Comments on abstract, title, references

Abstract section: 1-'' We have performed a comparative genomics analysis of clinical and environmental strains of V. parahaemolyticus. Our analyses could facilitate understanding of the phylogenetic diversity and niche adaptation of this bacterium''.

Comment: In English academic writing, it is important to avoid personal bias. Using “I” or “we” makes the essay about you and your experiences, instead of research and concrete details. ... This is not okay in formal writing, especially essays or research papers but it is okay when writing a personal letter, so the correct sentence suitable to be ''it has been sequenced ……'' , so the correct sentence suitable to be: ''it has been performed a comparative……………… the analyses could facilitate ……''..

Introduction section: 2-''the most prevalent in certain Asian areas and causes food poisoning, occasionally outbreaks, especially in the hot season ''

Comment: V.parahemolyticus causes seafood-borne gastroenteritis. In addition, warm temperature has been found to influence the incidence of this bacterium, the temperature ranged from 27.8 to 31.7C, so the correct sentences suitable to be:''…….causes seafood-borne gastroenteritis occasionally outbreaks, especially during the summer ''

3-'' The TDH is the major virulence gene of V. parahaemolyticus and present in most of the clinical Kanagawa phenonemon (KP)-positive strains''

Comment: TDH is a protein not a gene, so the correct sentence suitable to be ''The TDH is a major virulence factor that encoded by tdh gene……………''.

4-'' We sequenced the genomes of four O3:K6 and its serovariant clinical strains and five environmental strains of V. parahaemolyticus in Hong Kong''

Comment: as English academic writing, the sentence should be written ''the genomes of four O3:K6 have been sequenced ………….''

Materials and Methods section: Ethics statement and isolate collection 5-'' Nine isolates of V. parahaemolyticus were selected from the bacterial archive maintained at the microbiology laboratory of the Department of Health of Hong Kong''

Comment: a larger number of clinical and environmental of V. parahemolyticus isolates would be recommended. In addition, this study has not included isolates from the entire world.

6: '' We sequenced the genomes of four O3:K6 and its serovariant clinical strains and five environmental strains of V. parahaemolyticus in Hong Kong''

Comment: In academic writing, it's important to avoid personal bias. Using “I” or “we” makes the essay about you and your experiences, instead of research and concrete details.

7-'' Table 6 Distribution of prophages in V. parahaemolyticus strains''

Comment: the authors mentioned prophges in results section but did not mention examination for the presence of prophages in Methods.

Results and discussion Section Summary of genome sequencing data

8-'' Table 1 List of V. parahaemolyticus clinical and environmental isolates analyzed in this study''.

Comment: it would be better to add column Reference Strain/Clinical/Environmental, and the suitable title of this table is '' Table 1 List of V. parahaemolyticus isolates analyzed in this study'' '' Strain Reference Strain/Clinical/Environmental

VIP4-0395 Clinical
RIMD22163 Reference
VIP4-0430 Environmental

9- a-'' As summarized in Table 1, we have completed 454 genome sequencing of nine V. parahaemolyticus isolates obtained in Hong Kong, including four clinical and five environmental strains '' b-'' The clinical strains we sequenced were new O3:K6 and its serovariant (O3:K59), and they were positive for the tdh gene but negative for the trh gene'' c-'' Our environmental strains were all tdh and trh negative'' d- '' We have also included in our analyses six publicly available V. parahaemolyticus genomes'' Comment: In academic writing, it's important to avoid personal bias. Using “I” or “we” makes the essay about you and your experiences, instead of research and concrete details. So the correct sentences suitable to be as follow:- a:''…..the 454 genome sequencing of nine V. parahaemolyticus isolates obtained in Hong Kong, including four clinical and five environmental strains have been sequenced in this study'' b-''it has been found that the clinical strains have new O3:K6 and its serovariant (O3:K59)………….''
c:''However, all environmental strains were negative for tdh and trh'' d:'' it has been also included in this analyses six publicly available V. parahaemolyticus genomes''

Phylogenetic relationships 10-'' Moreover, our local clinical isolates were highly similar to RIMD 2210633 isolated'' Comment: the correct sentence suitable to be: ''Moreover, the local clinical isolates………….''

Pan-genome analysis 11- a:'' Our result shows that the number of pan-genome gene families increased with the number of genomes analysed,'' b:'' We have also analyzed the trend of new gene families, and we found that new genes will continue to be found with increasing of much more genomes''. Comment: the correct sentences suitable to be as follow:- a:''the results show that……….'' b:''it has been also analyzed…………, and it has been found that new genes…..'' Gene-content analysis of V. parahaemolyticus 12-a:'' By investigating the presence and absence of genes in V. parahaemolyticus, we found that most regions within their genomes were conserved'' b:'' We then further analyzed 24 genomic regions that are unique to V. parahaemolyticus RIMD 2210633'' Comment: the correct sentences suitable to be as follow:- a:''………, it has been found that……..'' b:''the further analyzed……..'' A novel genomic island commonly found in clinical strains 13- a:'' Here we analyzed the genome of our O3:K59 strain VIP4-0407'' b:'' We defined this genomic island as Vibrio parahaemolyticus island-8 (VPal-8)'' c:'' Therefore, we suggest that the genomic island found in this study may be related to the virulence of V. parahaemolyticus'' Comment: the correct sentences suitable to be as follow:- a:'' it has been analyzed the genome of O3:K59……..'' b:'' this genomic island has been defined as Vibrio parahaemolyticus….'' c:' Therefore, it has been suggested that the genomic ………'' sRNAs and CRISPR element analysis 14-'' We determined the sRNA sequences in our V. parahaemolyticus strains and found that most sRNAs were highly conserved (Additional file 2: Table S2)'' Comment: the correct sentence suitable to be: '' it has been determined the sRNA sequences in V. parahaemolyticus strains……'' Virulence potential of environmental strains 15-'' Here we report the distribution of virulence factors and prophages in the genomes of our V. parahaemolyticus strains to reveal their pathogenic potential'' Comment: the correct sentence suitable to be: ''it has been reported that the distribution…..of V. parahaemolyticus…………'' Conclusion section 16-a:'' We have three main conclusions. First, by comparing the genome sequences, we found that our clinical strains were phylogenetically distinct from the environmental strains'' b:'' We discovered a new gene cluster belonging to the biofilm associated proteins of V. parahaemolyticus'' c:'' We suggest that this novel gene cluster is a new virulence marker differentiating clinical from environmental strains'' d:'' We also found a novel genomic island (VPal-8) that frequently distributed in clinical strains'' Comment: the correct sentences suitable to be as follow: a:''in this study, there are three main……..,it has been found that the clinical……….'' b:''it has been discovered a new…….'' c:''it has been suggested that this novel ……..'' d:''it has been found a ………''