Here and elsewhere: an open resource for authors and peer reviewers of microbiology

Climbing wallWhen reviewing manuscripts prior to publication, many scientists become frustrated by identifying the same minor issues repeatedly. In my case, correcting common errors and inconsistencies became so repetitive that I gradually compiled recurring concerns into a single document, allowing rapid copy/paste/editing of these comments into reviews whenever needed. This reviewer “cheat sheet” has been a timesaver to me and there is a good chance that such a document might benefit other scientists as well.

In an effort to improve the quality of scientific writing, especially for our microbiology trainees, I am sharing my list of common minor corrections openly. I give full and unrestricted permission for any reviewer to pull from this list for future reviews. And, because this blog post accepts comments, please add your own "Here and elsewhere” scientific writing corrections for others to share as well.

Given that my first blog post advocated for anonymity in peer review, I recognize the potential irony/hypocrisy of publishing a list of common reviewer comments. That said, most of us use modified versions of these same statements, several were compiled from colleagues or reviews of my own papers, and all of these comments can be used anonymously and freely moving forward. In addition, my goal in publishing this list is to improve the quality of academic writing so that more time and attention can be devoted to evaluating the science itself, rather than reviewers being distracted or biased by the way a manuscript was (poorly) written.

Again, please feel welcome to add your own common corrections using the comment section below. I hope this list helps you as much as it has helped me:

Here and elsewhere, all recognized taxonomic levels should be italicized. Because phylum is not recognized by the Bacteriological Code, italics or not depends on preference.

Here and elsewhere, you do not need to capitalize or use italics for some taxonomic names when referring to the group of organisms themselves. For example, contrast “all detected bacteria and archaea were” with “all detected taxa affiliated with the <i>Bacteria</i> and <i>Archaea</i>"

Here and elsewhere, replace “next-generation sequencing” with "high-throughput sequencing”.

Here and elsewhere, please do not use “16s rDNA”, “rDNA”, "16S genes”, or “16S". The correct term is “16S rRNA genes” for DNA or "16S rRNA” for RNA.

Here and elsewhere, spell numbers less than 10 in full, unless in a series that includes at least one number >10.

Here and elsewhere, “while” and “since” imply time. Whenever time is not implied, replace with “whereas”, “although”, “even though”, or “because”, as appropriate.

Here and elsewhere, spp. refers to multiple species within a genus. Use sp. or spp. as appropriate throughout.

Here and elsewhere, do not use italics for sp. or spp.

Here and elsewhere, no dash after adverbs ending in -ly (e.g., "randomly collected soil samples").

Here and elsewhere, don’t use contractions in scientific writing.

Here and elsewhere, the R in R2 should be italicized and the p of p-value should be lowercase and in italics.

Here and elsewhere, please do not use “tag” or “pyrotag”. You sequenced 16S rRNA genes. We all sequence single-gene markers, and none of us sequence the full length genes in doing so; it goes without saying.

Here and elsewhere, please simply use “Shannon Index” (http://onlinelibrary.wiley.com/doi/10.1046/j.1466-822X.2003.00015.x/abstract).

Here and elsewhere, use “PCR amplification”, or some alternative, to avoid saying polymerase chain reaction reaction (“PCR reaction”). Redundant.

Here and elsewhere, what range of DNA quantities were added to the PCR (e.g., 1-10 ng of DNA template). The volume is irrelevant; the DNA quantity is important.

Here and elsewhere, be consistent with spacing between numbers and units.

Here and elsewhere, do not use "interesting" or "interestingly". Let the reader decide what is interesting.

Here and elsewhere, do a global find/replace of your document for double spaces “  “ and replace them with single spaces “ “.

Here and elsewhere, do not describe scientific results using the terms “dramatic” or “dramatically”.

Here and elsewhere, delete “etc.” from all scientific writing. “among others”, or “for example” can be used.

Here and elsewhere, use the Oxford comma, or not, but be consistent either way. Check journal format.

Here and elsewhere, “anaerobic” and “anoxic” used incorrectly. Anoxic is for the environment, anaerobic is for the metabolism. Same applies for “aerobic” and “oxic”.

Here and elsewhere, “population” refers to members of the same species. Use “community” when referring to assemblages of multiple species.

Here and elsewhere, (R), (C), and (Tm) symbols are not needed in scientific writing.

Here and elsewhere, don’t mention the data displays explicitly in the manuscript. Explain what your results showed, then cite data displays to support your claims (Fig. 1).

Here and elsewhere, please be consistent in following journal format convention for your references.

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Some suggestions for additional ones, Josh:

Here and elsewhere, "a number of samples" is ambiguous; consider specifying the actual number or using a less ambiguous phrase, such as "several samples".

Here and elsewhere, there is no need to use "In order to" when just "to" would do the same job!

Where possible, consider alternatives to long and convoluted sentences that require you to use the word "respectively". It makes for frustrating reading and compromises the accessibility of your manuscript to non-native-English-speakers.

Here and elsewhere, "M" (molar) and "mol" (moles) are used incorrectly. Do not use "M" as "X M of whichever-compound were added" because "M" refers to a molar concentration and not to an absolute value. Instead indicate one of: (1) the volume of an X M (X-molar) solution added; (2) the final molar concentration of the solution; or (3) the absolute number of moles added. 

Be consistent in descriptions of PCR mixtures. Just as with the DNA template, the volume of other components (MgCl2, primers and other components) is irrelevant. The molar quantity, or the final molar concentration, will be more important.

Make sure that you consider carefully, and understand the meaning of, words, such as "nonetheless", "conversely", "notwithstanding", "moreover", additionally, "subsequently", "consequently" and "concomitantly" before using them in your Discussion section. 

Here and elsewhere, "data" are plural.

Be consistent with the tense used in the Materials & Methods and Results sections of your manuscript. Usually, both sections should be written in the past tense, avoiding the active/personal (i.e. keeping it 'passive').

Here and elsewhere, use "double quotes", instead of 'single quotes', which are for quoting within quotes or article titles.

Here and elsewhere, include Genbank accession numbers.

Here and elsewhere, remove direct references to data presentations by searching for "shown in" and replacing with a comment about your results, or how they were generated.

Here and elsewhere, be consistent with significant digits. Also, perhaps only one decimal place is necessary?

Here and elsewhere, use italics for all taxa shown in the phylogenetic tree.

Here and elsewhere, remove shadow effect from under symbols.

Here and elsewhere, use Arial (or another sans serif font) for your figures. 
 
Here and elsewhere, right align table number columns and left alight text columns. Also, you only need horizontal lines above the title row, below the title row, and at the very bottom. 
 
Here and elsewhere, no title case in axis labels. 
 
Here and elsewhere, use "Proportion of x" followed by percent in brackets (the units) to avoid saying "Percent of x".
 
Here and elsewhere, color is not needed in this figure. And, if color kept, use colors that can be differentiated when printed in black and white.

Give the long form of acronyms at the first appearance in the main manuscript - the Abstract doesn't count. Don't abbreviate much, or use acronyms, in the Abstract unless these are repeatedly used in the Abstract.

Here and elsewhere, do not begin a sentence with a numeral or an acronym.

Modified from tweet by @angiegoesNL

Here and elsewhere, do not begin a sentence with an abbreviated species name. E. coli looks weird. Check journal format though.

Here and elsewhere, make sure that you consider carefully, and understand the meaning of, "principle" and "principal", particularly with respect to statistical analyses.

Here and elsewhere, do not confuse or conflate amplicon sequencing and metagenomics. They are not the same.  

This information is worth everyone's attention. How can I find out more?

My suggestions for more information would be Day and Gastel or Gustavii. Stephen Heard indicated that he has a book in the works that may be worth checking out.

I do indeed!  It's brand new (April 2016) and you can find out about it here: https://scientistseessquirrel.wordpress.com/the-scientists-guide-to-writing/  Thanks for mentioning it, Josh!

As far as I remember, only the genus and species should be in italics (as if they're foreign words). Other taxonomic levels go capitalized, but not in italics. Bacteria, Archaea, Firmicutes, Enterobacteriaceae, Escherichia coli, Bacillus subtilis...

This is a great idea - although I'd say the content of your list is a bit variable. Some points are clear factual issues (e.g., the meaning of 'spp.' vs. 'sp.'.  Others are matters of journal style (e.g. whether a P-value is upper or lower case, italic or not).  Still others are personal preferences (double spaces, which many find make reading easier).  Finally, a personal soapbox: why exactly is it that we "don’t use contractions in scientific writing"?  I've said the same thing many times but have realized I don't understand why.  I posted about this issue here: https://scientistseessquirrel.wordpress.com/2015/10/01/why-do-not-we-use-contractions-in-scientific-writing/

Thanks for adding the discussion, Steve. Important to point out that English is in flux and few rules set in stone. That said, my primary concerns are inconsistency and lack of attention to writing. Hopefully this post, your book, etc., can together help to correct these issues for the next generation.

Agreed, Josh!

As a non English speaking person (and for me always the question remains, what is "English" anyway? British Oxford? Jamaican? US? Aussie?), I think that the great majority of the above points, although they are correct, they should not be the responsibility of a reviewer.

Scientific reviewers are not there to do proof reading in English. For one we are not all native English speakers (although I have to admit that nationality does not necessary mean good writing skills).

We are already offering our services for free to journals. They should have someone else to do it (maybe it has to be someone trained as a scientist, look at all these ghost writers). I used to do such corrections but now I refuse to do them myself. If the journal is not interested to have well written articles, so be it (and one can find plenty of examples).

In the last journal I submitted as an author, they even wanted me to change the font size of the headings "among other" things, after the article had been found scientifically sound by the reviewers. And this even though in the end the journal would layout the article in their style (which is not the most difficult job either). In the end, they will ask us to send the paper as well to print the article. :-)

I will definitely use the list for my students to check before they pass me on their drafts.

You make a very good point, Sokratis. I agree that our job as reviewers should be 90%+ about the science itself. With respect to the quality of writing, my thinking is that sometimes English issues can be so distracting that some specific examples are helpful in directing authors to the major writing issues that they should be tackling during the revision stage. Just saying "The English is poor" is unhelpful for authors (and Editors) who wish for the paper to be as well received as possible when published eventually.

Overall though, I suspect that we are fully agreed that the most important goal of information like this is to help authors/students prepare initial submissions that are as well-written as possible, enabling an objective and unbiased review: "In an effort to improve the quality of scientific writing, especially for our microbiology trainees, I am sharing my list of common minor corrections openly."

Thanks for your feedback.