The Academic Hermit

  • Pre-print Review of 'Microbial Engraftment and Efficacy of FMT for C. difficile Patients With and Without IBD' My research group reviewed the preprint by Hirten and colleagues as part of our journal club and prepared this collaborative review. None of us have been asked to provide a review of the manuscript for a journal and we do not know its status 1. This preprint aims to describe...
  • Pre-print Review of 'Gut microbiota density influences host physiology and is shaped by host and microbial factors' The manuscript by Contijoch and colleagues presents a very intriguing collection of experiments that evaluate the variation in DNA density within the fecal material of sixteen mammalian species1. I am excited about this work because it highlights that microbial density may be a confounding variable in microbiome studies. Although it...
  • Your Personal Effort Report I’ve been on twitter now for a few years and have yet to step into the monthly “number of hours in the academic work week” flame wars 1. Instead of directly touching the academic Twitter third rail, I'd like to pivot the discussion. Let's say an academic works N hours....
  • Pre-print Review of 'Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome' Goltsman and colleagues present an ambitious longitudinal analysis of 10 pregnant women at three body sites - vagina, stool, mouth - at 10 time points collected every three weeks over their pregnancy 1. It should also be noted that I do not know the current status of this manuscript and...
  • Pre-print Review of NanoAmpli-Seq I was excited to see the preprint from Calus and colleagues describing NanoAmpli-Seq 1. This is a method of sequencing long amplicons using the Oxford Nanopore sequencing platform. For my set of applications within microbial ecology, this exciting sequencing platform still appears to be a method in search of an...
  • Pre-print Review of TaxAss Manuscript The preprint by Robin Rowher and colleagues seeks to develop a workflow that complements methods for classifying 16S rRNA gene sequences with greater precision than is found in the Wang naive Bayesian classifier 1. This is an issue that many people have raised with me. A lack of classification for...
  • Thinking About a Reproducible Research Topic Over the past 4 years, my lab has made a concerted effort to make all of the code that is associated with a paper publicly available in our lab’s GitHub project directory. This started because I was paranoid that people wouldn’t believe our analysis. I rationalized that you may not...
  • Pre-print Review of 97% Identity Threshold Manuscript The preprint by Robert Edgar sets out to take on the issue of what similarity threshold should be used to delineate bacterial species using partial and full-length 16S rRNA gene sequences 1. This is well covered territory and I’m not sure that many people would defend to the death the...
  • I Love Being a Professor About 10% of the proposals I’ve written have been accepted for funding. I’ve had one of about 80 papers accepted without further review. I’ve had papers rejected from third tier journals that regularly publish crap. I spend half my work hours either answering emails or in meetings. I’ve been negotiating...
  • Pre-print review of Cohesion manuscript The preprint from Herren and McMahon describes a new metric - cohesion - to describe the overall connectedness within a community using temporal data. I was excited to see this preprint because I am familiar with McMahon’s long history of developing rich time series data for microbial communities in Wisconsin...
  • The mSphereDirect Experiment Back in December mSphere, an open-access journal published by the American Society for Microbiology (ASM), announced that they would be trying a bold experiment: They would be allowing authors to essentially serve as editor of their own manuscripts. This experiment has been called mSphereDirect. A lot of emphasis has been...
  • Pre-print review of SmartGut manuscript At the end of October, uBiome put out a press release describing their product, SmartGut. The press release sounds a bit too good to be true. For example, “SmartGut empowers patients to take steps to understand their gut health and assess actionable information about their gut microbiome with their doctors”....
  • Labbies having babies The Schloss lab is growing! Ok, not really. For the first time in the history of my lab it isn’t me that’s having more kids, it’s members of my lab that are having their first kids. Of course, I’m very happy for them. I have been doing my best to...
  • What are you going to do with your tool? This is the talk I gave at my installation as the Frederick G. Novy Collegiate Professor of Microbiome Research at the University of Michigan. I was warmly introduced by Harry Mobley and Vince Young. A PDF version of the slides and text are available here and I will post the...
  • Deliberate practice as an academic Everyone has heard the phrase “practice makes perfect”. As a kid, my dad had his own spin on that line: “If you’re going to practice garbage, you’re going to play like garbage”. I lettered all four years in high school playing golf, but never seemed to get much better over...
  • The Unconference Last week the University of Michigan hosted a Michigan Meeting on Microbial Communities, “Unseen Partners: Manipulating Microbial Communities that Support Life on Earth”. The meeting was widely regarded as successful with an engaging debate by Norm Pace and Ford Doolittle, numerous talks, and discussion panels. At the bottom of the...
  • Ten Years On This week marks the 10 year anniversary of starting my independent academic career. Aside from meeting a few people during my interview, I knew no one in Amherst and our closest family was 400 miles away 1. We were fortunate to have had my mother-in-law help us drive and unpack....
  • Suck until you don't I am often asked how to get better at something. It is a great honor for someone else to recognize a set of skills that I work hard to hone, but I honestly want to answer “the hell if I know.” Last week I talked with someone that was interested...
  • What is your microbiome hypothesis worth? Last week I attended a symposium geared towards a general science audience where the topic of the day was the role of the microbiome in human health. I would exaggerate only slightly if I said that all of the presenters motivated their own interest in the microbiome by citing the...
  • Why did I publish in mSphere? On the morning of September 14th, I logged into mSphere’s manuscript submission page and uploaded a very cool paper describing our efforts to model the number of colonic tumors in a mouse model of colorectal cancer based on the composition of the animals’ microbiota 70 days earlier. I’m very proud...
  • Initial reactions to the UMU & IMI I must admit that I always feel a certain euphoria when I find people talking about microbiome research in the popular press or policy pieces. I’m a microbiome homer. So you can imagine my feelings yesterday when Science published an article by US scientists calling for a “interdisciplinary Unified Microbiome...
  • My response to the OSTP's RFI on the microbiome The Office of Science and Technology Policy (OSTP) recently released a request for information (RFI) to “to solicit feedback from industry, academia, research laboratories, and other stakeholder groups on both the overarching questions that unite all microbiome research and the tools, technologies, and training that are needed to answer these...
  • We don't read about dinosaurs To be perfectly frank, I think bioinformatics and the problems most of us are interested in are pretty abstract. Worse, they’re pretty boring. Try going to a party and talk about the latest greatest way of assembling a genome. Try going to your kids school and tell them about why...
  • MicroSeminar: A new way of doing conferences Why didn’t I think of that?! In the last few years I’ve pretty much lost all my drive to go to conferences to give talks. So when I saw a Twitter post from Jennifer Biddle (UDel) this summer announcing the creation of the MicroSeminar, I got excited. After seeing the...

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