July 16, 2021

Today’s digest features studies on environmental contamination of carbapenem-resistant Klebsiella pneumoniae in China (spoiler: extensive contamination, but has negligible impact on patient colonisation), the dynamic change and correlation of microbiome from different body sites to the treatment response as well as immune-related adverse events of immunotherapy in lung cancer patients, and more.

Also, check out a regularly-updated collection of FREE, ONLINE microbiome events. Happy Friday!

Human microbiome

*Prospective correlation between the patient microbiome with response to and development of immune-mediated adverse effects to immunotherapy in lung cancer – Justin Chau – BMC Cancer

Gut microbiome

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner – Emmanuel Montassier – Nature Microbiology

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Sandeep Verma – PlosOne

Differences in the individual curative effect of acupuncture for obese women with polycystic ovary syndrome based on metagenomic analysis: study protocol for a randomized controlled trial – Huaying Fan – Trials

Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes – Danielle Peterson – Frontiers in Microbiology

Resistome

*Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study – Li Wei – Microbiology Spectrum

*Linezolid- and multidrug-resistant enterococci in raw commercial dog food, Europe, 2019–2020 – Ana R. Freitas – Emerging Infectious Diseases

Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study – Huan Chen – PeerJ

Predicting antibiotic resistance gene abundance in activated sludge using shotgun metagenomics and machine learning – Yuepeng Sun – Water Research

Animal microbiome

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers – DΓ©borah Romaskevis Gomes Lopes – Journal of Animal Science and Biotechnology

Animal experiment

An osmotic laxative renders mice susceptible to prolonged Clostridioides difficile colonization and hinders clearance – Sarah Tomkovich – bioRxiv

Bioinformatics

Critical Assessment of Metagenome Interpretation – the second round of challenges – F. Meyer – bioRxiv

Disentangling environmental effects in microbial association networks – Maria Deutschmann – bioRxiv

Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

June 25, 2021

This week, the microbial sciences community worldwide (virtually) united at the World Microbe Forum – meeting highlights you can find here #WorldMicrobeForum.

Today’s digest features studies on group B Streptococcus pathogenesis, dental microbiota and aGVHD Risk, a book about writing and publishing papers, and more. Also, check out a collection of FREE, ONLINE microbiome events. Happy Friday!


Read about the experiences of 338 early career researchers from 36 countries with their mentors in Mentorship in life sciences: voices of mentees by A. Murat Eren (Meren)!


General microbiome

Behind the paper: Describing and naming bacteria in the 21st century – Thomas Hitch – Nature blog

Hierarchical control of microbial community assembly – Sammy Pontrelli – bioRxiv

Resistome

*L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli – Aleksandra Petrovic Fabijan – bioRxiv

Gut microbiome

A newly identified protein from Akkermansia muciniphila stimulates GLP-1 secretion – Patrice D. Cani and Claude Knauf – Cell Metabolism

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics – Anna Pryszlak – arXiv

Dispersal strategies shape persistence and evolution of human gut bacteria – Falk Hildebrand – Cell Host & Microbe

Urinary microbiome

Review: Urinary Microbiome: Yin and Yang of the Urinary Tract – Virginia Perez-Carrasco – Frontiers in Cellular and Infection Microbiology

Vaginal microbiome

Cysteine dependence in Lactobacillus iners constitutes a novel therapeutic target to modify the vaginal microbiota – Seth M. Bloom – bioRxiv

*A type VII secretion system in Group B Streptococcus mediates cytotoxicity and virulence – Brady L Spencer – bioRxiv

Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omics – Zhuye Jie – Genomics, Proteomics & Bioinformatics

Predictive functional analysis reveals inferred features unique to cervicovaginal microbiota of African women with bacterial vaginosis and high-risk human papillomavirus infection – Harris Onywera – PlosOne

Effect of metronidazole on vaginal microbiota associated with asymptomatic bacterial vaginosis – Daniel Ruiz-Perez – Access Microbiology

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 – Frontiers in Immunology

Fusobacterium nucleatum metabolically integrates commensals and pathogens in oral biofilms – Akito Sakanaka – bioRxiv

Animal microbiome

*Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches – Sharon A. Huws – Microbiome

Animal experiments

A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes – Marion Darnaud – bioRxiv

Bioinformatics

GUNC: detection of chimerism and contamination in prokaryotic genomes – Askarbek Orakov – BMC Genome Biology

metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies – Senying Lai – bioRxiv

Open challenges for microbial network construction and analysis – Karoline Faust – The ISME Journal 2021

STRipy: a graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data – Andreas Halman – bioRxiv

Adapting macroecology to microbiology: using occupancy modelling to assess functional profiles across metagenomes – Angus S Hilts – bioRxiv


Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

The International Conference on Group B Strep (ICGBS) – July 20-22

World Enterococcus Day – July 15 – Registration here

BiATA2021 Bioinformatics: from Algorithms to Applications – July 12–15 


LSfM Lecture Series & Workshops : “The Dark Side of Science: Misconduct in Biomedical Research” Dr. Elisabeth Bik – more info here – June 30

EMBARK Webinars – Kimberly Kline β€œPathogenesis and persistence during Enterococcus faecalis biofilm-associated infection” and Sofia Forslund β€œHigh-throughput measurement of host and microbiota” – EMBARK project – June 30


Writing

Writing and Publishing Scientific Papers: A Primer for the Non-English Speaker – GΓ‘bor LΓΆvei – OpenBook Publishers


Art

From Scientist to SciArtist – Eliza Wolfson


May 14, 2021

Today’s digest features Emu for microbial community profiling with expectation-maximization algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads, glycobiology of UTI, profiling canine fecal microbiome by long-read metagenomics with Nanopore sequencing, spatial-temporal assessment of drinking water microbiome in Puerto Rico, ancient microbial genomes from paleofeces (with 61 previously undescribed species), and more.

Check out a list of awesome webinars, courses and podcasts. Happy Friday!


Today is the last day for #NSURP2021 applications:

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.


Share your experience as an early career researcher with your academic mentor and take part in this important survey on mentorship!

Gut microbiome

Reconstruction of ancient microbial genomes from the human gut – Marsha C. Wibowo – Nature

Human and preclinical studies of the host–gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health – FranΓ§ois Brial – Gut Microbiota

Oral microbiome

*Mechanical biofilm disruption causes microbial and immunological shifts in periodontitis patients – William Johnston – Scientific Reports

Vaginal microbiome

Review: The Complex Link between the Female Genital Microbiota, Genital Infections, and Inflammation – Smritee Dabee – Infection and Immunity

Urinary microbiome

*Review: The glycobiology of uropathogenic E. coli infection: the sweet and bitter role of sugars in urinary tract immunity – Federico Lupo – Immunology

The Good and the Bad: Ecological Interaction Measurements Between the Urinary Microbiota and Uropathogens – Laurens E. Zandbergen – Frontiers in Microbiology

Urinary prostaglandin E2 as a biomarker for recurrent UTI in postmenopausal women – Tahmineh Ebrahimzadeh – Life Science Alliance

Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection – Carrie E. Jung – Female Pelvic Medicine & Reconstructive Surgery

Animal microbiome

*Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces – Anna CuscΓ³ – BMC Genomics

Perinatal exposure to tetracycline contributes to lasting developmental effects on offspring – Elizabeth M. Hill – Animal Microbiome

Drinking water microbiome

*Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria – Maria Catalina Sevillano – bioRxiv

Technique

Predicting the presence and abundance of bacterial taxa in environmental communities through flow cytometric fingerprinting – Jasmine Heyse – bioRixv

Sample preservation

Critical evaluation of faecal microbiome preservation using metagenomic analysis – Alena L. Pribyl – ISME Communications

Bioinformatics

*Emu: Species-Level Microbial Community Profiling for Full-Length Nanopore 16S Reads – Kristen D. Curry – bioRxiv

Microbiome differential abundance methods produce disturbingly different results across 38 datasets – Jacob T Nearing – bioRxiv

Improving metagenomic binning results with overlapped bins using assembly graphs – Vijini G. Mallawaarachchi – Algorithms for Molecular Biology

A method for achieving complete microbial genomes and improving bins from metagenomics data – Lauren M. Lui – Plos Computational Biology

Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions – J. Lima – Journal of Microbiological Methods

Webinars

EMBARK Spring Webinars – Heike Schmitt β€œInternational efforts for One Health surveillance of AMR (WHO Tricycle)” and Etienne RuppΓ© β€œOn the use of Tricycle in EMBARK” – EMBARK project – May 19
Registration here
More info here

BISMiS Live – GCM 2.0: WDCM 10K Sequencing Project for Type Strains by Juncai Ma – Bergey’s Intl. Society for Microbial Systematics – May 15
Registration here
More info here

Women in Data Science 2021 – Perspectives in Industry and Academia – Bayer AG and de.NBI, Elixir Germany Event – 18 June

PPGSND thesis seminar: The dark side os science: misconduct in biomedical research – Elisabeth Bik – 20 May

mSystems Thinking Series – ASM

Courses

Riffomonas Project – R tutorials and more – PatricK Schloss

Machine learning in Python with scikit-learn – Inria

Introduction to Computer Science and Programming in Python – MIT

Using MOFA for integration of omics data – Ricard Argelaguet – May 25

Data Visualization: Use R, ggplot2, and the principles of graphic design to create beautiful and truthful visualizations of data – Andrew Heiss

Conferences

1st Young AMICI Symposium – Austrian Microbiome Initiative – May 25-26

Microbes, Social Equity, and Rural Health – The Microbes and Social Equity working group and The University of Maine Institute of Medicine – June 14–18

Podcast

Differential gene expression and DESeq2 with Michael Love – The Bioinformatics Chat – Roman Cheplyaka and Jacob Schreiber

The Fake Science Detectives with David Sanders and Elisabeth Bik – Follow the Science – Faye Flam

Research, networking and public perception of science with Linda J Kenney – Microbes and Us – Joseph Shuttleworth

The microbiome: Delicious food and solutions to the climate crisis with Lene Lange – Science Stories – Jens Degett

April 16, 2021

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 12β€Š000-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

March 12, 2021

Today’s digest is HUGE.

Read about the healthy urogenital microbiome profiling by culturomics, gutSMASH (Specialized Primary Metabolite Analysis From Anaerobic Bacteria), (sub)strains evolution in mice, and AMPSphere (a comprehensive catalog of antimicrobial peptides).

There are interesting results of a new metaanalysis of the neonatal microbiome, maternal strain inheritance, and persistence into adolescence, evaluation of the effect of long-term freezing storage temperature on fecal samples, and estimation of the bioinformatic carbon footprint using the freely available Green Algorithms calculator. Find out more about statistics & challenges in molecular microbiology (with a reproducible research appendix!).

NEWS: The Transbiome project is a community driven research program using crowdfunding and co-creation to discover the diversity of the neo-vaginal microbiome. You can support the project here.

Check out a list of awesome webinars, courses and podcasts. Happy Friday!

Gut microbiome

*A systematic analysis of metabolic pathways in the human gut microbiota – VictΓ²ria Pascal Andreu – bioRxiv

*Strain inheritance and neonatal gut microbiota development: A meta-analysis – Daniel Podlesny and W. Florian Fricke – International Journal of Medical Microbiology

Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut – Andrea R. Watson – bioRixv

Effect of fecal microbiota transplantation on neurological restoration in a spinal cord injury mouse model: involvement of brain-gut axis – Yingli Jing – Microbiome

Review: Association between antibiotics and gut microbiome dysbiosis in children: systematic review and meta-analysis – Lucy McDonnell – Gut Microbes

Review: Salmonella versus the Microbiome – Andrew W. L. Rogers – Microbiology and Molecular Biology Reviews

Respiratory microbiome

Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis – Marija Dmitrijeva – mBio

Oral microbiome

Review: Resilience of the oral microbiome – William G. Wade – Periodontology 2000

Skin microbiome

Skin microbiota and clinical associations in Netherton sindrome – Veera SillanpÀÀ – JID Innovations

Urogenital microbiome

*Long-term stability of the urogenital microbiota of asymptomatic European women – Magdalena Ksiezarek – BMC Microbiology

Limosilactobacillus urinaemulieris sp. nov. and Limosilactobacillus portuensis sp. nov. isolated from urine of healthy women – Magdalena Ksiezarek – International Journal of Systematic and Evolutionary Microbiology

Vaginal microbiome

The structure and diversity of strain-level variation in vaginal bacteria – Brett A. Tortelli – Microbial Genomics

Obesity is associated with lower bacterial vaginosis prevalence in menopausal but not pre-menopausal women in a retrospective analysis of the Women’s Interagency HIV Study – Elizabeth Daubert – PlosOne

Bacterial biofilm formation on vaginal ring pessaries used for pelvic organ prolapse – Felicity G. Gould – International Urogynecology Journal

Animal microbiome

*Long-term storage of feces at βˆ’80 Β°C versus βˆ’20 Β°C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome – Stefan Gavriliuc – PeerJ

Differences in the gut microbiomes of dogs and wolves: roles of antibiotics and starch – Yuting Liu – BMC Veterinary Research

An Expanded Gene Catalog of Mouse Gut Metagenomes – Jiahui Zhu – mSphere

Animal experiments

*Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice – Bahtiyar Yilmaz – Cell Host & Microbe

The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet – Tahliyah S. Mims – Communications Biology

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments – Hualan Liu – Cell Reports

Tea polyphenols regulate gut microbiota dysbiosis induced by antibiotic in mice – Jie Li – Food Research International

Plant microbiome

Designing a home for beneficial plant microbiomes – Chunxu Song – Current Opinion in Plant Biology

Food

Review: Polymicrobial interaction between Lactobacillus and Saccharomyces cerevisiae: coexistence-relevant mechanisms – Zhenbo Xu – Critical Reviews in Microbiology

Viruses and phages

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities – Christian Santos-Medellin – The ISME Journal

Review: Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review – Julie Callanan – Microorganisms

Techniques

High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes – Florian Trigodet – bioRxiv

Bioinformatics

*AMPSphere: the worldwide survey of prokaryotic antimicrobial peptides – CΓ©lio Dias Santos-JΓΊnior – Zenodo

*A Statistical Perspective on the Challenges in Molecular Microbial Biology – Pratheepa Jeganathan and Susan P. Holmes – arXiv

*The carbon footprint of bioinformatics – Jason Grealey – bioRxiv

*Make Interactive Complex Heatmaps in R – Zuguang Gu and Daniel Huebschmann – bioRxiv

Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring – Ryan B.Ghannam and Stephen M.Techtmann – Computational and Structural Biotechnology Journal

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit – Fernando Meyer – Nature Protocols

STATegra: Multi-Omics Data Integration – A Conceptual Scheme With a Bioinformatics Pipeline – Nuria Planell – Frontiers in Genetics

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences – Grace A. Blackwell – bioRxiv

clinker & clustermap.js: automatic generation of gene cluster comparison figures – Cameron L M Gilchrist & Yit-Heng Chooi – Bioinformatics

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models – Johannes Zimmermann – Genome Biology

Webinars

mSystems Thinking Series: Diversity, Equity, and Inclusion in Microbiology – ASM – March 26

The Microbiome Centers Consortium Seminar Series – weekly seminars featuring early career researchers – Thursdays

Americas Webinar: Mother’s Milk & Baby’s Bacteria: Discoveries from the CHILD Cohort Study – Meghan Azad – April 14

Courses & Workshops

Get R Done: R Tutorials video series – Chad C. Williams

Machine Learning in Genomics: Tools, Resources, Clinical Applications and Ethics – the NHGRI Genomic Data Science Working Group of the National Advisory Council for Human Genome Research – April 13-14

Podcast

February 2021 Pod: Global Changβ€ͺe‬ – Bengtsson-Palme Lab – Microbiology Lab Pod

Enhancers with Molly Gasperini – Jacob Schreiber – The Bioinformatics Chat

Matthew Schechter: Metagenomics History Part 1 and 2 – Leo Elworth – The Bioinformatics and Beyond Podcast

Ep. 33 Oyster Microbiome with Dr. Rachel Diner – Julie Laurin – Planet B612

Art

UMich Microbial Masterpieces – Community for microbe enthusiasts and artists – Erica Gardner, Anna Urso, Bruna Iunes Sanches
*Check out their giant Winogradsky Panel in the Duderstadt Center gallery

February 12, 2021

Today’s quite diverse digest features: the role of gut commensal fungi mycobiota in shaping the human protective IgG antibody repertoire, Mouse Microbial Genome Collection, gut microbiome – lymphocytes – diet link, competition between Gardnerella species, microbiota-derived bile acids pool as a mediator of host–microbiota interactions, multiscale variation in genome graphs, and a list of awesome webinars, courses and podcasts. Check out two cool science and art projects, Bacterial Alphabet and Microbe Crayon. Happy Friday!

Gut microbiome

*Human gut mycobiota tune immunity via CARD9-dependent induction of anti-fungal IgG antibodies – Itai Doron – Cell

*Functional and taxonomic comparison of mouse and human gut microbiotas using extensive culturing and metagenomics – Benjamin S. Beresford-Jones – bioRxiv

*High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome – Cristina Menni – BMC Medicine

The Reactobiome Unravels a New Paradigm in Human Gut Microbiome Metabolism – Gholamreza Bidkhori – bioRxiv

Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer – Kellyanne Duncan – Gut Microbes

Review: Diversity and dynamism of IgAβˆ’microbiota interactions – Kelsey E. Huus – Nature Reviews Immunology

Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models – Francesco Strati – Microbiome

Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation – Monica Viladomiu – Cell Host & Microbe

Adults with Prader–Willi syndrome exhibit a unique microbiota profile – Wendy J. Dahl – BMC Research Notes

Vaginal microbiome

*Population density affects the outcome of competition in co-cultures of Gardnerella species isolated from the human vaginal microbiome – Salahuddin Khan and Janet E. Hill – bioRxiv

Review: Lactic acid-containing products for bacterial vaginosis and their impact on the vaginal microbiota: A systematic review – Erica L. Plummer – PlosOne

Urinary microbiome

Functional and Taxonomic Dysbiosis of the Gut, Urine, and Semen Microbiomes in Male Infertility – Scott D. Lundy – European Urology

Review: The microbiome and host mucosal interactions in urinary tract diseases – Bernadette Jones-Freeman – Mucosal Immunology

Epidemiology of urinary tract infections in children: Causative bacteria and antimicrobial therapy – Yuhei Tanaka – Paediatrics International

Human milk microbiome

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi – Microbiome

Respiratory microbiome

Review: Respiratory microbiome in mechanically ventilated patients: a narrative review – MΓ©lanie Fromentin – Intensive Care Medicine

Animal microbiome

Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes – Xuefeng Peng – Nature Microbiology

Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics – Paiboon Tunsagool – Applied and Environmental Microbiology

Unravelling the Role of Rumen Microbial Communities, Genes, and Activities on Milk Fatty Acid Profile Using a Combination of Omics Approaches – Sokratis Stergiadis – Frontiers in Microbiology

Evaluation of the ocular surface mycobiota in clinically normal horses – Mary L. Walsh – PlosOne

Animal experiments

Colonization at birth with human CST IV cervicovaginal microbiota alters development and increases neonatal mortality in mice – Eldin JaΕ‘areviΔ‡ – bioRxiv

Novel gut pathobionts confound results in a widely used mouse model of human inflammatory disease – Samuel C Forster – bioRxiv

Low-dose exposure of glyphosate-based herbicides disrupt the urine metabolome and its interaction with gut microbiota – Jianzhong Hu – Scientific Reports

Microbiota control of maternal behavior regulates early postnatal growth of offspring – Yujung Michelle Lee – Science Advances

Probiotics

Minireview: Lactic acid bacteria as probiotics for the nose? – Ilke De Boeck – Microbial Biotechnology

*Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization – Matthew H. Foley – PNAS

Probiotic nasal spray development by spray drying – Katarina Jokicevic – European Journal of Pharmaceutics and Biopharmaceutics

Water microbiome

Microbiota analysis of rural and urban surface waters and sediments in Bangladesh identifies human waste as driver of antibiotic resistance – Ross S. McInnes – bioRxiv

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika – Patricia Q. Tran – The ISME Journal

Soil microbiome

Trace gas oxidizers are widespread and active members of soil microbial communities – Sean K. Bay – Nature Microbiology

Bacterial communities regulate temporal variations of the antibiotic resistome in soil following manure amendment – Jianhua Cheng – Environmental Science and Pollution Research

Techniques

Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method – Pascal M. Frey – mSystems

Bioinformatics

*Enabling multiscale variation analysis with genome graphs – Brice Letcher – bioRxiv

HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes – Yu Li – Microbiome

BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence – Benjamin Hepp – Bioinformatics

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN) – Renaud Van Damme – Plos Computational Biology

PATO: Pangenome Analysis Toolkit – Miguel D. FernΓ‘ndez-de-Bobadilla – bioRxiv

Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets – Nicholas D. Youngblut and Ruth E. Ley – bioRxiv

Webinars

UCC Science Society STEMinar: The Gut Microbiome, Health & Disease. You truly are what you eat – Paul O’Toole – 15 February

SGBUG (Singapore Bacterial Ultra Group) seminar: Human Gut Bacteria, Bile Acids, and Host Physiology – Sloan Devlin – 18 February

MicroSeminars 2021 – Free Web-based Microbiology Seminar Series

Biofilm Baithak – An India-specific Meetup – India Biofilms Society- 20-27 February 2021.

Klebsiella Virtual Seminar Series 2021 #KlebClub2021 – Department of Microbiology and Immunology, University of Michigan

Courses

Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R – The Wellcome Genome Campus

Next Generation Sequencing Bioinformatics course – Wellcome Genome Campus Advanced Courses & Scientific Conferences – H3Abionet

Biobanking – Institut Pasteur

Podcasts

Season 2, Ep. 2: Building Biomes with Jack Gilbert – Ruairi Robertson – Biomes

Reverse mentoring with Martin Dougherty – Alice Matimba – Your Digital Mentor

Episode 17: Post-docs Part 2: Hiring – Stephanie Hicks and John Muschelli – The Corresponding Author

Episode 235: Green algae and fatty acids – Vincent Racaniello, Elio Schaechter, Michele Swanson, and Michael Schmidt – This week in microbiology podcast

Dr. Heer Mehta: Antibiotic Resistance and Experimental Evolution – Leo Elworth – The Bioinformatics and Beyond Podcast

Science and Art

Microbe Crayon Project – Anne A. Madden

Drawing the #BacterialAlphabet – NoΓ©mie Matthey

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 Ξ²-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 Ξ²-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-GonzΓ‘lez – 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 JaΕ‘areviΔ‡, 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

December 9, 2020

In today’s digest read about the selection and microdiversity in glacier-fed streams, Gardnerella vaginalis contribution to the increased rate of group B Streptococcus vaginal colonization, making F1 hybrids in Escherichia coli using MAE (Mass Allelic Exchange), smORFinder (annotation tool to identify small proteins in microbial genomes and metagenomes), and more.
Check out the new Science Friday podcast episode on microbial interactions in cheese rinds and Svetlana’s pick for happy holidays.
Cheers!

Human microbiome

Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver – Holly Lutz – Frontiers in Microbiology

Gut microbiome

Landscapes of bacterial and metabolic signatures and their interaction in major depressive disorders – Jian Yang – Science Advances

Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome – Dylan G. Maghini – Nature Protocols

Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses – Shu Yasuda – iScience

The Healthy Microbiome (What is the definition of a healthy gut microbiome?) – Fergus Shanahan – Gastroenterology

The gut microbiota is associated with immune cell dynamics in humans – Jonas Schluter
– Nature

Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure – Jonel Trebicka – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity – Alexander SF Berry – bioRxiv

Animal experiments

*Gardnerella vaginalis promotes group B Streptococcus vaginal colonization, enabling ascending uteroplacental infection in pregnant mice – Nicole M. Gilbert – American Journal of Obstetrics & Gynecology

Akkermansia muciniphila: A potential novel mechanism of nuciferine to improve hyperlipidemia – Yue Yu – Biomedicine & Pharmacotherapy

Gut microbiota modulation by both Lactobacillus fermentum MSK 408 and ketogenic diet in a murine model of pentylenetetrazole-induced acute seizure – Ju Young Eor – Epilepsy Research

Host-age prediction from fecal microbiome composition in laboratory mice – Adrian Low – bioRxiv

Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling Through The Aryl Hydrocarbon Receptor – Aayushi Uberoi – bioRxiv

Water microbiome

*Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome – Stilianos Fodelianakis – bioRxiv

Phages and viruses

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis – Andrey N. Shkoporov – bioRxiv

Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase – Marike Palmer – Frontiers in Microbiology

Broad Virus Detection and Variant Discovery in Fecal Samples of Hematopoietic Transplant Recipients Using Targeted Sequence Capture Metagenomics – Suze A. Jansen – Frontiers in Microbiology

Antimicrobial Resistance

Review: Multidrug-resistant high-risk Enterococcus faecium clones: can we really define them? – Ana R. Freitas – International Journal of Antimicrobial Agents

Review: Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance – Madangchanok Imchen – Frontiers in Genetics

Predicting clinical resistance prevalence using sewage metagenomic data – Antti Karkman – Communications Biology

Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants – John Leech – mSystems

Uncovering hidden antimicrobial resistance patterns within the hospital microbiome – Bastiaan W. Haak and W. Joost Wiersinga – Nature Medicine

Isolation and characterization of human pathogenic multidrug resistant bacteria associated with plastic litter collected in Zanzibar – Farah N. Rasool – Journal of Hazardous Materials

Integrated metagenomic and metatranscriptomic analyses of ultraviolet disinfection effects on antibiotic resistance genes and bacterial communities during wastewater treatment – Shuyu Jia – Ecotoxicology

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more – Magdalena SkarΕΌyΕ„ska – Plos One

Techniques

*Mass allelic exchange: enabling sexual genetics in Escherichia coli – Varnica Khetrapal – bioRxiv

Review: Microbial model communities: To understand complexity, harness the power of simplicity – Johan Bengtsson-Palme – Computational and Structural Biotechnology Journal

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae – Sivkheng Kann – BMC Microbiology

Bioinformatics

*Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes – Matthew G. Durrant and Ami S. Bhatt – Cell Host Microbe

Accurate Microbiome Sequencing with Synthetic Long Read Sequencing – Nico Chung – bioRxiv

Species level resolution of female bladder microbiota from marker gene surveys – Carter Hoffman – bioRxiv

Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis – Paul E. Smith – Frontiers in Microbiology

Events

H3ABioNet Seminars and Webinars – H3ABioNet Pan African Bioinformatics Network

Inspiring the next generation of scientists… online – The Young Microbiologists Symposium (YMS) 2020

MLCB 2020 Day 1 and 2 talks – Machine Learning in Computational Biology meeting

Podcast

Why We’re Giving Thanks To Microbes For Stinky Cheese with Benjamin Wolfe and Casey Cosetta – Katie Feather and Ira Flatow – Science Friday

Svetlana’s pick

Planning Our β€œHome-mas” this December – MissPond – Emma Pond

Holiday Gift Guide For Microbe Lovers – Justine Dees – Joyful Microbe

The 2020 cookbook giftlist – Fiona Beckett – Matching Food & Wine

November 20, 2020

Today’s digest features a systematic assessment of best practices for the sequencing-based characterization of the human vaginal microbiome, studies on link between the plaque microbiome and peri-implantitis, cutimycin [a Cutibacterium acnes-produced antibiotic that affects niche competition among the human skin microbiota] and antibiotic resistance genes in shower drains, washing machines, and dishwashers. There is a new Micro Binfie Podcast episode about moving from the wet lab into the dry lab to become a bioinformatician. Also, check out a list of interesting (freely available) events. Happy reading/listening!

Oral microbiome

*Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics – Paolo Ghensi – npj Biofilms and Microbiomes

Skin microbiome

*A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles – Jan Claesen – Science Translational Medicine

Review: Staphylococcus epidermidisβ€”Skin friend or foe? – Morgan M. Brown and Alexander R. Horswill – Plos Pathogen

Gut microbiome

Preterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts – Stephen A. James – Journal of Fungi

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology – Antonio Molinaro – Nature Communications

Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers – Allyson L. Byrd – Journal of experimental medicine

Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements – Rupasri Mandal – Metabolomics

Minireview: Communal Living: Glycan Utilization by the Human Gut Microbiota – Jonathon A. Briggs – Environmental Microbiology

Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut – Leszek Michalak – Nature Communications

Vaginal microbiome

*Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome – Luisa W. Hugerth – mSphere

Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Conor Feehily – npj Biofilms and Microbiomes

Intercepting genomic variability of Gardnerella vaginalis species through comparative genomics analyses: evolutionary and ecological implications – Chiara Tarracchini – Applied and Environmental Microbiology

Engineered phage endolysin eliminates Gardnerella in bacterial vaginosis without damaging the healthy vaginal microbiome – Christine Landlinger – medRxiv

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid – Katelyn Brandt & Rodolphe Barrangou – BMC Microbiology

Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species – Wendy Li and Zhanshan Sam Ma – Computational and Structural Biotechnology Journal

Animal microbiome

The haybiome: Characterising the viable bacterial community profile of four different hays for horses following different pre-feeding regimens – Simon Daniels – Plos One

Review: Value of Probiotics in Canine and Feline Gastroenterology – Silke Salavati Schmitz – Veterinary Clinics of North America: Small Animal Practice

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel – Marco Gerdol – Genome Biology

Technique

Phylotype-Level Characterization of Complex Lactobacilli Communities Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach – Shaktheeshwari Silvaraju – Applied and Environmental Microbiology

Metagenomics

Metagenomic assessment of the global distribution of bacteria and fungi – Mohammad Bahram – Environmental Microbiology

Bioinformatics

On the complexity of haplotyping a microbial community – Samuel M Nicholls – Bioinformatics

Challenges in Benchmarking Metagenomic Profilers – Zheng Sun – bioRxiv

Unifying the global coding sequence space enables the study of genes with unknown function across biomes – Chiara Vanni – bioRxiv

Nucleotide-resolution bacterial pan-genomics with reference graphs – Rachel M Colquhoun – bioRxiv

Efficient storage and analysis of quantitative genomics data with the Dense Depth Data Dump (D4) format and d4tools – Hao Hou – bioRxiv

An Integrated Workflow for Enhanced Taxonomic and Functional Coverage of the Mouse Faecal Metaproteome – Nicolas Nalpas – bioRxiv

The misuse of colour in science communication – Fabio Crameri – Nature Communications

Antimicrobial Resistance

*The Household Resistome: Frequency of Ξ²-Lactamases, Class 1 Integrons, and Antibiotic-Resistant Bacteria in the Domestic Environment and Their Reduction during Automated Dishwashing and Laundering – Laura Schages – Applied and Environmental Microbiology

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm – Shireen M Kotay – bioRxiv

fosM, a new family of fosfomycin resistance gene identified in bacterial species isolated from human microbiota – Sami Khabthani – Antimicrobial Agents and Chemotherapy

Heme is crucial for medium-dependent metronidazole resistance in clinical isolates of C. difficile – Ilse M. Boekhoud – bioRxiv

Events

Black In Immuno Week – Black in Immuno – 22-28 November 2020
*A collective of scientists to celebrating, amplifying, and promoting the work of Black Immunologists across the globe.

Webinar: Antibiotic Resistance in the Environment – Organizer: Resistomap – Date: Tuesday, 24 November 2020

Webinar: Microbiology Webinars – FEMS – webinar recordings available

Virtual course and symposium: Harnessing Our Inner Ecology To Track and Treat Disease – Institute for Systems Biology – October 15 and 16, 2020
*all course materials/tutorials and talks are available for free on the website

Virtual Conference on Prokaryotic Small Proteins – Organizers: Todd Gray, Kai Papenfort, Gigi Storz and Joe Wade – January 12-14, 2021

Podcast

*Moving from wet to dry with Phil Ashton – Hosts: Andrew Page, Nabil-Fareed Alikhan and Lee Katz – Micro Binfie Podcast

Real-time quantitative proteomics with Devin Schweppe – Host: Jacob Schreiber – The Bioinformatics Chat

Interspecies collaborations with Mindaugas GapΕ‘evičius – Host: Aga Pokrywka – Ferment Radio

Microbiome as Organ: Researcher Colin Hill Talks Bacteria and Bacteriophages in Human Body with Colin Hill – Host: Richard Jacobs – The Finding Genius Podcast

What Does Your Microbiome Say About You? with Colin Hill – Host: Andrea Hardy – Let’s Gut Real

Colouring booklet

Microbes, diet and beyond by Microbiome Support EU project; Illustrations by Maria Pock

Boardgame

Drugs vs Bugs, a free and exciting Print’n’Play boardgame developed by CΓ©lia Souque

October 16, 2020

In today’s digest read about how food additives affect the intestinal microbiota and induce intestinal inflammation, the role of the gut microbiome in honey bee nestmate recognition, how to use gene-level analysis to identify microbial “genome islands” associated with human health, and more. Check out the list of audiobooks about microbes. Happy Friday!

General microbiome

Time as a microbial resource – Karen G. Lloyd – Environmental Microbiology Reports

Review: The Central Role of Interbacterial Antagonism in Bacterial Life – S. Brook Peterson – Current Biology

Gut microbiome

*Dietary Emulsifiers Directly Impact Adherent-Invasive E. coli Gene Expression to Drive Chronic Intestinal Inflammation – Emilie Viennois – Cell Reports

Microbial Strain Engraftment, Persistence and Replacement after Fecal Microbiota Transplantation – Daniel Podlesny – medRxiv

Characterization of presumptive vancomycin-resistant enterococci recovered during infection control surveillance in Dallas, Texas – Sara Ping – bioRxiv

Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria – Samir Giri – bioRxiv

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria – Mathilde Lebas – Microorganisms

A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within Vibrio cholerae infected patients – InΓ¨s Levade – bioRxiv

Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial – Anne-Sophie Alvarez – Scientific Reports

Skin microbiome

Microbial and transcriptional differences elucidate atopic dermatitis heterogeneity across skin sites – Noora Ottman – Allergy

Respiratory microbiome

Multicenter analysis of sputum microbiota in tuberculosis patients – Claudia Sala – PlosOne

Lacticaseibacillus casei AMBR2 modulates the epithelial barrier function and immune response in a donor-derived nasal microbiota manner – Charlotte De Rudder – Scientific Reports

Animal microbiome

*The gut microbiome defines social group membership in honey bee colonies – Cassondra L. Vernier – Science Advances

Early-life gut dysbiosis linked to juvenile mortality in ostriches – Elin Videvall – Microbiome

Animal experiment

The Immune System Fails to Mount a Protective Response to Gram-Positive or Gram-Negative Bacterial Prostatitis – Federico Lupo – Journal of Immunology

The aging mouse microbiome has obesogenic characteristics – Dana Binyamin – Genome Medicine

Tetracycline Antibiotics Induce Host-Dependent Disease Tolerance to Infection – Henrique G. ColaΓ§o – Immunity

Water microbiome

Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks – Isabel Douterelo – Water Research

Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria – Ekaterina Y. Gottshall – bioRxiv

Viruses and phages

Culturing novel and abundant pelagiphages in the ocean – Zefeng Zhang – Environmental Microbiology

High-throughput mapping of the phage resistance landscape in E. coli – Vivek K. Mutalik – PlosBiology

Fungi

Minireview: Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance – Brianna Ball – mBio

Technique

Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment – Andrea Sajuthi – bioRxiv

Bioinformatics

*Gene-level metagenomics identifies genome islands associated with immunotherapy response – Samuel S Minot – bioRxiv

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom – Keith Mitchell – Frontiers in Microbiology

Raman2imzML converts Raman imaging data into the standard mass spectrometry imaging format – Stefania Alexandra Iakab – BMC Bioinformatics

Scientific writing

Eight problems with literature reviews and how to fix them – Neal R. Haddaway – Nature Ecology & Evolution

Scientific art

Inktober2020 #PathogenPortraits by Dr Eliza Wolfson

Citizen science

The Human Diets & Microbiome Initiative in the US (THDMI): A unique opportunity to become a citizen scientist. Join for FREE to uncover the secret of the gut microbiome.

Books

11 Audiobooks About Microbes – Justine Dees – Joyful Microbe