Gut microbes and the brain: paradigm shift in neuroscience

EA Mayer, R Knight, SK Mazmanian…�- Journal of�…, 2014 - Soc Neuroscience
The discovery of the size and complexity of the human microbiome has resulted in an
ongoing reevaluation of many concepts of health and disease, including diseases affecting�…

[HTML][HTML] Analysis of microbial compositions: a review of normalization and differential abundance analysis

H Lin, SD Peddada�- NPJ biofilms and microbiomes, 2020 - nature.com
Increasingly, researchers are discovering associations between microbiome and a wide
range of human diseases such as obesity, inflammatory bowel diseases, HIV, and so on�…

The pancreatic cancer microbiome promotes oncogenesis by induction of innate and adaptive immune suppression

S Pushalkar, M Hundeyin, D Daley, CP Zambirinis…�- Cancer discovery, 2018 - AACR
We found that the cancerous pancreas harbors a markedly more abundant microbiome
compared with normal pancreas in both mice and humans, and select bacteria are�…

The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL

B Aykut, S Pushalkar, R Chen, Q Li, R Abengozar…�- Nature, 2019 - nature.com
Bacterial dysbiosis accompanies carcinogenesis in malignancies such as colon and liver
cancer, and has recently been implicated in the pathogenesis of pancreatic ductal�…

[HTML][HTML] Waste not, want not: why rarefying microbiome data is inadmissible

PJ McMurdie, S Holmes�- PLoS computational biology, 2014 - journals.plos.org
Current practice in the normalization of microbiome count data is inefficient in the statistical
sense. For apparently historical reasons, the common approach is either to use simple�…

Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice

K Berer, LA Gerdes, E Cekanaviciute…�- Proceedings of the�…, 2017 - National Acad Sciences
There is emerging evidence that the commensal microbiota has a role in the pathogenesis
of multiple sclerosis (MS), a putative autoimmune disease of the CNS. Here, we compared�…

A microbial signature for Crohn's disease

V Pascal, M Pozuelo, N Borruel, F Casellas, D Campos…�- Gut, 2017 - gut.bmj.com
Objective A decade of microbiome studies has linked IBD to an alteration in the gut microbial
community of genetically predisposed subjects. However, existing profiles of gut microbiome�…

Qiita: rapid, web-enabled microbiome meta-analysis

A Gonzalez, JA Navas-Molina, T Kosciolek…�- Nature�…, 2018 - nature.com
Multi-omic insights into microbiome function and composition typically advance one study at
a time. However, in order for relationships across studies to be fully understood, data must�…

[HTML][HTML] Characterization of the gut microbiome using 16S or shotgun metagenomics

J Jovel, J Patterson, W Wang, N Hotte…�- Frontiers in�…, 2016 - frontiersin.org
The advent of next generation sequencing (NGS) has enabled investigations of the gut
microbiome with unprecedented resolution and throughput. This has stimulated the�…

[HTML][HTML] Enhancing diversity analysis by repeatedly rarefying next generation sequencing data describing microbial communities

ES Cameron, PJ Schmidt, BJM Tremblay, MB Emelko…�- Scientific reports, 2021 - nature.com
Amplicon sequencing has revolutionized our ability to study DNA collected from
environmental samples by providing a rapid and sensitive technique for microbial�…