Some are more equal than others : the role of ‘keystone’ species in the degradation of recalcitrant substrates

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Process-based modelling of Microbial community dynamics in the human colon

Acknowledgments We thank the Scottish Goverment’s Rural and Environment Science and Analytical Services Division (RESAS) for funding this research. Funding Statement The Scottish Goverment’s Rural and Environment Science and Analytical Ser581 vices Division (RESAS) funded this researchPeer reviewedPostprin

Contribution of diet to the composition of the human gut microbiota

This paper is part of the Proceedings from the 2013 ENGIHR Conference in Valencia, Spain. More papers from this supplement can be found at http://www.microbecolhealthdis.net Microbial Ecology in Health & Disease 2015. © 2015 Daniela Graf et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial 3.0 Unported License (http://creativecommons.org/licenses/by-nc/3.0/), permitting all non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ACKNOWLEDGEMENTS The authors acknowledge the support of the European Science Foundation (ESF), in the framework of the Research Networking Programe, The European Network for Gastrointestinal Health Research.Peer reviewedPublisher PD

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

Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis

Copyright © 2015 Travis et al. ACKNOWLEDGMENTS We thank Gillian Campbell, Pauline Young, Karen Garden, and Sylvia Duncan for contributing to this work, which was supported by Scottish Government RESAS (Rural and Environmental Sciences and Analytical Services).Peer reviewedPublisher PD

microPop: modelling microbial populations and communities in R

We thank the Scottish Goverment’s Rural and Environment Science and Ana-lytical Services Division (RESAS) for funding this research. Also many thanks to Rafael Munoz-Tamayo for sharing his matlab code for the rumen modelPeer reviewedPostprin

Faecalibacterium prausnitzii Strain HTF-F and Its Extracellular Polymeric Matrix Attenuate Clinical Parameters in DSS-Induced Colitis

Date of Acceptance: 26/02/2015 Funding: The authors received no specific funding for this work.Peer reviewedPublisher PD

Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions

This work was supported in part by the European Union, Area NMP.2013.1.1–2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project number: 604530, and by the EU Seventh Framework Programme (FP7 2007–2013) under the WallTraC project (Grant Agreement no 263916), and BioStruct-X (grant agreement no 283570). This paper reflects the author’s views only. The European Community is not liable for any use that may be made of the information contained herein. CMGAF is also supported by Fundação para a Ciência e a Tecnologia (Lisbon, Portugal) through grants PTDC/BIA-PRO/103980/2008 and EXPL/BIA-MIC/1176/2012. EAB is also funded by a grant (No. 1349/13) from the Israel Science Foundation (ISF), Jerusalem, Israel and by a grant (No. 2013284) from the U.S.-Israel Binational Science Foundation (BSF). E.A.B. is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic Chemistry.Peer reviewedPublisher PD

Rumen cellulosomics : divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains

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β-Glucan is a major growth substrate for human gut bacteria related to Coprococcus eutactus

A clone encoding carboxymethyl cellulase activity was isolated during functional screening of a human gut metagenomic library using Lactococcus lactis MG1363 as heterologous host. The insert carried a glycoside hydrolase family 9 (GH9) catalytic domain with sequence similarity to a gene from Coprococcus eutactus ART55/1. Genome surveys indicated a limited distribution of GH9 domains among dominant human colonic anaerobes. Genomes of C. eutactus-related strains harboured two GH9-encoding and four GH5-encoding genes, but the strains did not appear to degrade cellulose. Instead, they grew well on β-glucans and one of the strains also grew on galactomannan, galactan, glucomannan and starch. Coprococcus comes and Coprococcus catus strains did not harbour GH9 genes and were not able to grow on β-glucans. Gene expression and proteomic analysis of C. eutactus ART55/1 grown on cellobiose, β-glucan and lichenan revealed similar changes in expression in comparison to glucose. On β-glucan and lichenan only, one of the four GH5 genes was strongly upregulated. Growth on glucomannan led to a transcriptional response of many genes, in particular a strong upregulation of glycoside hydrolases involved in mannan degradation. Thus, β-glucans are a major growth substrate for species related to C. eutactus, with glucomannan and galactans alternative substrates for some strains