DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan,Paul J. McMurdie,Michael J. Rosen,Andrew W. Han,Amy Jo A. Johnson,Susan Holmes +5 more
TLDR
The open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors is presented, revealing a diversity of previously undetected Lactobacillus crispatus variants.Abstract:
We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.read more
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Gut microbiome transition across a lifestyle gradient in Himalaya.
Aashish R. Jha,Emily R. Davenport,Yoshina Gautam,Dinesh Bhandari,Sarmila Tandukar,Katharine M. Ng,Gabriela K. Fragiadakis,Susan Holmes,Guru Prasad Gautam,Jeff Leach,Sherchand Jb,Carlos Bustamante,Justin L. Sonnenburg +12 more
TL;DR: The gut microbiomes of Raute and Raji reveal an intermediate state between the Chepang and Tharu, indicating that divergence from a stereotypical foraging microbiome can occur within a single generation, and environmental factors such as drinking water source and solid cooking fuel are significantly associated with the gut microbiome.
Journal ArticleDOI
Ubiquity of polystyrene digestion and biodegradation within yellow mealworms, larvae of Tenebrio molitor Linnaeus (Coleoptera: Tenebrionidae).
Shan-Shan Yang,Wei-Min Wu,Anja Malawi Brandon,Hanqing Fan,Joseph P. Receveur,Yiran Li,Zhiyue Wang,Fan Rui,Rebecca L. McClellan,Shu-Hong Gao,Daliang Ning,Debra Phillips,Bo-Yu Peng,Hongtao Wang,Shen-Yang Cai,Ping Li,Weiwei Cai,Ling-Yun Ding,Jun Yang,Min Zheng,Jie Ren,Yalei Zhang,Jie Gao,Defeng Xing,Nanqi Ren,Robert M. Waymouth,Jizhong Zhou,Hu-Chun Tao,Christine J. Picard,Mark Eric Benbow,Craig S. Criddle +30 more
TL;DR: It is confirmed that yellow mealworms, the larvae of Tenebrio molitor Linnaeus, can survive by eating polystyrene (PS) foam and the hypothesis that this capacity is independent of the geographic origin of the mealworms is supported, and is likely ubiquitous to members of this species.
Journal ArticleDOI
The gut microbiota as a novel regulator of cardiovascular function and disease.
TL;DR: The aim of the current review is to summarize the available data regarding the role of the gut microbiome in regulating CVD function and disease processes, with particular emphasis placed on nutrition-related alterations in the microbiome.
Journal ArticleDOI
Microbiota from young mice counteracts selective age-associated behavioral deficits
Marcus Boehme,Katherine E. Guzzetta,Thomaz F.S. Bastiaanssen,Marcel van de Wouw,Gerard M. Moloney,Andreu Gual-Grau,Simon Spichak,Loreto Olavarría-Ramírez,Patrick Fitzgerald,Enrique Morillas,Nathaniel L. Ritz,Minal Jaggar,Caitlin S. M. Cowan,Fiona Crispie,Fiona Crispie,Francisco Donoso,Evelyn Halitzki,Marta C Neto,Marzia Sichetti,Anna V. Golubeva,Rachel S. Fitzgerald,Marcus J. Claesson,Paul D. Cotter,Paul D. Cotter,Olivia F. O’Leary,Timothy G. Dinan,John F. Cryan +26 more
TL;DR: It is shown that rejuvenation of the gut microbiome by fecal microbiota transplantation from young mice reverses aging-induced deficits in the hippocampal immune system, metabolome and transcriptome, and rescues selective cognitive deficits.
Journal ArticleDOI
Tiny microbes, enormous impacts: what matters in gut microbiome studies?
Justine W. Debelius,Se Jin Song,Se Jin Song,Yoshiki Vázquez-Baeza,Zhenjiang Zech Xu,Antonio Gonzalez,Rob Knight +6 more
TL;DR: The presentation of quantitative effect sizes in addition to P values will improve the ability to perform meta-analysis and to evaluate potentially relevant biological effects and lead to more robust biological conclusions in microbiome studies.
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TL;DR: The Human Microbiome Project Consortium reported the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome as discussed by the authors.
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