Journal ArticleDOI
UPARSE: highly accurate OTU sequences from microbial amplicon reads
TLDR
The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% correct bases commonly reported by other methods.Abstract:
Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.read more
Citations
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Journal ArticleDOI
Altered Gut Microbiota in a Mouse Model of Alzheimer’s Disease
Ling Zhang,Ying Wang,Xia Xiayu,Changhua Shi,Wei Chen,Nan Song,Xinjing Fu,Rui Zhou,Yanfeng Xu,Lan Huang,Hua Zhu,Yunlin Han,Chuan Qin +12 more
TL;DR: It is shown that AD pathology might not only affect brain function directly, but also exacerbate cognitive deficits through reducing the level of SCFAs via alterations of gut microbiota induced by intestinal amyloid deposition, suggesting a novel route for therapeutic intervention in AD.
Journal ArticleDOI
The biogeography of the atlantic salmon (Salmo salar) gut microbiome
Martin S. Llewellyn,Philip McGinnity,Melanie Dionne,Justine Letourneau,Florian Thonier,Gary R. Carvalho,Simon Creer,Nicolas Derome +7 more
TL;DR: Patterns of Mycoplasmataceae phylotype recruitment to the intestinal microbial community among sites and life-cycle stages support a dual role for deterministic and stochastic processes in defining the composition of the S. salar gut microbiome.
Journal ArticleDOI
Altered Mucosal Microbiome Diversity and Disease Severity in Sjögren Syndrome
Cintia S. de Paiva,Daniel B. Jones,Michael Stern,Fang Bian,Quianta Moore,Shani Corbiere,Charles F. Streckfus,Diane S. Hutchinson,Nadim J. Ajami,Joseph F. Petrosino,Stephen C. Pflugfelder +10 more
TL;DR: It is suggested that SS is marked by a dysbiotic intestinal microbiome driven by low relative abundance of commensal bacteria and high Relative abundance of potentially pathogenic genera that is associated with worse ocular mucosal disease in a mouse model of SS and in SS patients.
Journal ArticleDOI
Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum
Mie Crusell,Tue H. Hansen,Trine Nielsen,Kristine H. Allin,Kristine H. Allin,Malte C. Rühlemann,Peter Damm,Henrik Vestergaard,Henrik Vestergaard,Christina Rørbye,Niklas Rye Jørgensen,Ole Bjarne Christiansen,Ole Bjarne Christiansen,Femke-Anouska Heinsen,Andre Franke,Torben Hansen,Jeannet Lauenborg,Oluf Pedersen +17 more
TL;DR: The gut microbiota composition of women with GDM, both during and after pregnancy, resembles the aberrant microbiota composition reported in non-pregnant individuals with type 2 diabetes and associated intermediary metabolic traits.
Journal ArticleDOI
Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production
Edward C. Deehan,Chen Yang,Maria Elisa Perez-Muñoz,Nguyen K. Nguyen,Christopher C. Cheng,Lucila Triador,Zhengxiao Zhang,Jeffrey A. Bakal,Jens Walter,Jens Walter +9 more
TL;DR: It is found that crystalline and phosphate cross-linked starch structures induce divergent and highly specific effects on microbiome composition that are linked to directed shifts in the output of either propionate or butyrate.
References
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