January 15, 2021

Today’s digest features a collection of reviews, opinion pieces, discussion on prenatal microbiome, pipeline to extract metabolic models from whole metagenome sequencing data (metaGEM), novel type of colistin resistance genes, mechanisms that shape microbial pangenomes, and more. Check out a list of free web-based microbial seminars. Happy reading/listening!

General microbiome

*Mechanisms That Shape Microbial Pangenomes – Maria Rosa Domingo-Sananes
and James O. McInerney – Trends in Microbiology

Evolution to alternative levels of stable diversity leaves areas of niche space unexplored – Ilan Naftali Rubin – bioRxiv

Prenatal microbiome

*The prenatal in utero microbiome controversy: Microbiome or no microbiome: are we looking at the prenatal environment through the right lens? – W. Florian Fricke and Jacques Ravel – BMC Microbiome

Urinary microbiome

The Urinary Microbiome in Postmenopausal Women with Recurrent Urinary Tract Infections – Monique H. Vaughan – bioRxiv

Alterations in Urobiome in Patients With Bladder Cancer and Implications for Clinical Outcome: A Single-Institution Study – Jiarong Zeng – Frontiers in Cellular and Infection Microbiology

Bare Versus Hair: Do Pubic Hair Grooming Preferences Dictate the Urogenital Microbiome? – Geynisman-Tan J – Female Pelvic Medicine & Reconstructive Surgery

Vaginal microbiome

Amylases in the Human Vagina – Kenetta L. Nunn – mSphere

Gut microbiome

Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes – Moamen M. Elmassry – PlosOne

Microbiome and ischemic stroke: A systematic review – Yee Teng Lee – PlosOne

Antimicrobial resistance

*A novel type of colistin resistance genes selected from random sequence space – Michael Knopp – Plos Genetics

Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance – Kara K. Tsang – Microbial Genomics

A framework for identifying the recent origins of mobile antibiotic resistance genes – Stefan Ebmeyer – Communications Biology

Minimal biophysical model of combined antibiotic action – Bor Kavčič – Plos Computational Biology

Mobilization of antibiotic resistance genes differ by resistance mechanism – Tue Kjaergaard Nielsen – bioRxiv

Carbapenem and Colistin Resistance in Enterobacter: Determinants and Clones – Zhiyong Zong – Trends in Microbiology

Animal microbiome

Fermented traditional Chinese medicine alters the intestinal microbiota composition of broiler chickens – Peng Huang – Research in Veterinary Science

Plant/root/soil microbiome

Coordination between microbiota and root endodermis supports plant mineral nutrient homeostasis – Isai Salas-González – Science

Food microbiome

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community – Sonja Blasche – Nature Microbiology

Generation of lactose and protease positive probiotic Lacticaseibacillus rhamnosus GG by conjugation with Lactococcus lactis NCDO 712 – Nazar Hussain – Applied and Environmental Microbiology

Phages and Viruses

Engineered Phage Endolysin Eliminates Gardnerella Biofilm without Damaging Beneficial Bacteria in Bacterial Vaginosis Ex Vivo – Christine Landlinger – Pathogens

Bioinformatics

*metaGEM: reconstruction of genome scale metabolic models directly from metagenomes – Francisco Zorrilla – bioRxiv

Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species – Thomas Sakoparnig – eLife

CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data – Anna Abramova – Bioinformatics

Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it – Huy N Nguyen – Bioinformatics

Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge – Runzhi Zhang – Biology Direct

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation – Wenjun Li – Nucleic Acids Research

Techniques

A co-culture microplate for real-time measurement of microbial interactions – Charles Jo – bioRxiv

Webinars

Mind, Mood & Microbes Expert Q&A: From Mechanisms to Clinical Applications – Jane Foster, Mauro Costa-Mattioli, John Cryan, Eldin Jašarević, Aletta D. Kraneveld, Filip Scheperjans, Elaine Hsiao – 21 January

SGBUG (Singapore Bacterial Ultra Group) seminar: Silencing bacterial genes with CRISPR-dCas9: from basic insights to high-throughput screens – David Bikard – 21 January

LoopSeq Solo Webinar: High Resolution Metagenomic Sequencing using DADA2 and LoopSeq Long-Read Sequencing – Benjamin Callahan – 21 January

FEMS Yeast Research Webinar on Genomic Insights into Yeast Diversity and Evolution – FEMS – 28 January

SSB Seminar: Double Trouble: Inappropriate Image Duplications in Biomedical Publications – Elisabeth Bik – 29 January

Geomicrobiology Network Seminar Series – The Mineralogical Society of Great Britain and Ireland

Winter 2021 WESTalks – Weekly seminars related to Water and the Environment with speakers from around the globe – IC-IMPACTS Student Engagement Committee (SEC) and the University of British Columbia’s Future Waters

MicroSeminars 2021 – Free Web-based Microbiology Seminar Series

Conferences &c

1st Microbiome PT Summit – The Portuguese Microbiome Community – 4 February

The 2021 UK Cellular Microbiology Network meeting – The Francis Crick Institute – 1-2 March

The Biology and Physics of Bacterial Chromosomes meeting – 4 March

Symposium Celebrating 100th Birthday and Research Accomplishments of Dr. Evelyn M. Witkin – Waksman Institute of Microbiology – 13 April

Podcast

TWiM 233: Antivirals made by bacteria – Hosts: Vincent Racaniello, Elio Schaechter, Michele Swanson, and Michael Schmidt – This week in microbiology podcast

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