On 2014 Jul 28, Changting Liu commented:

Hi Willem, thanks for your attention on our manuscript. Some of your questions are really important and here is my answering. Firstly, the large differences on genome size. We noticed that the assembly results of these two strains were not good and some genome sequences were not obtained. But it was shown that the sequences of repeats and plasmids were much longer in strain LCT-KP289 and the some of the results were exhibited in Table1 and Table2. And the assembly results of repeats and plasmids can be affected by the sequencing data size and software parameters distinctively. On the other hand, the strains with special phenotypes were sequenced after space-travelling and laboratory-culturing, so there could be some mutations laid in the genome of LCT-KP289. Secondly, the acquisition of several antibiotic resistance genes and plasmids (some of enterococcal origin) in strain LCT-KP289. The manuscript has illustrated that the gene sul1 was multi-copy gene in Klebsiella pneumonia and there was one more copy exhibited in LCT-KP289. And other drug resistance genes which contained in integron were found both in LCT-KP214 and LCT-KP289, so it only explained the multiple drug resistances of Klebsiella pneumonia. As for the enterococcal plasmids, we should notice that it exist both in LCT-KP214 and LCT-KP289, so the plasmid should be captured by Klebsiella pneumonia before space traveling and it was not acquired from the medium or sequencing contaminant. Thirdly, the manuscript contains several errors (including a reported %GC of 84.42% for one of the strains). I apologize for this writing error, and the GC% of LCT-KP289 should be 56.78% and we are contacting the editor of BMC for the typo correction. Thanks again for your question. And if you have any more problems, please don't be hesitated to contact us. Thank you.

On 2014 Jul 15, Willem Schaik commented:

This paper attempts to show genomic differences between a Klebsiella pneumoniae strain that was incubated in the Shenzhou VIII unmanned spacecraft for 17 days and a control that remained on Earth. The reported differences between the two strains are large and include a 200 kbp difference in genome size and the acquisition of several antibiotic resistance genes and plasmids (some of enterococcal origin). These data are highly unlikely because when strains are grown in isolation, they should not be able to acquire foreign DNA from the medium. The authors do not explain these observations and simply claim that this is a result of spaceflight. In my opinion it is more likely that strains have been mixed-up or a contaminant has been sequenced. I also note that the manuscript contains several errors (including a reported %GC of 84.42% for one of the strains) and unsubstantiated claims.

On 2014 Jul 15, Willem Schaik commented:

This paper attempts to show genomic differences between a Klebsiella pneumoniae strain that was incubated in the Shenzhou VIII unmanned spacecraft for 17 days and a control that remained on Earth. The reported differences between the two strains are large and include a 200 kbp difference in genome size and the acquisition of several antibiotic resistance genes and plasmids (some of enterococcal origin). These data are highly unlikely because when strains are grown in isolation, they should not be able to acquire foreign DNA from the medium. The authors do not explain these observations and simply claim that this is a result of spaceflight. In my opinion it is more likely that strains have been mixed-up or a contaminant has been sequenced. I also note that the manuscript contains several errors (including a reported %GC of 84.42% for one of the strains) and unsubstantiated claims.