June 13, 2022

Today’s digest features metagenomics for clinical UTI diagnostics, microbial diversity in kombucha tea, microbial source tracking using single nucleotide variants, and more. Happy reading!

Neonatal microbiome

Editorial: More data needed on neonatal microbiome seeding – W. Florian Fricke & Jacques Ravel – Microbiome

Urinary microbiome

The Urobiomes of Adult Women With Various Lower Urinary Tract Symptoms Status Differ: A Re-Analysis – Cara Joyce – Frontiers in Cellular and Infection Microbiology

*Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study – Victoria A Janes – The Lancet Microbe

Gut microbiome

Perspective: Tiny Gatekeepers: Microbial Control of Host Drug Transporters – Than S. Kyaw and Peter J. Turnbaugh – Clinical Pharmacology & Therapeutics

Host hepatic metabolism is modulated by gut microbiota-derived sphingolipids – Henry H. Le – Cell Host & Microbe

Linking gastrointestinal microbiota and metabolome dynamics to clinical outcomes in paediatric haematopoietic stem cell transplantation – Gintare Vaitkute – Microbiome

Animal microbiome

Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis – Vittorio Boscaro – Nature Microbiology

Water microbiome

Cyanopeptides restriction and degradation co-mediate microbiota assembly during a freshwater cyanobacterial harmful algal bloom (CyanoHAB) – Han Gao – Water Research

Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster – Irmarie Cotto – bioRxiv

Soil microbiome

Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies – Ying Wang – Frontiers in Microbiology

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra – Igor S. Pessi – bioRxiv

Food

*Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations – Elizabeth A. Landis – mSystems

Spontaneous Riboflavin-Overproducing Limosilactobacillus reuteri for Biofortification of Fermented Foods – Irina Spacova, Sarah Ahannach – Frontiers in Nutrition

Bioinformatics

coda4microbiome: compositional data analysis for microbiome studies – M.Luz Calle & Antoni Susin – bioRxiv

GeneToList: A web application to assist with gene identifiers for the non-bioinformatics-savvy scientist – Joshua D. Breidenbach – bioRxiv

*Microbiome source tracking using single nucleotide variants – Leah Briscoe – bioRxiv

May 5, 2022

Today’s digest features a review on the role of bacterial translocation (especially oral-gut axis) in health and disease, a proof-of-concept study on probiotics on processing of negative emotions in humans, and more. Happy reading!

Let’s talk microbiome science at the next #MVIF!

Sterile (?) environment

Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis – HanChen Wang – Scientific Reports

Probiotics

Lactobacillus acidophilus, L. plantarum, L. rhamnosus, and L. reuteri Cell-Free Supernatants Inhibit Candida parapsilosis Pathogenic Potential upon Infection of Vaginal Epithelial Cells Monolayer and in a Transwell Coculture System In Vitro – Luca Spaggiari – Microbiology Spectrum

*Probiotic Mixture Containing Lactobacillus helveticus, Bifidobacterium longum and Lactiplantibacillus plantarum Affects Brain Responses Toward an Emotional Task in Healthy Subjects: A Randomized Clinical Trial – Julia Rode – Frontiers in Nutrition

Vaginal microbiome

Identification and characterization of novel endolysins targeting Gardnerella vaginalis biofilms to treat bacterial vaginosis – Sara Arroyo-Moreno – npj Biofilms and Microbiomes

Gut microbiome

*Review: Deciphering mechanisms and implications of bacterial translocation in human health and disease – Shen Jin – Current Opinion in Microbiology

Two Competing Guilds as a Core Microbiome Signature for Chronic Diseases – Guojun Wu – bioRxiv

Neonatal Immune Challenge influences the Microbiota and Behaviour in a Sexually Dimorphic Manner – A. Cuskelly – Brain, Behavior, and Immunity

Review: Diet- and microbiota-related metabolite, 5-aminovaleric acid betaine (5-AVAB), in health and disease – Retu Haikonen – Trends in Endocrinology & Metabolism

Gut mycobiome

Review: “Molding” immunity—modulation of mucosal and systemic immunity by the intestinal mycobiome in health and disease – Mackenzie W. Gutierrez – Nature Mucosal Immunology

Animal experiments

Evolution of the murine gut resistome following broad-spectrum antibiotic treatment – Laura de Nies – Nature Communications & Behind the paper here.

Plant, root/soil microbiome

*Sugars dominate the seagrass rhizosphere – E. Maggie Sogin – Nature Ecology & Evolution

Viruses

A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use – Bridget Hegarty – Water Research

Techniques

Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification – Charlotte C. van de Velde – ISME Communications

Bioinformatics

A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments – Shaojun Pan – Nature Communications

HiFine: integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs – Yuxuan Du and Fengzhu Sun – Bioinformatics

happi: a Hierarchical Approach to Pangenomics Inference – Pauline Trinh – bioRxiv

Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome – Rebecca H. Smit – bioRxiv

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles – Varuni Sarwal – bioRxiv

April 6, 2022

Today’s digest features studies on microbial genes of unknown function, oral microbiome of smokeless tobacco consumers, non-industrialized infant microbiome, and more news. Happy reading!

Microbiome Forum FOR EVERYONE
Each event is replicated shortly thereafter to reach a global audience.
ALL microbiome research & career levels welcome
!
Free registration.

Global microbiome

Global Distribution of mcr Gene Variants in 214K Metagenomic Samples – Hannah-Marie Martiny – mSystems

Symposium Review: After the storm—Perspectives on the taxonomy of Lactobacillaceae – Nanzhen Qiao – JDS Communications

Oral microbiome

Assessing the Effect of Smokeless Tobacco Consumption on Oral Microbiome in Healthy and Oral Cancer Patients – Rituja Saxena – Frontiers in Cellular and Infection Microbiology

Gut microbiome

Unravelling specific diet and gut microbial contributions to inflammatory bowel disease – Gabriel Vasconcelos Pereira – bioRxiv

Effects of caloric restriction on the gut microbiome are linked with immune senescence – Julia Sbierski-Kind – Microbiome

Tap water as a natural vehicle for microorganisms shaping the human gut microbiome – Gabriele Andrea Lugli – Environmental Microbiology

Review: Diet-gut microbiota interactions on cardiovascular disease – Xufei Zhang and Philippe Gérard – Computational and Structural Biotechnology Journal

*Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles – Matthew R Olm – bioRxiv

Animal microbiome

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Yunyan Zhou – Microbiome

Animal experiment

Modulation of the gut microbiome by novel synthetic glycans for the production of propionate and the reduction of cardiometabolic risk factors – Yves A Millet – bioRxiv

Plant microbiome

The phyllosphere microbiome shifts toward combating melanose pathogen – Pu-Dong Li – Microbiome

Wastewater microbiome

Near-neutral pH increased n-caprylate production in a microbiome with product inhibition of methanogenesis – Rodolfo Palomo-Briones – bioRxiv

Techniques

Review: Next-generation sequencing: insights to advance clinical investigations of the microbiome – Caroline R. Wensel – The Journal of Clinical Investigations

Metagenomics-enabled microbial surveillance – Karrie K. K. Ko – Nature Microbiology

Bioinformatics

Software testing in microbial bioinformatics: a call to action – Boas C.L. van der Putten – Microbial Genomics

Review: Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation – Alban Mathieu – Frontiers in Microbiology

*Unifying the known and unknown microbial coding sequence space – Chiara Vanni – eLife

NSURP is a community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the Microbiology, Immunology, and Cancer Biology Sciences.

March 7, 2022

hard to do science

Originally tweeted by Peter Fabian (@PeterFabianLab) on March 4, 2022.


General microbiome

Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves – Philippe Piccardi – bioRxiv

Could a Focus on the “Why” of Taxonomy Help Taxonomy Better Respond to the Needs of Science and Society? – Leighton Pritchard – Preprints

Vaginal microbiome

Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation – Seth M. Bloom – Nature Microbiology

Citizen-science map of the vaginal microbiome – Sarah Lebeer – Research Square

Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data – Michael T France – Genome Biology

Urinary microbiome

Review: The gut, vaginal, and urine microbiome in overactive bladder: a systematic review – Christina Sze – International Urogynecology Journal

Gut microbiome

Identification of antimicrobial peptides from the human gut microbiome using deep learning – Yue Ma – Nature Biotechnology

Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders – Amira Metwaly – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Temporal variations shape the gut microbiome ecology of the moth Brithys crini – Jesús Marín-Miret – Environmental Microbiology

Bioinformatics

Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research – Braden T. Tierney – PlosBiology

MultiBaC: An R package to remove batch effects in multi-omic experiments – Manuel Ugidos – Bioinformatics

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps – Yuxuan Du & Fengzhu Sun – Genome Biology


TOMORROW MVIF #7 and the latest microbiome science!

Hey #microbiome people! 🦠
In MARCH there is #MVIF #7!

You can register for free here:
https://hopin.com/events/microbiome-vif-n-7

⭐️Keynote Speaker: prof Willem De Vos ⭐️

📅Check out day and time in your city here:
https://www.microbiome-vif.org/program/

See you there! 😎

Originally tweeted by Microbiome Virtual International Forum (@MicrobiomeVIF) on February 17, 2022.

February 4, 2022

Today’s digest is super diverse (read cool!): novel genes from uncultivated prokaryotes, a new Latilactobacillus species isolated from leaves of a strawberry plant (read the full 🍓 story behind the paper!), the benchmarking study of taxonomic profilers for long-read shotgun metagenomic datasets, and more. The first Issue of a new international peer-reviewed, open access, microbiome-oriented journal – the Microbiome Research Reports – is out with one original article, one perspective and four reviews.
And, a bit of shameless self-promotion, check out my preprint on urinary microbiome of healthy European women!
Happy Friday!

Global microbiome

*Functional and evolutionary significance of unknown genes from uncultivated taxa – Alvaro Rodríguez – bioRxiv

Ear microbiome

The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes – Maria Burton – PlosOne

Respiratory microbiome

Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer – Lisa Derosa – Nature Medicine

Associations and recovery dynamics of the nasopharyngeal microbiota during influenza‑like illness in the aging population – Sudarshan A. Shetty – Scientific Reports

Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways – Kasey A. Webb – Microbial Genomics

Gut microbiome

Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project – Esteban A. Lopera-Maya – Nature Genetics


The gut bacterial community potentiates Clostridioides difficile infection severity – Nicholas A Lesniak – bioRxiv

Emergent evolutionary forces in spatial models of microbial growth in the human gut microbiota – Olivia M. Ghosh and Benjamin H. Good – bioRxiv

Review: Microbiome-based therapeutics – Matthew T. Sorbara and Eric G. Pamer – Nature Reviews Microbiology

Review: Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota –Anna E. Lindell – Nature Reviews Microbiology

Review: Gut microbiome and health: mechanistic insights – Willem M de Vos – Gut

Vaginal microbiome

Gardnerella vaginalis induces matrix metalloproteinases in the cervicovaginal epithelium through TLR-2 activation – Kristin D. Gerson – American Journal of Obstetrics & Gynecology/SMFM 42nd Annual Meeting: The Pregnancy Meeting

Urinary microbiome

*Extended bacterial diversity of the urinary microbiome of reproductive-age healthy European women captured by culturomics and long-read amplicon sequencing – Svetlana Ugarcina Perovic – bioRxiv


Phylogenetic analysis and antimicrobial susceptibility profile of uropathogens – Hanif Ullah – PlosOne

Multidrug-resistant Uro-associated Escherichia coli Populations and Recurrent Urinary Tract Infections in Patients Performing Clean Intermittent Self-catheterisation – Catherine Mowbray – European Urology Open Science

Plant microbiome

*Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa) – Marie Legein – International Journal of Systematic and Evolutionary Microbiology

Ecology and potential functions of plant-associated microbial communities in cold environments – Malek Marian – FEMS Microbiology Ecology

Animal microbiome

Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides – Lucelia Cabral – Nature Communications

Review: Pesticide-induced disturbances of bee gut microbiotas – Michelle Z Hotchkiss – FEMS Microbiology Reviews

Animal experiments

Effect of a freeze-dried coffee solution in a high-fat diet-induced obesity model in rats: Impact on inflammatory response, lipid profile, and gut microbiota – Marilia Hermes Cavalcanti – PlosOne

Gut microbiota and butyrate contribute to nonalcoholic fatty liver disease in premenopause due to estrogen deficiency – Limin Liu – PlosOne

Techniques

BIOME-Preserve: A novel storage and transport medium for preserving anaerobic microbiota samples for culture recovery – Embriette R. Hyde – PlosOne

Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions – Samuel Bellais – Microbiome

Bioinformatics

*Evaluation of taxonomic profiling methods for long-read shotgun metagenomic sequencing datasets – Daniel M Portik – bioRxiv

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite – Giorgos Skoufos – Genome Biology

McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems – André Bogdanowski – Plos Computational Biology

VeChat: Correcting errors in long reads using variation graphs – Xiao Luo – bioRxiv

ReadBouncer: Precise and Scalable Adaptive Sampling for Nanopore Sequencing – Jens-Uwe Ulrich – bioRxiv


📻

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

November 12, 2021

Today’s digest features the study on the Amazon River microbiome, Spanish gut microbiome, review on nanopore sequencing, 16S rRNA metabarcoding study to characterize the responses of the active gut microbiome of fathead minnows to exposure with a model contaminant (benzo[a]pyrene), and more. Happy Friday!

Lung microbiome

Review: The composition of lung microbiome in lung cancer: a systematic review and meta-analysis – Sadaf Najafi – BMC Microbiology

Skin microbiome

Charting host-microbe co-metabolism in skin aging and application to metagenomics data – Wynand Alkema – PlosOne

Gut microbiome

*The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet – Adriel Latorre-Pérez – Scientific Reports

Autism-related dietary preferences mediate autism-gut microbiome associations – Chloe X. Yap – Cell

Animal microbiome

*16S rRNA metabarcoding unearths responses of rare gut microbiome of fathead minnows exposed to benzo[a]pyrene – Abigail DeBofsky – Science of The Total Environment

Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs – Morag Clinton – BMC Microbiology

Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing – Xiaofen Hu – BMC Microbiology

Animal experiment

The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model – Eldin Jašarević – Nature Communications

Polyamine metabolism links gut microbiota and testicular dysfunction – Qi Zhao – Microbiome

A fiber-deprived diet causes cognitive impairment and hippocampal microglia-mediated synaptic loss through the gut microbiota and metabolites – Hongli Shi – Microbiome

Water microbiome

*Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters – Célio Dias Santos-Júnior – Molecular Ecology

Bioinformatics

*Review: Nanopore sequencing technology, bioinformatics and applications – Yunhao Wang – Nature Biotechnology

mBodyMap: a curated database for microbes across human body and their associations with health and diseases – Hanbo Jin – Nucleic Acids Research

Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper – Alexander G McFarland – Bioinformatics

OptiFit: an improved method for fitting amplicon sequences to existing OTUs – Kelly L Sovacool – bioRxiv

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!