Query  630  IRAIYDKPTANIILNGQKLEAFPLKTGTRQGCPLSPLLFNIVLEVLARAIRQEKEIKGIQ  689
             RAIYDKPTANIILNGQKLEAFPLKTGTRQGCPLSPLLFN+VLEVLARAIR+EKE+KGIQ
Sbjct  61   TRAIYDKPTANIILNGQKLEAFPLKTGTRQGCPLSPLLFNVVLEVLARAIRREKEVKGIQ  120
 
Query  690  LGKEEVKLSLFADDMIVYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQAFLYTNNRQT  749
            LGKEEVKLSLFADDMIVYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQAFLYTNNRQT
Sbjct  121  LGKEEVKLSLFADDMIVYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQAFLYTNNRQT  180
 
Query  750  ESQIMGELPFTIASKRIKYLGIQLTRDVKDLFKENYKPLLKEIKEDTNKWKNIPCSWVGR  809
            ESQIM ELPFTIASKRIKYLGIQLTRDVKDLFKENYKPLLKEIKEDTNKWKNIPCSWVGR
Sbjct  181  ESQIMSELPFTIASKRIKYLGIQLTRDVKDLFKENYKPLLKEIKEDTNKWKNIPCSWVGR  240
 
Query  810  INIVKMAILPKVIYRFNAIPIKLPMTFFTELEKTTLKFIWNQKRARIAKSILSQKNKAGG  869
            INIVKMAILPKVIYRFNAIPIKLPMTFFTELEKTTLKF+WNQKRA IAKSILSQKNKAGG
Sbjct  241  INIVKMAILPKVIYRFNAIPIKLPMTFFTELEKTTLKFMWNQKRACIAKSILSQKNKAGG  300
 
Query  870  ITLPYFKLYYKATVTK  885
            ITLP FKLYYKATVTK
Sbjct  301  ITLPDFKLYYKATVTK  316
 
 
>ref|ZP_04563087.1|  conserved hypothetical protein [Mollicutes bacterium D7]
Length=131
 
 Score =  211 bits (536),  Expect = 8e-52
 Identities = 104/121 (86%), Positives = 112/121 (93%), Gaps = 0/121 (0%)
 
Query  945   RKLKLDLFLTPYTKINSRWIKDLNVKPKTIKTLEENLGITIQDIGVGKDFMSKTPKAMAT  1004
             +K +   FLTPYTKI+SRWIKDL+V+PKTIKTLEENLGITIQDI +GKDFMSKTPKAMAT
Sbjct  2     QKTETGPFLTPYTKIHSRWIKDLHVRPKTIKTLEENLGITIQDIXMGKDFMSKTPKAMAT  61
 
Query  1005  KDKIDKWDLIKLKSFCTAKETTIRVNRQPTTWEKIFATYSSDKGLISRIYNELKQIYKKK  1064
             K KIDKWDLIKLKSFCTA+ETTIRVNRQPT WEKIFATYSSDKGLISRI  ELKQIY+KK
Sbjct  62    KAKIDKWDLIKLKSFCTAEETTIRVNRQPTEWEKIFATYSSDKGLISRICKELKQIYRKK  121
 
Query  1065  T  1065
             T
Sbjct  122   T  122
 
 
>ref|ZP_04563088.1|  conserved hypothetical protein [Mollicutes bacterium D7]
Length=91
 
 Score =  206 bits (524),  Expect = 2e-50
 Identities = 90/91 (99%), Positives = 91/91 (100%), Gaps = 0/91 (0%)
 
Query  1104  MQIKTTMRYHLTPVRMAIIKKSGNNRCWRGCGEIGTLLHCWWDCKLVQPLWKSVWRFLRD  1163
             MQIKTTMRYHLTPVRMAIIKKSGNNRCWRGCGEIGTLLHCWWDCKLVQPLWKSVWRFLRD
Sbjct  1     MQIKTTMRYHLTPVRMAIIKKSGNNRCWRGCGEIGTLLHCWWDCKLVQPLWKSVWRFLRD  60
 
Query  1164  LELEIPFDPAIPLLGIYPEDYKSCCYKDTCT  1194
             LELEIPFDPAIPLLGIYP+DYKSCCYKDTCT
Sbjct  61    LELEIPFDPAIPLLGIYPKDYKSCCYKDTCT  91
 
 
>ref|ZP_02004659.1|  conserved hypothetical protein [Beggiatoa sp. PS]
Length=95
 
 Score =  179 bits (455),  Expect = 2e-42
 Identities = 91/92 (99%), Positives = 91/92 (99%), Gaps = 0/92 (0%)
 
Query  595  MIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKIIRAIYDKPTANIILNGQKLEAFPLK  654
            MIISIDAEKAFDKIQQPFMLKTLNKLGIDGTY KIIRAIYDKPTANIILNGQKLEAFPLK
Sbjct  1    MIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYLKIIRAIYDKPTANIILNGQKLEAFPLK  60
 
Query  655  TGTRQGCPLSPLLFNIVLEVLARAIRQEKEIK  686
            TGTRQGCPLSPLLFNIVLEVLARAIRQEKEIK
Sbjct  61   TGTRQGCPLSPLLFNIVLEVLARAIRQEKEIK  92
 
 
>ref|ZP_02544187.1|  hypothetical protein cdiviTM7_00465 [candidate division TM7 single-cell
isolate TM7c]
Length=84
 
 Score =  167 bits (424),  Expect = 8e-39
 Identities = 83/84 (99%), Positives = 83/84 (99%), Gaps = 0/84 (0%)
 
Query  466  PTKKSPGPDGFTAEFYQRYKEELVPFLLKLFQSIEKEGILPNSFYEASIILIPKPGRDTT  525
            PTKKSPGPDGFTAEFYQRYKEELV FLLKLFQSIEKEGILPNSFYEASIILIPKPGRDTT
Sbjct  1    PTKKSPGPDGFTAEFYQRYKEELVQFLLKLFQSIEKEGILPNSFYEASIILIPKPGRDTT  60
 
Query  526  KKENFRPISLMNIDAKILNKILAN  549
            KKENFRPISLMNIDAKILNKILAN
Sbjct  61   KKENFRPISLMNIDAKILNKILAN  84
 
 
>ref|ZP_02532187.1|  hypothetical protein Epers_00800 [Endoriftia persephone 'Hot96_1+Hot96_2']
Length=89
 
 Score =  166 bits (419),  Expect = 3e-38
 Identities = 85/89 (96%), Positives = 86/89 (97%), Gaps = 0/89 (0%)
 
Query  595  MIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKIIRAIYDKPTANIILNGQKLEAFPLK  654
            MIISIDAEKAFDKIQQ FMLKTLNKL IDGTY KIIRAIYDKPTANIILNG+KLEAFPLK
Sbjct  1    MIISIDAEKAFDKIQQHFMLKTLNKLYIDGTYLKIIRAIYDKPTANIILNGKKLEAFPLK  60
 
Query  655  TGTRQGCPLSPLLFNIVLEVLARAIRQEK  683
            TGTRQGCPLSPLLFNIVLEVLARAIRQEK
Sbjct  61   TGTRQGCPLSPLLFNIVLEVLARAIRQEK  89
 
 
>ref|ZP_01265305.1|  hypothetical protein PU1002_07017 [Candidatus Pelagibacter ubique
HTCC1002]
Length=120
 
 Score =  152 bits (385),  Expect = 3e-34
 Identities = 83/122 (69%), Positives = 94/122 (78%), Gaps = 2/122 (1%)
 
Query  943   ICRKLKLDLFLTPYTKINSRWIKDLNVKPKTIKTLEENLGITIQDIGVGKDFMSKTPKAM  1002
             +CRKLKLD FLT YTKINSRWI++LNVK KTIK LEENLG TI+ IG+GK FM K+PKA+
Sbjct  1     MCRKLKLDPFLTLYTKINSRWIQNLNVKSKTIKILEENLGNTIKGIGMGKYFMIKSPKAI  60
 
Query  1003  ATKDKIDKWDLIKLKSFCTAKETTIRVNRQPTTWEKIFATYSSDKGLISRIYNELKQIYK  1062
             ATK KIDKWDLIKLKSFCTA+ET+          E +     +DK LISRIY ELKQI K
Sbjct  61    ATKAKIDKWDLIKLKSFCTAEETSQHKQTIYRMGENV--CNLTDKSLISRIYKELKQIKK  118
 
Query  1063  KK  1064
             KK
Sbjct  119   KK  120
 
 
>ref|ZP_02873580.1|  hypothetical protein cdivTM_25184 [candidate division TM7 single-cell
isolate TM7a]
Length=58
 
 Score =  101 bits (251),  Expect = 9e-19
 Identities = 50/58 (87%), Positives = 52/58 (90%), Gaps = 0/58 (0%)
 
Query  109  LTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSILDRSTRQKVNKDTQ  166
            LTILNIYAPNTGAPRFIKQVL DLQRDLDS T+I+GD NTPLSI DRS RQKVNKD Q
Sbjct  1    LTILNIYAPNTGAPRFIKQVLRDLQRDLDSRTIIVGDINTPLSISDRSMRQKVNKDIQ  58
 
 
>ref|ZP_07929653.1|  LOW QUALITY PROTEIN: conserved hypothetical protein [Fusobacterium
ulcerans ATCC 49185]
 gb|EFS27679.1|  LOW QUALITY PROTEIN: conserved hypothetical protein [Fusobacterium
ulcerans ATCC 49185]
Length=57
 
 Score =  100 bits (250),  Expect = 1e-18
 Identities = 48/57 (85%), Positives = 51/57 (90%), Gaps = 0/57 (0%)
 
Query  214  LSKCKRTEIITNYLSDHSAIKLELRIKNLTQSRSTTWKLNNLLLNDYWVHNEMKAEI  270
            LSKCKRTEIITN LSDHS IKLEL+IK LTQ+ S TW+LNNLLLNDYWVHNEM AEI
Sbjct  1    LSKCKRTEIITNCLSDHSEIKLELKIKKLTQNCSATWRLNNLLLNDYWVHNEMNAEI  57
 
 
>ref|ZP_02873206.1|  hypothetical protein cdivTM_23289 [candidate division TM7 single-cell
isolate TM7a]
Length=82
 
 Score = 97.1 bits (240),  Expect = 2e-17
 Identities = 43/60 (72%), Positives = 51/60 (85%), Gaps = 0/60 (0%)
 
Query  1204  IAKTWNQPKCPTMIDWIKKMWHIYTMEYYAAIKNDEFISFVGTWMKLETIILSKLSQEQK  1263
             +AKTWNQPKCP+++D IKKMW IYTMEY AA+K +E + F GTWM+LE IILSKL QEQK
Sbjct  1     MAKTWNQPKCPSVVDCIKKMWFIYTMEYNAAMKKNEIMFFAGTWMELEAIILSKLMQEQK  60
 
 
>ref|ZP_02873863.1|  hypothetical protein cdivTM_26611 [candidate division TM7 single-cell
isolate TM7a]
Length=54
 
 Score = 95.1 bits (235),  Expect = 6e-17
 Identities = 47/52 (91%), Positives = 50/52 (97%), Gaps = 0/52 (0%)
 
Query  61   KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTIL  112
            +IYQANGK+KKAG+AILVSDKTDFKPTKIKRDKE H IMVKGSIQQEELTIL
Sbjct  3    EIYQANGKEKKAGIAILVSDKTDFKPTKIKRDKERHDIMVKGSIQQEELTIL  54
 
 
>ref|ZP_04563056.1|  conserved hypothetical protein [Mollicutes bacterium D7]
Length=44
 
 Score = 87.8 bits (216),  Expect = 1e-14
 Identities = 42/42 (100%), Positives = 42/42 (100%), Gaps = 0/42 (0%)
 
Query  61   KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKG  102
            KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKG
Sbjct  3    KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKG  44
 
 
>ref|ZP_02871216.1|  hypothetical protein cdivTM_13184 [candidate division TM7 single-cell
isolate TM7a]
Length=78
 
 Score = 83.2 bits (204),  Expect = 3e-13
 Identities = 42/72 (59%), Positives = 50/72 (70%), Gaps = 0/72 (0%)
 
Query  971   PKTIKTLEENLGITIQDIGVGKDFMSKTPKAMATKDKIDKWDLIKLKSFCTAKETTIRVN  1030
             P  +KT +  LG  I  I +GKDFM K PKA+A K K++KWDLI+ KS CTAKET  RVN
Sbjct  1     PSLLKTWKTILGNIILGIEMGKDFMMKMPKAIAKKGKVEKWDLIEQKSLCTAKETINRVN  60
 
Query  1031  RQPTTWEKIFAT  1042
             +QPT  EKI  T
Sbjct  61    KQPTEGEKILQT  72
 
 
>gb|ADV08625.1|  hypothetical protein NGTW08_1668 [Neisseria gonorrhoeae TCDC-NG08107]
Length=58
 
 Score = 76.3 bits (186),  Expect = 3e-11
 Identities = 35/52 (68%), Positives = 46/52 (89%), Gaps = 0/52 (0%)
 
Query  333  KASRRQEITKIRAELKEIETQKTLQKINESRSWFFERINKIDRPLARLIKKK  384
            + SRR+EI KIRAE+   ET++T+ KIN+++SWFFERINKID+PLARLIKK+
Sbjct  5    RVSRRKEILKIRAEINAKETKETIAKINKAKSWFFERINKIDKPLARLIKKQ  56

All of these are in dinky little contigs, again suggesting contamination of the bacterial DNA with human DNA rather then genuine HGT.

All that is, apart from the gonococcal Line-1 RT sequence!! This sits slap bang in the middle of the TCDC-NG08107 gonococcal chromosome, next to an invertase-related gene (just like in the paper!), providing clear evidence that there is more going on here than the authors report.

Now, I was prepared to leave it there, but for some reason, I decided to look for hits to the RT CDS just in Neisseria and then discovered over a dozen matches to the Line-1 RT among proteins from the Neisseria polysaccharea ATCC 43768 genome. These all appear to be in small contigs, so look like contamination!

So the take away message is that, yes, it seems plausible that Line-1 DNA has made its way into gonococcal genomes, but given that Line-1 DNA has also contaminated many bacterial genomes, I think we should say that the verdict is so far rests on the balance of probabilities, rather than being beyond all reasonable doubt.

P.S. Oh, and I just checked and the marine metagenome in the environmental DNA archive is also chock full of Line 1 sequences!

 
ResearchBlogging.org Mark T. Anderson, & H. Steven Seifert (2001). Opportunity and Means: Horizontal Gene Transfer from the Human Host to a Bacterial Pathogen mBio, 2 (1)

13 Responses

  1. krobison
    February 16, 2011 at 5:02 pm |

    While the pure sequence data might be unconvincing, what about the PCR validation using one bacterial-specific primer and one LINE-specific primer?

  2. RosieRedfield
    RosieRedfield
    February 16, 2011 at 5:45 pm |

    The Line-1 sequence is in a part of the genome coding for a Neisseria prophage, and is at the same location in the. I wonder if the prophage is still functional – if so, the Line-1 fragment might have inserted into prophage or phage DNA and subsequently spread by lysogeny. The paper doesn’t give enough information to clarify this, so I’m going to email the authors.

  3. Jonathan Badger
    February 16, 2011 at 6:59 pm |

    There was quite a bit of buzz about Alu sequences in the Sargasso Sea metagenome a few years ago (The now moribund blog Suicyte Notes jokingly claimed that it was evidence of tiny aquatic primates; true “sea monkeys”). As I recall, people more seriously attributed it to contamination.

  4. HSS
    HSS
    February 16, 2011 at 8:10 pm |

    We appreciate the insightful bioinformatic analysis performed by Dr. Pallen and agree that it is possible that L1 sequences may be present in other bacterial species or perhaps even in other Neisseria species. It is also possible that the L1 sequences presented by Dr. Pallen’s analysis are examples of sequence contamination. The authenticity of these sequences could certainly be determined experimentally, as we have done conclusively for the nL1 fragment in Neisseria gonorrhoeae using PCR and direct sequence analysis of the genomic locus. We hope our report stimulates the search for other such events. While we have no way to prove that the jump was direct from a mammalian genome into the bacterial genome, the 100% match of these sequences with a human L1 copy coupled with the absence of this sequence in the closely related Neisseria meningitidis and the close association of Neisseria gonorrhoeae and human cells, makes direct transfer the most likely explanation.
    Hank Seifert

  5. Transitioning into “real” science journalism « Culturing Science – biology as relevant to us earthly beings

    [...] down to read my Research Blogging RSS feeds in the morning.  And what did I come across?  A blog post with the title: “Human DNA in bacterial genomes? Yes? No? Maybe?”  Could this be a [...]

  6. HannahWaters
    HannahWaters
    February 17, 2011 at 5:32 pm |

    Thanks again for all your help. Just wanted to correct the link f0r The Scientist article – it’s http://www.the-scientist.com/news/display/57990/

    Best,
    Hannah

  7. Joe H.
    February 17, 2011 at 11:40 pm |

    I haven’t given these sequences a very careful look over, but have you eliminated the possibility that the hits coming back are just other RT- or endonuclease-containing bacterial ORFs? For instance, many group II introns encode RTs that are in the same non-LTR family as LINE-1, and bacteria contain many GpII’s, both partial and full.

    This has no implication on the Neisseria findings, but perhaps a consideration for expanding that observed gene transfer to something broader.

  8. ResearchBlogging.org News » Blog Archive » Editor’s Selections: Human DNA in bacterial genomes (?), primate vaccines, and deep sea carbon cycling

    [...] the genome of the obligate human pathogen, Neisseria gonorrhoeae. But is this really an example of horizontal gene transfer, or contamination of bacterial DNA with human [...]

  9. Cliff Beall
    Cliff Beall
    February 18, 2011 at 8:45 pm |

    The TM7 single cells were isolated from a human mouth, although as you mention it is a dinky contig and is likely to be contamination.

  10. Des bactéries avec des gènes humains? | Bactérioblog

    [...] travaux, comme cela semble être le cas pour un nombre important de séquençages? Il est vrai que la séquence LINE1 se retrouve dans de nombreux génomes bactériens, sur des fragments d’ADN séquencé (les contigs) de petite taille ou chez des bactéries [...]

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