Studying the microbiome and its complexities : an interview with Alan Walker

Acknowledgements AWW would like to thank his collaborating co-authors on the 2014 contamination paper for all of their excellent work. Funding AWW is supported by core funding from the Scottish Government Rural & Environment Science & Analytical Services (RESAS).Peer reviewedPublisher PD

A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses

A.W.W. receives core research funding from the Scottish Government’s Rural and Environment Science and Analytical Services (RESAS) division. I thank Paul Scott, Wellcome Sanger Institute, for his title suggestions for this commentary.Peer reviewedPublisher PD

Dietary Uncoupling of Gut Microbiota and Energy Harvesting from Obesity and Glucose Tolerance in Mice

The authors gratefully acknowledge Doctoral Training Partnership funding from the BBSRC (M.J.D.) and funding from the Scottish Government (P.J.M., A.W.R., and A.W.W.). We also thank the Centre for Genome-Enabled Biology and Medicine for help with next-generation sequencing and Karen Garden and the Rowett’s Analytical Services for SCFA analysis. SUPPLEMENTAL INFORMATION Supplemental Information includes four figures and two tables and can be found with this article online at https://doi.org/10.1016/j.celrep.2017.10.056.Peer reviewedPublisher PD

Special issue : The Human Intestinal Microbiota

Peer reviewedPublisher PD

Bayesian estimation of bacterial community composition from 454 sequencing data

Peer reviewe

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

Acknowledgements The authors acknowledge the assistance of Grietje Holtrop (RINH-BioSS) with the statistical analysis of the data and the Wellcome Trust Sanger Institute’s 454 pyrosequencing team for generating 16S rRNA gene data. AWW, PS and JP received core funding support from the Wellcome Trust [grant number 098051]. AWW, JCM, HJF and KPS are funded by the Scottish Government (SG-RESAS).Peer reviewedPublisher PD

TPL-2 restricts Ccl24-dependent immunity to Heligmosomoides polygyrus

Funding: This work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001220), the UK Medical Research Council (FC001220), and the Wellcome Trust (FC001200). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Acknowledgments We are indebted to The Francis Crick Institute Flow Cytometry facility, and in particular Bhavik Patel, Graham Preece, Wayne Turnbull and Phil Hobson. We would also like to thank The Francis Crick Institute Procedural Service Section for production of GA lines and Biological Services, especially Trisha Norton, Keith Williams and Adebambo Adekoya for animal husbandry and technical support; to Riccardo Guidi for constructive discussions and technical assistance. We would like to thank Gitta Stockinger and AhR Immunity Laboratory for providing technical support and reagents throughout this study. We also thank Richard Rance and the Wellcome Trust Sanger Institute’s 454 pyrosequencing team for generating 16S rRNA gene data.Peer reviewedPublisher PD

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment

Acknowledgements The authors wish to thank Mark Stares, Richard Rance, and other members of the Wellcome Trust Sanger Institute’s 454 sequencing team for generating the 16S rRNA gene data. Lili Fox Vélez provided editorial support. Funding IA, JNP, and MP were partly supported by the NIH, grants R01-AI-100947 to MP, and R21-GM-107683 to Matthias Chung, subcontract to MP. JNP was partly supported by an NSF graduate fellowship number DGE750616. IA, JNP, BRL, OCS and MP were supported in part by the Bill and Melinda Gates Foundation, award number 42917 to OCS. JP and AWW received core funding support from The Wellcome Trust (grant number 098051). AWW, and the Rowett Institute of Nutrition and Health, University of Aberdeen, receive core funding support from the Scottish Government Rural and Environmental Science and Analysis Service (RESAS).Peer reviewedPublisher PD

Nonlinear Asymptotic Integration Algorithms for One-dimensional Autonomous Dissipative First-order Odes

Nonlinear asymptotic integrators are applied to one-dimensional, nonlinear, autonomous, dissipative, ordinary differential equations. These integrators, including a one-step explicit, a one-step implicit, and a one- and two-step midpoint algorithm, are designed to follow the asymptotic behavior of a system approaching a steady state. The methods require that the differential equation be written in a particular asymptotic form. This is always possible for a one-dimensional equation with a globally asymptotic steady state. In this case, conditions are obtained to guarantee that the implicit algorithms are well defined. Further conditions are determined for the implicit methods to be contractive. These methods are all first order accurate, while under certain conditions the midpoint algorithms may also become second order accurate. The stability of each method is investigated and an estimate of the local error is provided