Stool microbiome, pH and short/branched chain fatty acids in infants receiving extensively hydrolyzed formula, amino acid formula, or human milk through two months of age

Authors

• Car Reen Kok, University of Nebraska-LincolnFollow
• Bradford Brabec, Midwest Children’s Health Research Institute
• Maciej Chichlowski, Global Nutrition Science, Mead Johnson Nutrition, Evansville, IN
• Cheryl L. Harris, Clinical Research, Department of Medical Affairs, Mead Johnson Nutrition, Evansville, IN
• Nancy Moore, Department of Medical Affairs, Mead Johnson Nutrition, Evansville, IN
• Jennifer L. Wampler, Department of Medical Affairs, Mead Johnson Nutrition, Evansville, IN
• Jon Vanderhoof, Boston Children’s Hospital, Gastroenterology
• Devin Rose, University of Nebraska-LincolnFollow
• Robert Hutkins, University of Nebraska-LincolnFollow

Date of this Version

2020

Document Type

Article

Citation

Kok et al. BMC Microbiology (2020) 20:337 https://doi.org/10.1186/s12866-020-01991-5

Comments

CC-BY-NC

Abstract

CRISPR–Cas is an anti-viral mechanism of prokaryotes that has been widely adopted for genome editing. To make CRISPR–Cas genome editing more controllable and safer to use, anti-CRISPR proteins have been recently exploited to prevent excessive/prolonged Cas nuclease cleavage. Anti-CRISPR (Acr) proteins are encoded by (pro)phages/(pro)viruses, and have the ability to inhibit their host’s CRISPR–Cas systems. We have built an online database AcrDB (http://bcb.unl.edu/AcrDB) by scanning ∼19 000 genomes of prokaryotes and viruses with AcrFinder, a recently developed AcrAca (Acr-associated regulator) operon prediction program. Proteins in Acr-Aca operons were further processed by two machine learning-based programs (AcRanker and PaCRISPR) to obtain numerical scores/ranks. Compared to other anti-CRISPR databases, AcrDB has the following unique features: (i) It is a genome-scale database with the largest collection of data (39 799 Acr-Aca operons containing Aca or Acr homologs); (ii) It offers a user-friendly web interface with various functions for browsing, graphically viewing, searching, and batch downloading Acr-Aca operons; (iii) It focuses on the genomic context of Acr and Aca candidates instead of individual Acr protein family and (iv) It collects data with three independent programs each having a unique data mining algorithm for cross validation. AcrDB will be a valuable resource to the anti-CRISPR research community.