Restoration of cefixime-induced gut microbiota changes by Lactobacillus cocktails and fructooligosaccharides in a mouse model.
Ying Shi,Qixiao Zhai,Dongyao Li,Mao Bingyong,Xiaoming Liu,Jianxin Zhao,Hao Zhang,Wei Chen,Wei Chen +8 more
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TLDR
The results show that the use of cefixime caused a reduction in the diversities of the microbial community and led to significantly decreasing to one preponderant Firmicutes phylum, which was difficult to restore naturally in the short term.About:
This article is published in Microbiological Research.The article was published on 2017-07-01 and is currently open access. It has received 49 citations till now. The article focuses on the topics: Lactobacillus & Gut flora.read more
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Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix
TL;DR: FastTree as mentioned in this paper uses sequence profiles of internal nodes in the tree to implement neighbor-joining and uses heuristics to quickly identify candidate joins, then uses nearest-neighbor interchanges to reduce the length of the tree.
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Lactobacillus plantarum with Functional Properties: An Approach to Increase Safety and Shelf-Life of Fermented Foods.
TL;DR: This review emphasizes that the Lb.
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A Review on Gut Remediation of Selected Environmental Contaminants: Possible Roles of Probiotics and Gut Microbiota
TL;DR: The current understanding of the remediation mechanisms of some probiotic bacteria and the combined effects of probiotics and gut microbiota on remediation of foodborne contaminants in vivo is summarized.
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Molecular mechanisms of probiotic prevention of antibiotic-associated diarrhea.
TL;DR: What is currently known about how probiotics reduce the risk for antibiotic-associated diarrhea via modulating the gut microbiota, altering nutrient and bile acid metabolism, inducing epithelial solute transporter activity, supporting intestinal barrier function, and influencing the immune system is examined.
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Structural and Functional Alterations in the Microbial Community and Immunological Consequences in a Mouse Model of Antibiotic-Induced Dysbiosis
Ying Shi,Lee Kellingray,Qixiao Zhai,Gwénaëlle Le Gall,Arjan Narbad,Jianxin Zhao,Hao Zhang,Wei Chen,Wei Chen +8 more
TL;DR: The bacterial ecology of antibiotic exposure model in combination with host physiological characteristics at a detailed level of microbial taxa is described, and key taxa were identified as CTDA-specific.
References
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QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
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Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
TL;DR: The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
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UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Catherine A. Lozupone,Rob Knight +1 more
TL;DR: The results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.
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Enterotypes of the human gut microbiome
Manimozhiyan Arumugam,Jeroen Raes,Eric Pelletier,Denis Le Paslier,Takuji Yamada,Daniel R. Mende,Gabriel Fernandes,Julien Tap,Thomas Brüls,Jean-Michel Batto,Marcelo Bertalan,Natalia Borruel,Francesc Casellas,Leyden Fernández,Laurent Gautier,Torben Hansen,Masahira Hattori,Tetsuya Hayashi,Michiel Kleerebezem,Ken Kurokawa,Marion Leclerc,Florence Levenez,Chaysavanh Manichanh,H. Bjørn Nielsen,Trine Nielsen,Nicolas Pons,Julie Poulain,Junjie Qin,Thomas Sicheritz-Pontén,Sebastian Tims,David Torrents,Edgardo Ugarte,Erwin G. Zoetendal,Jun Wang,Francisco Guarner,Oluf Pedersen,Willem M. de Vos,Søren Brunak,Joël Doré,Jean Weissenbach,S. Dusko Ehrlich,Peer Bork +41 more
TL;DR: Three robust clusters (referred to as enterotypes hereafter) are identified that are not nation or continent specific and confirmed in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous.
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Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
Harry Sokol,Bénédicte Pigneur,Laurie Watterlot,Omar Lakhdari,Luis G. Bermúdez-Humarán,Jean-Jacques Gratadoux,Sébastien Blugeon,Chantal Bridonneau,Jean-Pierre Furet,Gérard Corthier,Corinne Grangette,Nadia Vasquez,Philippe Pochart,Germain Trugnan,Ginette Thomas,Hervé M. Blottière,Joël Doré,Philippe Marteau,Philippe Seksik,Philippe Langella +19 more
TL;DR: The results suggest that counterbalancing dysbiosis using F. prausnitzii as a probiotic is a promising strategy in CD treatment and exhibits anti-inflammatory effects on cellular and TNBS colitis models, partly due to secreted metabolites able to block NF-κB activation and IL-8 production.