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Welcome to the Neufeld lab, where we explore and exploit microbial communities. We try to understand microbial community diversity and function and do this by developing and applying methods that help us circumvent a longstanding challenge of microbial ecology: how do you study something you can barely see, or experiment with organisms that don’t like to grow in the lab. This site highlights people and publications that demonstrate progress we’ve made toward exploring the “unseen majority”, microorganisms that inhabit our bodies and our environment.

  1. Sep. 5, 2016Mushmallows

    Mushmallows

    Josh Neufeld (Twitter: @joshdneufeld)

    Mushmallows are healthy vegetarian campfire alternatives to marshmallows and s’mores. They taste great, are very easy to make, use few ingredients, yet you can create a variety of combinations to suit your taste. Consider making this mycology-inspired culinary creation your go-to campfire staple.

    Ingredients
    White button mushrooms, any size (cremini will also work)


    Flavoured cream cheese (garlic and herb is delicious, many other flavours to choose from)

    Directions
    1. Remove stem from mushroom by rocking back and forth until it detaches. The stem contains moisture that is best removed and the hole will later be used for the filling.


    2. Place mushroom on end of a metal marshmallow-roasting stick. A double-pronged stick is best for stability.


    3. Roast both sides for ~2.5 minutes a side. Timing is flexible, as is heat. The goal is to gently crinkle the outside and dry the mushroom a little in the process. One benefit is that a mushmallow does not burst into flames like a marshmallow does. It takes effort to overly char the outside.


    4. When nicely "toasted" (browned both sides), carefully remove from  the metal prongs. A mushmallow does not retain heat well so this is not usually a difficult step. However, be careful of any liquid that might drip from holes - liquid drips will be hot.


    5. Fill the mushmallow hole with flavoured cream cheese. "Garlic and herb" flavour is great. Jalapeno is also delicious (and spicy!). Be adventurous.


    6. Enjoy.


    Optional: placing cream-cheese filled mushmallow onto a thin circular rice cracker or round melba toast simulates a s'more. This is a crunchy and delicious alternative to a standard mushmallow (s'mushmallow?).

  2. Nov. 18, 2015Here and elsewhere: an open resource for authors and peer reviewers of microbiologyClimbing wall

    When 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.

  3. Nov. 12, 2015Albus Dumbledore and the importance of anonymous peer reviewAlbus Dumbledore

    Peer review is the cornerstone of academic publishing. The process provides a relatively unbiased assessment of scientific research to verify that manuscript claims about experimental discoveries are supported by robust data and statistical analyses. Without peer review, scientific literature would become misleading, error prone, and untrustworthy. Peer review involves a journal editor selecting one or more peer reviewers who evaluate a manuscript critically, which results in a decision to reject or accept, or postpone a decision while authors make revisions.

    Recently, a manuscript I submitted to a journal came back with two reviews. Reading through these positive and brief reports, I was considering each comment and planning changes I would make in response. And there, at the very end of the second review, was the name of Reviewer 2: Albus Dumbledore. Well, it wasn’t actually Professor Dumbledore, but my point will be that the name isn’t important nor should it have been included.

    Although I argue in favour of either single-blind (reviewer names removed) or double blind (both reviewer and author names removed) anonymous peer review, it is worth considering why a reviewer might choose to sign a review. Some argue that open peer review promotes integrity and transparency in the dissemination of scientific discoveries. By signing a review and relinquishing anonymity, a reviewer makes a strong statement about being accountable, being confident about the quality of the review, promoting openness, and being constructive in the review process. Some might sign reviews because they might otherwise be more negative and critical behind the protective wall of anonymity. Although Mick Watson published a blog post here that discusses the benefits of signing reviews, and drawbacks of anonymous peer review, I find that most of my rationale in support of anonymous peer review is distinct from his discussion.

    Here are several reasons why I advocate for anonymous peer review.

    1. Anonymous peer review works. Having read hundreds of reviews of my own research papers, and being involved in the review process of many other articles, I have only flagged a handful of poor reviews, where the reviewer was obviously out to lunch or had an axe to grind. The remainder were well-considered and fair criticisms of the work. As a reviewer, my reviews usually agree with the other reviewers. Rejections, even for many of my own papers, have almost always been well founded, despite the upset and frustration that accompany such negative outcomes. I do not see how the vast majority of my reviews, or the countless others I’ve seen, would have been improved substantially by signatures at the bottom.

    2. Accountability is inherent in the system. Editors are leaders in the field who monitor the review process and those who review for them. Strong reviewers garner favour and are eventually asked to become editorial board members or editors themselves. Weak reviewers do not get called on again and, I suspect, risk their professional reputation. A signature is not needed, nor should be needed, to ensure that a scientist performs a review task professionally and in an unbiased manner. If, on the other hand, a scientist would be overly critical or biased in the absence of a signature, this is an ethical concern; I would not want that scientist reviewing my work regardless.

    3. The editor as "good cop". Many papers should be rejected. It is not uncommon to see authors demonstrate poor judgment, submit experimental work that was poorly designed or conducted, misjudge the “impact" of their work, neglect to edit their manuscript sufficiently prior to submission, or prepare figures and tables of unacceptable quality. For many reasons, authors often disagree with the critical comments of reviewers, even when the criticisms are well founded. Being critical of the science, reviewers serve as “bad cops”. In contrast, editors are the good cops, the messengers, the bearers of bad news. Editors may take a lot of flack for rejecting papers, but they can stand behind the reviews to justify their decision. Because reviewers are asked to be bad cops in this process, I do not think that they should also be in the firing line of those who stand subjectively behind their questionable manuscripts and data. Worse still, many journals make decisions to reject based on perceived impact. In those cases, the authors are justifiably upset and I would not want them angry with reviewers for not "raving" about their paper sufficiently to the editor of a high impact factor journal. Given the enormous professional stakes involved with publishing (e.g., job security, promotion, salary, reputation among peers, awards, student success), signing reviews adds an unnecessary element of risk of "bad blood" between reviewers and authors.

    4. Let my review be unbiased. Environmental Microbiology had an unfortunate tradition of publishing some of the silly things reviewers said in their evaluations. I was critical of this practice and asked the editors that I never be cited like this because it would make me self conscious about my reviews. For example, I might think that if I just tweak this sentence to be a little more funny, or damning, or tongue in cheek, maybe I'd be quoted in the referees’ quotes section next year. Likewise, if my peer review was signed, I might worry just a little more about the wording of my review, what the authors might think, what I will say to them later, whether they might hold a grudge. If reviewing the paper of a senior scientist in my field, one who might evaluate my next paper, grant proposal, or application for promotion, I might be tempted to sugar coat my concerns a little, even when I know that firmness and objective criticism is essential. Because I'm a "nice guy”, it is particularly important to depersonalize the process of evaluating science. In other words, I would worry too much about not being perceived as a jerk, which could detract from my duty to express very serious concerns about the quality of data I see in many manuscripts that cross my desk. In contrast, if I review a manuscript briefly and favourably, a signature could be perceived as a conflict of interest (see point 5).

    5. No reviewer kickbacks. In my case, Albus Dumbledore offered a favourable and brief review of my manuscript. Professor Dumbledore is now in my good books and I will certainly suggest this reviewer again. Perhaps I will send a thank you card, bottle of butterbeer, or an invitation to speak at an upcoming conference. Perhaps I will be generous when reviewing the next paper or grant proposal from this colleague. Conversely, any overly critical reviewers will be on my blacklist. I will avoid recommending them as reviewers in the future or, worse yet, I might ask an editor that they not review my next submission. Would I do all of this? No. Could I? Yes, very easily. Preventing kickbacks may be the single most important reason why anonymous peer review is essential.

    6. I don’t need it. That Professor Dumbledore reviewed my paper has little value to me as an author. Without the reviewer name, I am still fully able to work with an editor to incorporate recommended changes and respond to criticism. In my recent example, anonymous Reviewer #1 provided a highly similar review to Albus Dumbledore and both reviewers identified two of the same primary weaknesses that needed addressing in our manuscript.

    7. There are better ways to improve science publishing. Although there are many things that can be done to improve the scientific publishing process, signing reviews is not a step in the right direction. A poor review that is signed is still a poor review. A common goal here is to improve the quality of the review process and there are steps that scientific mentors and journals can take to improve the system. Supervisors should partner with senior graduate students and postdocs on joint peer reviews, complementing other forms of early career training. I would also like to see increased efforts by journals and academic societies to educate scientists to be effective reviewers. For example, professional workshops organized by academic societies could focus on peer review skills, much as online reviewer training courses could help provide the basics. Editors should work with reviewers to ensure that poor quality reviews do not end up on authors’ desks. Importantly, journals should do much more to provide reviewers and editorial board members with regular performance metrics, seeking ways to incentivize the review process for faster turnaround times and higher quality reviews. Rewarding strong reviewers for their contributions could help, perhaps through a point system that can be used toward offsetting open access publication charges. In other words, providing training and incentives for reviewers to increase their performance would help address the root of the peer review problem better than signing reviews.

    For the reasons outlined above, I will include a request in future cover letters that any reviewer names be removed prior to returning my manuscript for revision. In addition, I will no longer review for journals that publish reviewer names alongside each article and, as much as possible, avoid publishing in those same journals. My preference is for reviewers to remain anonymous, for journals and editors to promote and uphold the integrity of anonymous peer review, and for scientists to take the role of reviewer seriously, whether we sign our reviews or not, continually seeking to improve our performance for the betterment of science.

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