Draft genome sequence of a Lactiplantibacillus pentosus strain isolated from traditionally fermented rice
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Lactiplantibacillus pentosus is a probiotic bacterium reported to be present in various fermented foods, such as fermented olives, and it significantly influences human health. The present study concerns a lactic acid bacterial strain designated L. pentosus krglsrbmofpi2, isolated from traditional fermented rice, and which has been shown to have an assortment of beneficial attributes. Using Illumina technologies, we have sequenced and investigated the whole genome sequence of L. pentosus krglsrbmofpi2 to understand its functionality and safety. The chromosomal genome was 3.7 Mb in size with 46% GC content and 3192 protein-coding genes. Additional extensive bioinformatics investigations were carried out involving whole genome sequence assembly and annotation.
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All comments by the reviewers were satisfactorily addressed.
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The manuscript is interesting and well-written. It focuses on a sequence analysis of L. pentosus from fermented rice and it is important for the field of probiotics. The literature review contains many relevant recent papers of good quality and the methodology is quite sound. Few minor corrections: Line 46: What were the incubation conditions? Line 46: "The strain was isolated" - Not clear; provide details Line 47: What was the incubation temperature? Lines 46-48: It is not clear how L. pentosus was specifically isolated from the fermented rice, considering that there may be several other bacterial species present Lines 57-58: It is not clear why these three citations have been lumped together, rather than broken up. Table 2 and Figure 1 appear to present the same information. It is not clear why this duplication is needed. In Figure …
The manuscript is interesting and well-written. It focuses on a sequence analysis of L. pentosus from fermented rice and it is important for the field of probiotics. The literature review contains many relevant recent papers of good quality and the methodology is quite sound. Few minor corrections: Line 46: What were the incubation conditions? Line 46: "The strain was isolated" - Not clear; provide details Line 47: What was the incubation temperature? Lines 46-48: It is not clear how L. pentosus was specifically isolated from the fermented rice, considering that there may be several other bacterial species present Lines 57-58: It is not clear why these three citations have been lumped together, rather than broken up. Table 2 and Figure 1 appear to present the same information. It is not clear why this duplication is needed. In Figure 1, the subsystem coverage bar does not seem to add anything; please provide additional details to clarify. Lines 71-76: It is not clear why you are describing in terms of "Indian" and "European" Line 72: If you are going to make comparisons, then the comparative data should be presented in Table, e.g. as part of Table 1 perhaps Line 73: "one Indian strain" - Which one? Are there more? Line 73: "a single plasmid DNA" - Details of the plasmid should be presented in Table 1 Lines 34-35: Italicise "Lactobacillus" "Bacillus" "Bifidobacterium" Lines 34-36: The sentence is not clear. Furthermore, what is the purpose of highlighting yeast cultures? Line 44: "Various fermented food samples have been obtained from numerous places in Himachal Pradesh, India." - It is not clear whether this is a general statement or a statement about the reported study. Consider rewording.
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Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data Methods appear appropriate, but there are aspects where further detail is required. Line 46: What were the incubation conditions? Line 46: "The strain was isolated" - Not clear; provide details Line 47: What was the incubation temperature? Lines 46-48: It is not clear how L. pentosus was specifically isolated from the fermented rice, considering that there may be several other bacterial species present Lines 57-58: It is not clear why these three citations have been lumped together, rather than broken up. 2. Presentation of results Results are generally well presented, but some aspects need further clarification / amendment. Lines 61-62: Write 07 and 04 in words Line 63: It is not clear what the purpose of this citation …
Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data Methods appear appropriate, but there are aspects where further detail is required. Line 46: What were the incubation conditions? Line 46: "The strain was isolated" - Not clear; provide details Line 47: What was the incubation temperature? Lines 46-48: It is not clear how L. pentosus was specifically isolated from the fermented rice, considering that there may be several other bacterial species present Lines 57-58: It is not clear why these three citations have been lumped together, rather than broken up. 2. Presentation of results Results are generally well presented, but some aspects need further clarification / amendment. Lines 61-62: Write 07 and 04 in words Line 63: It is not clear what the purpose of this citation is. Line 64: "RAST annotation reveals 350 subsystems......(Figure 1)" - Where is this detail shown in Figure 1? It does not seem obvious. Lines 65-66: "sub-framework" "non-subsystem" - What do these terms mean? Table 2 and Figure 1 appear to present the same information. It is not clear why this duplication is needed. In Figure 1, the subsystem coverage bar does not seem to add anything; please provide additional details to clarify. 3. How the style and organization of the paper communicates and represents key findings Aspects of the narrative in relation to "probiotic" needs to be amended. The narrative (mainly the abstract) alludes to L. pentosus as a probiotic, but ignores that for an organism to be referred to as probiotic, there should be robust evidence supported by clinical trials. Also, only specific strains, rather than entire species, should be referred to as probiotic. The narrative should instead indicate that it is potentially probiotic. The actual name of the fermented rice product should be included in the manuscript. 4. Literature analysis or discussion Line 67: "pathways" - It is not clear what you mean by "pathways" Lines 70-71: This sentence is not clear Lines 71-76: It is not clear why you are describing in terms of "Indian" and "European" Line 72: If you are going to make comparisons, then the comparative data should be presented in Table, e.g. as part of Table 1 perhaps Line 73: "one Indian strain" - Which one? Are there more? Line 73: "a single plasmid DNA" - Details of the plasmid should be presented in Table 1 Line 74: "The most unique feature....." - Why is this considered unique and what is the potential significance? Line 75:"....that are identical to vertebrate ferritin complexes." - Provide a citation Lines 77-78: "...emerges as a compelling contender for a functional food with possible probiotic features." - This assertion is based on which information specifically? 5. Any other relevant comments The manuscript needs to follow Vancouver style appropriately. In-text citations should be presented as numbers, and the references should be numbered/listed in the order that they appear in the text. Line 28: Should be "16S rRNA" Line 28: Write WGS in full Lines 34-35: Italicise "Lactobacillus" "Bacillus" "Bifidobacterium" Lines 34-36: The sentence is not clear. Furthermore, what is the purpose of highlighting yeast cultures? Line 44: "Various fermented food samples have been obtained from numerous places in Himachal Pradesh, India." - It is not clear whether this is a general statement or a statement about the reported study. Consider rewording. Line 107: The article title is incomplete Lines 145 and 157: This should be "general characteristics", not general characters
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Poor
To what extent are the conclusions supported by the data?
Not at all
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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