January 10, 2022

Today’s digest features studies on glycosaminoglycans degradation by urinary microbiome, social network of honeybees, improved DNA extraction for low biomass samples, the LotuS2 tool for amplicon sequencing analysis, and more. Happy Monday!


Gut microbiome

Review: The role of the microbiota in the management of intensive care patients – Piotr Szychowiak – Annals of Intensive Care

Review: The Gut Microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS) – Rahel S. König – Frontiers in Immunology

Review: Opioid Use, Gut Dysbiosis, Inflammation, and the Nervous System – Richa Jalodia – Journal of Neuroimmune Pharmacology

Urinary microbiome

*A Semi-Quantitative Assay to Measure Glycosaminoglycan Degradation by the Urinary Microbiota – Vivian H. Nguyen – Frontiers in Cellular and Infection Microbiology

Vaginal microbiome

Composition and Stability of the Vaginal Microbiota of Pregnant Women With Inflammatory Bowel Disease – Janet E Hill – Inflammatory Bowel Diseases

Skin microbiome

*Anatomy promotes neutral coexistence of strains in the human skin microbiome – Arolyn Conwill – Cell Host & Microbe

Water microbiome

Tenets of a Holistic Approach to Drinking Water-Associated Pathogen Research, Management, and Communication – Caitlin Proctor – Water Research

Animal microbiome

Review: Possibilities and limits for using the gut microbiome to improve captive animal health – Jessica Diaz & Aspen T. Reese – Animal Microbiome

The mosquito microbiome includes habitat-specific but rare symbionts – Hans Schrieke – Computational and Structural Biotechnology Journal

*The gut microbiota affects the social network of honeybees – Joanito Liberti – bioRxiv

Techniques and methods

Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome – Guoshun Xu – BMC Genomics

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

When to suspect contamination rather than colonization – lessons from a putative fetal sheep microbiome – Simone Bihl – Gut Microbes

*Microvolume DNA extraction methods for microscale amplicon and metagenomic studies – Anna R. Bramucci – ISME Communications

Bioinformatics

*LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis – Ezgi Özkurt – bioRxiv

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities – Derek M. Bickhart – Nature Biotechnology



December 16, 2021

Today’s digest features the Global Microbial Gene Catalog, studies on group B Streptococcus vaginal colonization in a murine model and Patescibacteria in oxic and anoxic groundwater, and more. Happy holidays!

Important NEWS from the Microbiome Virtual International Forum:
The recordings of the MVIF #4 with Jonathan Eisen and other speakers are available here.
The registration for the MVIF #5 with Eran Elinav is open.
The abstract submission for the MVIF #6 with Susan Holmes is open.


Global microbiome

*Towards the biogeography of prokaryotic genes – Luis Pedro Coelho – Nature

Review: Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research – Imane Allali – Microbiome


Human milk microbiome

Factors influencing the microbial composition of human milk – Anastasia Mantziaria and Samuli Rautavab – Seminars in Perinatology


Animal experiments

*Group B Streptococcus CAMP Factor Does Not Contribute to Interactions with the Vaginal Epithelium and Is Dispensable for Vaginal Colonization in Mice – Mallory B. Ballard – Microbiology Spectrum

Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing – Jongoh Shin – Microbiome


Water microbiome

*The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers – Narendrakumar M. Chaudhari – Environmental Microbiome


Bioinformatics

EXPERT: Transfer Learning-enabled context-aware microbial source tracking – Hui Chong – bioRxiv
https://www.biorxiv.org/content/10.1101/2021.01.29.428751v2


NEWS from NCBI taxonomy

October 22, 2021

Happy Friday!

Today’s digest includes an article on the role of age in the human intestinal microbiome, research on the role of a novel Acidobacteriota in seafloor sulfur cycling, work demonstrating the use of machine learning to predict camplyobacter source data, and much more! I also included the link to a page on “The Secret World Inside You”, a science exhibit focused on the human microbiome that is at the Witte Museum in San Antonio, Texas from now until April 10, 2022. If anyone ends up checking it out, I’d love to hear about it!

Events

A microbiome science exhibit, “The Secret World Inside You,” is at The Witte Museum in San Antonio, Texas from October 16, 2021 to April 10, 2022 .

Human gut microbiome

Bile acid-independent protection against Clostridioides difficile infection – Aguirre et al. – PLOS PATHOGENS

The importance of age in compositional and functional profiling of the human intestinal microbiome – Herzog et al. – PLOS ONE

Plant, root, and soil microbiome

The chosen few—variations in common and rare soil bacteria across biomes – Bickel & Or – The ISME Journal

The fungus Kalmusia longispora is able to cause vascular necrosis on Vitis vinifera – Karácsony et al. – PLOS ONE

Water and extremophile microbiome

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling – Flieder et al. – The ISME Journal

Beach sand oil spills select for generalist microbial populations – Heritier-Robbins et al. – The ISME Journal

Preprint: Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA – Matsuoka et al. – bioRxiv

Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake – Reboul et al. – The ISME Journal

Phages and viruses

Review: Community context matters for bacteria-phage ecology and evolution – Blazanin & Turner – The ISME Journal

Bioinformatics

Machine learning to predict the source of campylobacteriosis using whole genome data – Arning et al. – PLOS GENETICS

October 12th, 2021

Bonjour from Paris, France ! Today’s digest contains a selection of really interesting preprints and published studies. In their review, Heilbronner and collaborators explore the role of bacteriocins, small antibacterial molecules produced by many commensal bacteria in human-associated microbiomes. The role of the bacteriocins in the human microbiome is of particular importance since they could be leveraged to specifically target colonizing pathogens while sparing mutualistic patners.

If you are interested in exploring new bioinformatic methods, I recommend taking a look at the study from Cheng and collaborators, who applied a novel iterative random forest approach to explore marine microbiome during algal blooms. They show how this model allow to identify conditions that are important causal factors of algal bloom dynamics.

Today’s non-microbiology pick is an opinion piece reflecting on the possible methods to develop the field of computational biology, ensure proper training and career development in this discipline and allow a greater collaboration between domain biologist and data scientists in multidisciplinary teams.

Have a great Tuesday!


Events and jobs

Virtual conference: Harnessing the plant microbiome – October 22-24, 2021
University of California, Davis, USA

Virtual conference: Reshaping the Microbiome through nutrition – November 17-19, 2021


General microbiome

Review: The microbiome-shaping roles of bacteriocins – Heilbronner et al. – Nature Reviews Microbiology

Human gut microbiome

Preprint: Gut Bacterial Dysbiosis and Instability is Associated with the Onset of Complications and Mortality in COVID-19 – Schult et al. – BioRXiv

Review: Nurturing the Early Life Gut Microbiome and Immune Maturation for Long Term Health – Dogra et al. – microorganisms


Animal experiments

Preprint: Mice with a humanized immune system are resilient to transplantation of human microbiota – Zhou et al. – BioRXiv

Animal microbiome

Preprint: Inter-species microbiota transplantation recapitulates microbial acquisition and persistence in mosquitoes – Coon et al. – BioRXiv

Water and extremophile microbiome

A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms – Cheng et al. – Scientific reports

Built environment

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years – Wang et al. – Microbiome


Phages and viruses

Preprint: A Snapshot of the Global Drinking Water Virome: Diversity and Metabolic Potential Vary with Residual Disinfectant Use – Hegarty et al. – BioRXiv

Bioinformatics

Preprint: SynTracker: a synteny based tool for tracking microbial strains – Enav and Ley – BioRXiv


My non-microbiology pick

A field guide to cultivating computational biology – Way et al – PLOS biology

October 8, 2021

Today’s digest features a metagenomic meta-study on faecal microbiota transplantation, RibDif for count and compare 16S rRNA genes within a genus, and more. Also, there is a new FEMS Microbiology Letters collection of articles highlighting the evolution of education during the COVID-19 pandemic.

There is still time to join in the second 🌎 Microbiome Virtual International Forum 🌏. Recordings from previous MVIF can be found here.

And, the #Microber2021 just started! Check out this microbe edition of #Inktober drawing challenge – during October, every day a new scientific art on microbiology topic.


Global microbiome

Cultivating Healthy Connections: Exploring and Engineering the Microbial Flow That Shapes Microbiomes – Travis J. Wiles – mSystems

Neonatal microbiome

Presence of distinctive microbiome in the first-pass meconium of newborn infants – Jenni Turunen – Scientific Reports

Respiratory microbiome

Divergence of bacterial communities in the lower airways of CF patients in early childhood – John B. O’Connor – PlosOne

Gut microbiome

Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation – Thomas Schmidt – bioRxiv

Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis – Vishnu Prasoodanan P. K. – npj Biofilms and Microbiomes

Animal microbiome

Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms – Sara E. Pidcock – Microbial Genomics

Animal experiment

Metabolic modulation of tumours with engineered bacteria for immunotherapy – Fernando P. Canale – Nature

Citrobacter amalonaticus Inhibits the Growth of Citrobacter rodentium in the Gut Lumen – Caroline Mullineaux-Sanders – mBio

Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide – Lesley Hoyles – bioRxiv

Effects of prebiotic oligofructose-enriched inulin on gut-derived uremic toxins and disease progression in rats with adenine-induced chronic kidney disease – Ebru Melekoglu – PlosOne

Plant microbiome

Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria – Claudia Sanchis-López – mSystems

Food

Bacteriocinogenic lactic acid bacteria in the traditional cereal-based beverage Boza: a genomic and functional approach – Luciano Lopes Queiroz – bioRxiv

Bioinformatics

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes – Francisco Zorrilla – Nucleic Acids Research

RibDif: can individual species be differentiated by 16S sequencing? – Mikael Lenz Strube – Bioinformatics Advances

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale – Carlos P Cantalapiedra – Molecular Biology and Evolution

Sequencing DNA with nanopores: Troubles and biases – Clara Delahaye and Jacques Nicolas – PlosOne

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – October 14 (Pacific Live)/15 (Atlantic Reply)

Webinar: EMBARK Fall Webinars – a webinar series focused on AMR research

Microscopy Live! – Geology – an hour of live electron microscopy, guided by the audience – Plymouth Electron Microscopy Centre (October 29)

For more, check out a collection of microbiome events HERE!


Happy #Microber2021, sci-art October!

September 10, 2021

In today’s digest read about a discovery of new Bordetella bronchiseptica-specific temperate and highly abundant siphoviruses that lead to the creation of a new genus Vojvodinavirus, biases in public human microbiome data, infant gut strain persistence, and more. Also, check out a list of upcoming microbiome events. Happy Friday!

Global microbiome

*Public human microbiome data dominated by highly developed countries – Richard J. Abdill – bioRxiv

Gut microbiome

Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization – Jing Lu – npj Biofilms and Microbiomes

Gut microbiota alterations in response to sleep length among African-origin adults – Na Fei – PlosOne

Bioaccumulation of therapeutic drugs by human gut bacteria – Martina Klünemann – Nature

*Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition – Yue Clare Lou – Cell Reports Medicine

Skin microbiome

Cotton and Surgical Face Masks in Community Settings: Bacterial Contamination and Face Mask Hygiene – Lize Delanghe – Frontiers in Medicine

Animal microbiome

The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps? – Chiara Crestani – Microbial Genomics

Viruses and phages

*Are Bordetella bronchiseptica Siphoviruses (Genus Vojvodinavirus) Appropriate for Phage Therapy—Bacterial Allies or Foes? – Aleksandra Petrovic Fabijan – Viruses

Water microbiome

Functional Redundancy in Ocean Microbiomes Controls Trait Stability – Taylor M. Royalty and Andrew D. Steen – bioRxiv

Bioinformatics

SHOOT: phylogenetic gene search and ortholog inference – David Emms and Steven Kelly – bioRxiv

Ultra-resolution Metagenomics: When Enough Is Not Enough – Falk Hildebrand – mSystems

Computational challenges and opportunities in spatially resolved transcriptomic data analysis – Lyla Atta & Jean Fan – Nature Communications

*BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data – Chenhao Li – Plos Computational Biology

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – September 14/16 (Atlantic/Pacific)

Course + Symposium: 2021 ISB Virtual Microbiome Series – October 13-15

Webinar: EMBARK Fall Webinars – a webinar series where invited speakers will be presenting their AMR research and be contrasted to EMBARK members presenting the work performed in the project.

For more, check out a collection of microbiome events HERE!

August 6, 2021

Today’s digest features a detailed temporal profiling of the rhizosphere and endosphere microbiomes of rice plants exposed to different drought durations, a review on microbiome and recurrent urinary tract infections, a new therapeutic strategy for treating pregnancy disorders via modulation of the maternal gut microbiome in mice, and more. Also, check out a collection of microbiome podcasts. Happy Friday!

First, important NEWS:
If you've recently published an Open-Access paper or Green-OA in peer-reviewed journals or a preprint on a publicly available repository, you can SUBMIT it as Open-Access Paper Highlight and present your work to the worldwide audience at the Microbiome Virtual International Forum!
And, today you can join the 2021 NSURP Closing Ceremony or later you can check out the presentations by NSURP students and their summer internship work on microbiology and immunology here!
New studies:

Global microbiome

A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity – Gongchao Jing – mSystems


Gut microbiome

Perspective: Crosstalk between γδ T cells and the microbiota – Pedro H. Papotto – Nature Microbiology

Opinion: Microbiota and sleep: awakening the gut feeling – Paromita Sen – Trends in Molecular Medicine

Structural and quantitative alterations of gut microbiota in experimental small bowel obstruction – Jiali Mo – PlosOne

Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle – Hilary P. Browne – Genome Biology


Urinary microbiome

*Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs – Jonathan Josephs-Spaulding – Frontiers in Cellular and Infection Microbiology


Vaginal microbiome

The association between the vaginal microenvironment and fecundability: a register-based cohort study among Chinese women – X Hong – BJOG


Animal experiments

*Maternal microbiota Bifidobacterium promotes placental vascularization, nutrient transport and fetal growth in mice – Jorge Lopez-Tello – bioRxiv

Early invasion of the bladder wall by solitary bacteria protects UPEC from antibiotics and neutrophil swarms in an organoid model – Kunal Sharma – Cell Reports


Root microbiome

*Prolonged drought imparts lasting compositional changes to the rice root microbiome – Christian Santos-Medellín – Nature Plants


Bioinformatics

COPLA, a taxonomic classifier of plasmids – Santiago Redondo‑Salvo – BMC Bioinformatics

Strainberry: automated strain separation in low-complexity metagenomes using long reads – Riccardo Vicedomini – Nature Communications

STRONG: metagenomics strain resolution on assembly graphs – Christopher Quince – Genome Biology

HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data – Pranvera Hiseni – Microbiome

YouTube Tutorial: How to Critically Evaluate Machine Learning Methods – Thomas P. Quinn


Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – September 14

Hackathon: Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon – Application deadline August 20; Event Dates: Sept. 27-Oct. – The National Institutes of Health (NIH) Office of Data Science Strategy, the National Center for Biotechnology and Information at the National Library of Medicine, and the Department of Energy’s (DOE) Office of Biological and Environmental Research.

Conference: Microbiome Superheroes Connect – September 8 – Australasian Human Microbiome Research Network

Webinar: EMBARK Fall Webinars – a webinar series where invited speakers will be presenting their AMR research and be contrasted to EMBARK members presenting the work performed in the EMBARK project.

For more, check out a collection of microbiome events HERE!

Podcasts

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 – Déborah 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 “Pathogenesis and persistence during Enterococcus faecalis biofilm-associated infection” and Sofia Forslund “High-throughput measurement of host and microbiota” – EMBARK project – June 30


Writing

Writing and Publishing Scientific Papers: A Primer for the Non-English Speaker – Gábor Lövei – 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 – François 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 Cuscó – 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 “International efforts for One Health surveillance of AMR (WHO Tricycle)” and Etienne Ruppé “On 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