In today’s digest read about the presence/absence of ACBP orthologues in human gut metagenomes and how the gut microbiome links nutrition with cardiometabolic health, LEGO-based microscope, SIAMCAT for statistical inference of associations between microbial communities and host phenotypes, bacteriophage plaques size tool, and more. Check out a list of awesome webinars and courses. Happy Friday!
OPEN #NSURP2021 CALL for mentors and mentees: The National Summer Undergraduate Research Project – A community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the microbial sciences.
Microbiome in the news
*Microbiome research in general and business newspapers: How many microbiome articles are published and which study designs make the news the most? – Andreu Prados-Bo and Gonzalo Casino – PlosOne
General
Prokaryotic taxonomy and nomenclature in the age of big sequence data – Philip Hugenholtz – The ISME Journal
The metabolic network of the last bacterial common ancestor – Joana C. Xavier – Communications Biology
Techniques
*Designing a high-resolution, LEGO-based microscope for an educational setting – Bart Eduard Vos – bioRxiv
Genome-Based Targeted Sequencing as a Reproducible Microbial Community Profiling Assay – Jacquelynn Benjamino – mSphere
Gut microbiome
*Microbial ACBP/DBI-like genes are rare in the human gut microbiome and show no links with obesity – Andrew Maltez Thomas – Applied and Environmental Microbiology
The long-term genetic stability and individual specificity of the human gut microbiome – Lianmin Chen – Cell
Review: Emulating the gut–liver axis: Dissecting the microbiome’s effect on drug metabolism using multiorgan-on-chip models – Mara Lucchetti – Current Opinion in Endocrine and Metabolic Research
Urinary microbiome
The human urobiome – Linda Brubaker – Mammalian Genome
Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods – Baylie R. Hochstedler – International Urogynecology Journal
Vaginal microbiome
Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil – Marcelle Oliveira de Almeida – PeerJ
Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment – Leonardo Mancabelli – Applied and Environmental Microbiology
Probiotics
Review: Lacticaseibacillus rhamnosus GR-1, a.k.a. Lactobacillus rhamnosus GR-1: Past and Future Perspectives – Mariya I.Petrova – Trends in Microbiology
Probiotic Lactobacillus sp. Strains Inhibit Growth, Adhesion, Biofilm Formation, and Gene Expression of Bacterial Vaginosis-Inducing Gardnerella vaginalis – Zhixiang Qian – Microorganisms
Oral microbiome
Dental biofilm microbiota dysbiosis is associated with the risk of acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation – Vitor Heidrich – medRxiv
Soil microbiome
Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps) – Carla Perez-Mon – Microbial Genomics
Phages and viruses
*Plaque Size Tool: an automated plaque analysis tool for simplifying and standardising bacteriophage plaque morphology measurements – Ellina Trofimova and Paul R Jaschke – bioRxiv
The gut virome of healthy children during the first year of life is diverse and dynamic – Blanca Taboada – PlosOne
Bioinformatics
Taxonomic analysis of metagenomic data with kASA – Silvio Weging – Nucleic Acids Research
*Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox – Jakob Wirbel – Genome Biology
Review: Integrating pan-genome with metagenome for microbial community profiling – Chaofang Zhong – Computational and Structural Biotechnology Journal
Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing – Caitlin M. Singleton – Nature Communications
Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles – Christopher Gaulke – bioRxiv
Democratising deep learning for microscopy with ZeroCostDL4Mic – Lucas von Chamier – Nature Communications
Webinars
Offered talks on Plasmids and Mobile Elements for 2021 – Plasmids around the globe – International Society for Plasmid Biology and Other Mobile Genetic Elements
Spring 2021 Microbiome Informatics webinars – OSU Center of Microbiome Science
EMBARK Spring Webinars – AMR focused webinars – EMBARK project
BISMiS Live – Microbial taxonomy: where are we now and where are we going? Iain Sutcliffe – Bergey’s Intl. Society for Microbial Systematics; registration here
Berkeley Lab Live Science – Exploring Earth – Berkeley Lab – April 23
Conferences
ISAPP 2021 Virtual Annual Meeting – International Scientific Association for Probiotics and Prebiotics – June 1–2
Courses
Open Online R Stream – Wolfgang Viechtbauer
RaukR: Advanced R for Bioinformatics Summer School – NBIS/SciLifeLab – June 14-24
