preprint reviews by Patrick Schloss

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

Sourced from https://www.biorxiv.org/content/early/2018/02/18/266700.

Daniela S. A. Goltsman, Christine L. Sun, Diana M. Proctor, Daniel B. DiGiulio, Anna Robaczewska, Brian C. Thomas, Gary M. Shaw, David K. Stevenson, Susan P. Holmes, Jillian F Banfield, David A. Relman

Review posted on 20th February 2018

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 pregnan...

See full review here.


NanoAmpli-Seq: A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform

Sourced from https://www.biorxiv.org/content/early/2018/01/07/244517.

Szymon T Calus, Umer Zeeshan Ijaz, Ameet J Pinto

Review posted on 14th February 2018

I was excited to see the preprint from Calus and colleagues describing NanoAmpli-Seq. This is a method of sequencing long amplicons using the Oxford Nanopore sequencing platform. For my set of appl...

See full review here.


TaxAss: Leveraging Custom Databases Achieves Fine-Scale Taxonomic Resolution

Sourced from https://www.biorxiv.org/content/early/2017/11/05/214288.

Robin Rebecca Rohwer, Joshua J Hamilton, Ryan J Newton, Katherine D McMahon

Review posted on 09th November 2017

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 Bayes...

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Updating the 97% identity threshold for 16S‌ ribosomal RNA OTUs

Sourced from https://www.biorxiv.org/content/early/2017/09/21/192211.

Robert C Edgar

Review posted on 11th October 2017

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. This is ...

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Meta Analysis Of Microbiome Studies Identifies Shared And Disease-Specific Patterns

Sourced from http://biorxiv.org/content/early/2017/05/08/134031.

Claire Duvallet, Sean M. Gibbons, Thomas Gurry, Rafael A. Irizarry, Eric J. Alm

Review posted on 09th June 2017

My research group reviewed the preprint version of this manuscript on May 18, 2017 and we prepared this joint review.

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See full review here.


Cohesion: A method for quantifying the connectivity of microbial communities

Sourced from http://biorxiv.org/content/early/2017/02/28/112391.

Cristina Herren, Katherine McMahon

Review posted on 07th March 2017

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 a...

See full review here.


16S rRNA Gene Sequencing as a Clinical Diagnostic Aid for Gastrointestinal-related Conditions

Sourced from http://biorxiv.org/content/early/2016/10/31/084657.

Daniel E Almonacid, Laurens Kraal, Francisco J Ossandon, Yelena V Budovskaya, Juan Pablo Cardenas, Jessica Richman, Zachary S Apte

Review posted on 06th December 2016

To be clear, I was not asked to review this manuscript by a journal and have no connection to uBiome. This review has been cross posted at here.