Journal ArticleDOI
Microbiota restoration: natural and supplemented recovery of human microbial communities
Gregor Reid,Jessica A. Younes,Henny C. van der Mei,Gregory B. Gloor,Rob Knight,Henk J. Busscher +5 more
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TLDR
The mechanisms underlying microbiota restoration following insult (antibiotic or otherwise) to the skin, oral cavity, and gastrointestinal and urogenital tracts are explored, highlighting recovery by natural processes and after probiotic administration.Abstract:
In a healthy host, a balance exists between members of the microbiota, such that potential pathogenic and non-pathogenic organisms can be found in apparent harmony. During infection, this balance can become disturbed, leading to often dramatic changes in the composition of the microbiota. For most bacterial infections, nonspecific antibiotics are used, killing the non-pathogenic members of the microbiota as well as the pathogens and leading to a substantial delay in the restoration of a healthy microbiota. However, in some cases, infections can self-resolve without the intervention of antibiotics. In this Review, we explore the mechanisms underlying microbiota restoration following insult (antibiotic or otherwise) to the skin, oral cavity, and gastrointestinal and urogenital tracts, highlighting recovery by natural processes and after probiotic administration.read more
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Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic
Colin Hill,Francisco Guarner,Gregor Reid,Glenn R. Gibson,Daniel Merenstein,Bruno Pot,Lorenzo Morelli,Roberto Berni Canani,Harry J. Flint,Seppo Salminen,Philip C. Calder,Mary Ellen Sanders +11 more
TL;DR: An expert panel was convened in October 2013 by the International Scientific Association for Probiotics and Prebiotics (ISAPP) to discuss the field of probiotics and the appropriate use and scope of the term probiotic.
Journal ArticleDOI
Microbial Co-occurrence Relationships in the Human Microbiome
Karoline Faust,J. Fah Sathirapongsasuti,Jacques Izard,Jacques Izard,Nicola Segata,Dirk Gevers,Jeroen Raes,Curtis Huttenhower,Curtis Huttenhower +8 more
TL;DR: This article applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome.
Microbial Co-occurrence Relationships in the Human Microbiome
Karoline Faust,J. Fah Sathirapongsasuti,Jacques Izard,Jacques Izard,Nicola Segata,Dirk Gevers,Jeroen Raes,Curtis Huttenhower,Curtis Huttenhower +8 more
TL;DR: An ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort resulted in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome.
Journal ArticleDOI
Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection.
TL;DR: Effectiveness varied by route of instillation, relationship to stool donor, volume of IMT given, and treatment before infusion, but findings can guide physicians interested in implementing the procedure until better designed studies are conducted to confirm best practices.
Journal ArticleDOI
Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis
Andrew D. Fernandes,Jennifer Reid,Jean M. Macklaim,Thomas A McMurrough,David R. Edgell,Gregory B. Gloor +5 more
TL;DR: Statistical analysis of high-throughput sequencing datasets composed of per feature counts showed that the ALDEx2 R package is a simple and robust tool, which can be applied to RNA-seq, 16S rRNA gene sequencing and differential growth datasets, and by extension to other techniques that use a similar approach.
References
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A core gut microbiome in obese and lean twins
Peter J. Turnbaugh,Micah Hamady,Tanya Yatsunenko,Brandi L. Cantarel,Alexis E. Duncan,Ruth E. Ley,Mitchell L. Sogin,William J. Jones,Bruce A. Roe,Jason P. Affourtit,Michael Egholm,Bernard Henrissat,Andrew C. Heath,Rob Knight,Jeffrey I. Gordon +14 more
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