Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana

Round 1

Reviewer 1 Report

I have some general comments for the manuscript submitted to the CIMB journal.

Line 229-233: Nanopore platform classified as Apicomplexa positive 10 out of 14 samples, according to a scoring rule we developed, which classifies a sample as Apicomplexa positive in case the number of reads assigned to Apicomplexa is at least 5-fold the average number of reads assigned to Apicomplexa for negative controls. ¿What criterion did the authors use to determine/develop this classification into positive and negative?

According to the results, the Illumina platform presents higher sensitivity than the nanopore system (14/14 vs. 10/14, respectively); the authors also mention that at the genus level, there is a high correlation between both platforms, and that may be attributed to lower sequencing yield or differential efficiency of PCR primers. Additionally, the authors mention proposals for sensitivity improvement, among other things. ¿Could the authors elaborate on the sensitivity improvements of the test? If this methodology is intended to be applied for diagnostic purposes, it should be discussed in a better way.

General:

Lines 50-51 Indeed, humans can be contaminated through activities such as hunting, fishing or consumption of soiled water, raw or uncooked game meat (12–14), greatly enjoyed by the population.

Suggestion: Contaminated is misused; the correct term is infected, as contamination is towards non-living beings (e.g., materials or surfaces), and enjoyed is misused as it refers to preference, and the correct term is usually or commonly.

Minor editing of English language required

Author Response

Thank you very much for taking the time to review our manuscript "Meat-Borne-Parasite: a Nanopore-based meta-barcoding work-flow for parasitic microbiodiversity assessment in the wild fauna of French Guiana". Please find the detailed responses in attachment. 

Author Response File: Author Response.docx

Reviewer 2 Report

Dear Editor, I have reviewed  the manuscript “Meat-Borne-Parasite: a Nanopore-based meta-barcoding work-flow for parasitic microbiodiversity assessment in the wild fauna of French Guiana” submitted to be published on Current Issues in Molecular biology. Here are my observations:

Line 39 . currently the name of the phylum is Apicomplexa, please remove the sentence “also called Sporozoa”.

Line 44 replace the authors' names ((Beck et al., 2009) with the number of reference

Lines 43-44 I’m not agree with the following sentence ”potentially causing chronic asymptomatic diseases or severe acute diseases in endemic areas”. The cited Apicomplexa, Sarcocystis, Cryptosporidium and Toxoplasma,  are  worldwide protozoa and in my opinion it cannot be said that endemic areas exist. Please rephrase.

Line 50 the word “contaminated” is not appropriate, please replace with “infected” in all over the manuscript

Lines 59-64 IFAT is not a tool for the detection of protozoa in wild animals as it allows the detection of antibodies. Please rephrase

Table 1 change column headers and/or add columns. Cuniculus paca is a species then the column header should be Species and not Genus species.

Line 248 use italic for Theileria

Line 251 use italic for T. gondii

Line 326  change Dasyprocta Leoprina with Dasyprocta leporina

General comments

The authors developed a workflow based  on Nanopore sequencing, to target the 18S rRNA gene for  Apicomplexa detection.  They describe the technique very well but the results are not sufficiently described. Specifically, they do not report which species of Apicomplexa they found in the hosts analyzed and whether there are differences based on the tissues used as matrix. In figure 2 only the animal code is indicated but the species is not shown.

Author Response

Thank you very much for taking the time to review our manuscript "Meat-Borne-Parasite: a Nanopore-based meta-barcoding work-flow for parasitic microbiodiversity assessment in the wild fauna of French Guiana". Please find the detailed responses in attachment. 

Author Response File: Author Response.pdf