December 10, 2020

Good morning from New Jersey! Only a few new research articles to share with you today, but FOUR new reviews on the microbiome’s role in cancers and periodontal disease. And if you’re feeling adventurous, PLOS ONE just published an article on human postmortem decomposition that includes a brief evaluation of the buried corpse microbiome.

Jobs

A new postdoctoral position was just posted at the University of Minnesota for research on new methods of fecal microbiota transplantation.

General microbiome

Review – Unexpected guests in the tumor microenvironment: microbiome in cancer, Abigail Wong-Rolle et al., Protein Cell

Review – Understanding the microbial components of periodontal diseases and periodontal treatment-induced microbiological shifts, Ioannis Fragkioudakis et al., Journal of Medical Microbiology

Human gut microbiome

Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia muciniphila, Kenny C. Mok et al., mBio

Interpretable Machine Learning Framework Reveals Robust Gut Microbiome Features Associated With Type 2 Diabetes, Wanglong Gou et al., Diabetes Care

Gut microbial ecosystem in Parkinson’s disease: New clinico‐biological insights from multi‐omics, Ai Huey Tan et al., Annals of Neurology

Review – Intervention on Gut Microbiota May Change the Strategy for Management of Colorectal Cancer, Sedigheh Taghinezhad‐S et al., Gastroenterology and Hepatology

Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson’s Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder, Hiroshi Nishiwaki et al., mSystems

Animal experiments

Respiratory tissue-associated commensal bacteria offer therapeutic potential against pneumococcal colonization, Soner Yildiz et al., eLife

Effects of Pinus massoniana pollen polysaccharides on intestinal microenvironment and colitis in mice, Niu and Shang et al., Food & Function

A Subset of Roux-en-Y Gastric Bypass Bacterial Consortium Colonizes the Gut of Nonsurgical Rats without Inducing Host-Microbe Metabolic Changes, Zhigang Liu et al., mSystems

Plant, root, and soil microbiome

Preprint – Rapid evolution of bacterial mutualism in the plant rhizosphere, Erqin Li et al., bioRxiv

Review – Coffee Microbiota and Its Potential Use in Sustainable Crop Management, Benoit Duong et al., Frontiers in Sustainable Food Systems

Bioinformatics

Review – Tissue-associated microbial detection in cancer using human sequencing data, Rebecca M. Rodriguez et al., BMC Bioinformatics

Techniques

Preprint – BIOME-Preserve: A Novel Storage and Transport Medium for Preserving Anaerobic Microbiota Samples for Culture Recovery, Embriette R. Hyde et al., bioRxiv

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 Skarżyńska – 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 “Home-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

December 08, 2020

General microbiome

The Microbial Conveyor Belt: Connecting the Globe through Dispersion and Dormancy – Mestre & Höfer – Trends in Microbiology

Microbiomes for All – Muth & Caplan – Frontiers in Microbiology

Human oral microbiome

[REVIEW]The Oral Host–Microbial Interactome: An Ecological Chronometer of Health? – Freire, Nelson & Edlund – Trends in Microbiology

Human vaginal microbiome

Impact of vaginal microbiome communities on HIV antiretroviral-based pre-exposure prophylaxis (PrEP) drug metabolism – Cheu et al. – PLOS Pathogens

Human gut microbiome

The Effect of Probiotics Supplementation on Gut Microbiota After Helicobacter pylori Eradication: A Multicenter Randomized Controlled Trial – Tang et al. – Infectious Diseases and Therapy

Therapeutic potential of natural products against atherosclerosis: Targeting on gut microbiota – Zhao et al. – Pharmacological Research

Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries – Tamura & Brumer – Current Opinion in Structural Biology

Animal microbiome (for animals in the wild)

Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica – Kim, Cho & Lee – Journal of Microbiology

Plant, root, and soil microbiome

Soil texture and properties rather than irrigation water type shape the diversity and composition of soil microbial communities – Obayomi et al. – Applied Soil Ecology

Microbes in space

[BOOK CHAPTER]Antarctic Bacteria as Astrobiological Models – Abbott & Pearce – Extremophiles as Astrobiological Models

Bioinformatics

MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data – Chen et al. – PLOS One

[REVIEW]Measuring the microbiome: best practices for developing and benchmarking microbiomics methods – Bokulich et al. – Computational and Structural Biotechnology Journal

[REVIEW]Seeing the forest for the trees: retrieving plant secondary biochemical pathways from metabolome networks – Desmet et al. – Computational and Structural Biotechnology Journal

Evaluation of Single Sample Network Inference Methods for Metabolomics-Based Systems Medicine – Jahagirdar & Saccenti – Journal of Proteome Research

December 04, 2020

General microbiome

Highly multiplexed spatial mapping of microbial communities – Shi et al. – Nature

Human respiratory microbiome

Comparison of the human microbiome in adults and children with chronic rhinosinusitis – Park et al. – PLOS One

Human gut microbiome/mycobiome

Gut mycobiomes are altered in people with type 2 Diabetes Mellitus and Diabetic Retinopathy – Jayasudha et al. – PLOS One

Mucosa-Associated Microbiota in Patients with Irritable Bowel Syndrome: A Comparison of Subtypes – Matsumoto et al. – Digestion

[REVIEW]The Role of the Gut Microbiota and the Immune System in the Development of Autism – Lungba et al. – Cureus Journal of Medical Science

Animal microbiome

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows – Ekman et al. – PLOS One

Gut microbiota is associated with protection against Marek’s disease virus infection in chickens – Bavananthasivam – Virology

Stingless bees and microbial interactions – de Paula et al. – Current Opinion in Insect Science

Bioinformatics

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis – Hupfauf et al. – PLOS One

December 02, 2020

General microbiome

The Interplay of Sex Steroids, the Immune Response, and the Intestinal Microbiota – Pace & Watnick – Trends in Microbiology

[REVIEW]Circulating 16S RNA in Biofluids: Extracellular Vesicles as Mirrors of Human Microbiome? – Ricci et al. – Int. J. Mol. Sci.

[REVIEW]Microbiota and Obesity: Where Are We Now? – Ballini et al. – Biology

Human vaginal microbiome

Vaginal Microbiome-Based Bacterial Signatures for Predicting the Severity of Cervical Intraepithelial Neoplasia – Lee et al. – Diagnostics

Human gut microbiome

A functional ecological network based on metaproteomics responses of individual gut microbiomes to resistant starches – Li et al. – Computational and Structural Biotechnology Journal

[REVIEW]Personalized Nutrition Through The Gut Microbiota: Current Insights And Future Perspectives – Vandeputte – Nutrion Reviews

[REVIEW]Harnessing the gut microbiota to promote metabolic health – Zmora – Nutrion Reviews

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Cage bedding modifies metabolic and gut microbiota profiles in mouse studies applying dietary restriction – Gregor et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Influence of Environmental Stressors on the Microbiota of Zebra Mussels (Dreissena polymorpha) – Mathai et al. – Invertebrate Microbiology

Gut microbiota protects honey bees (Apis mellifera L.) against polystyrene microplastics exposure risks – Wang et al. – Journal of Hazardous Materials

Plant, root, and soil microbiome

Variable characteristics of microbial communities on the surface of sweet cherries under different storage conditions – Zhang et al. – Postharvest Biology and Technology

Biodiversity of pesticides degrading microbial communities and their environmental impact – Kumar et al. – Biocatalysis and Agricultural Biotechnology

Bioinformatics

[REVIEW]Evaluating and minimizing batch effects in metabolomics – Han & Li – Mass Spectrometry Reviews

November 30, 2020

Hello from Luebeck! Today we selected among others maternal obesity and neurodevelopment, infant growth, breastfeeding and c-section, dental microbiome, gut microbiome and diseases/cancer, a couple of animal and plant microbiome studies. Of particular interest is a study diet and problem solving in a bird species (Parus major).

General microbiome

[REVIEW]The dynamic wound microbiome – Liu et al. – BMC Medicine

[REVIEW]Microbiome and Cervical Cancer – Castanheira et al. – Pathobiology

Pregnancy and early life

[REVIEW]The impact of maternal obesity on childhood neurodevelopment – Tong & Kalish – Journal of Perinatology

Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function – Selma-Royo et al. – Microbiome

Breastfeeding restored the gut microbiota in caesarean section infants and lowered the infection risk in early life – Guo et al. BMC Pediatrics

Human oral microbiome

Dental plaque microbiota profiles of children with caries-free and caries-active dentition – Qudeimat et al. – Journal of Dentistry

[REVIEW]Microbiomics: Were we all wrong before? – Kumar – Periodontology 2000

[REVIEW]Metaproteome and metabolome of oral microbial communities – Bostanci et al. – Periodontology 2000

Human gut microbiome

Gutmicrobiota, immunity and pain – Santoni, Miccini & Batelli – Immunology Letters

The Healthy Microbiome (What is the definition of a healthy gut microbiome?) – Shanahan, Ghosh & O’Toole – Gastroenterology

Altered gut bacterial and metabolic signatures and their interaction in gestational diabetes mellitus – Wang et al. – Gut Microbes

Animal microbiome (for animals in the wild)

Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird – Davidson et al. Scientific Reports

Wild black bears harbor simple gut microbial communities with little difference between the jejunum and colon – Gillman, McKenney & Lafferty – Scientific Reports

Age Patterning in Wild Chimpanzee Gut Microbiota Diversity Reveals Differences from Humans in Early Life – Reese et al. – Current Biology

Plant, root, and soil microbiome

Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream – Piazzon et al. – Microbiome

A comparison of the functional diversity of microbial communities in maize rhizosphere soils in the North West Province of South Africa – Chinenyenwa Fortune Chukwuneme, Ayansina Segun Ayangbenro, Olubukola Oluranti Babalola – Rhizosphere

[REVIEW]Beyond the extremes: Rocks as ultimate refuge for fungi in drylands – Coleine et al. – Mycologia

Bioinformatics

[REVIEW]Emerging computational tools and models for studying gut microbiota composition and function – Park et al. – Current Opinion in Biotechnology

November 27, 2020

Hello from Luebeck!

Today’s digest covers the connection between human diseases and gut microbiome, the gut feeling, secrets about plant growth and vertical stratification in urban spaces. Happy reading and happy black Friday!

General microbiome

Human microbiome and allergy – Montecchiani & Fanos – Pediatric Allergy and Immunology

Early life and childhood

Early Gut Fungal and Bacterial Microbiota and Childhood Growth – Schei et al. – Frontiers in Pediatrics

Oral human microbiome

Characterization of Lactobacilli isolated from carious dentin after selective caries removal and cavity sealing – Damé-Teixeira et al. – Archives of Oral Biology

Human gut microbiome

A Pilot Study: Changes of Intestinal Microbiota of Patients With Non-small Cell Lung Cancer in Response to Osimertinib Therapy – Cong et al. – Frontiers in Microbiology

What connection is there between intestinal microbiota and heart disease? – Poli – European Heart Journal Supplements

The Student-Centered Classroom: The New Gut Feeling – Lyles & Oli – FEMS Microbiology Letters

Animal microbiome

Comparison of the fecal microbiota composition between the blue Sheep (Pseudois nayaur) fed with Lolium perenne and Sorghum sudanense – Wu, Yuan & Pan – Canadian Journal of Microbiology

Plant, root, and soil microbiome

[REVIEW]The plant microbiome: The dark and dirty secrets of plant growth – Tkacz & Poole – Pants People Plant

Water and extremophile microbiome

[PREPRINT]Rapid shift in microbial community structure in a neutral hydrothermal hot spring from Costa Rica – Rojas-Gätjens et al. – bioRxiv

Environment

Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al. – Environmental Health Perspectives

Techniques

Power calculations for detecting differences in efficacy of fecal microbiota donors – Olesen – Contemporary Clinical Trials Communications

November 25, 2020

Human respiratory microbiome

[PREPRINT] Genomic diversity and antimicrobial resistance of Haemophilus colonising the airways of young children with cystic fibrosis – Watts et al. – bioRxiv

Human vaginal microbiome

VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition – France et al. – Microbiome

Human gut microbiome

Diet influences the functions of the human intestinal microbiome – De Angelis et al. – Scientific Reports

Dietary probiotic and metabolites improve intestinal homeostasis and prevent colorectal cancer – Peng et al. – Food & Function

Animal microbiome

The synergistic tumor growth-inhibitory effect of probiotic Lactobacillus on transgenic mouse model of pancreatic cancer treated with gemcitabine – Chen et al. – Scientific Reports

16S rRNA sequence data of Bombyx mori gut bacteriome after spermidine supplementation – Rajan et al. – BMC Research Notes

Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly – Näsvall et al. – Molecular Ecology

Effect of sterilization on the canine vaginal microbiota: a pilot study – Rota et al. – BMC Veterinary Research

Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters – Stothart et al. – Molecular Ecology

Changes in the faecal bacterial microbiota during hospitalisation of horses with colic and the effect of different causes of colic – Stewart et al. – Equine Veterinary Journal

Microbiome‐Metabolomic Analyses of the Impacts of Dietary Stachyose on Fecal Microbiota and Metabolites in Infants Intestinal Microbiota‐associated Mice – Xi et al. – Science of Food and Agriculture

Bioinformatics

MetaGeneHunt for protein domain annotation in short-read metagenomes – Berlemont et al. – Scientific Reports

SuRF: A new method for sparse variable selection, with application in microbiome data analysis – Liu – et al. – Statistics in Medicine

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 epidermidis—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 β-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 WeekBlack 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 Gapševičius – 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 Célia Souque

November 14, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find great papers, in particular in soil and water microbiology but also in bioinformatics! As an example, Mara and collaborators are exploring the viruses found in the oxygen-deficient water column of the Cariaco basin. Interestingly, a large diversity of viral Auxilliary Metabolic Genes (AMGs) were found and give new insights in how phages may interact with their bacterial hosts in this understudied ecosystem.

In the bioinformatics section, I recommend anyone interested in phage metagenomics to take a look at the paper from Ren and collaborators. The authors have developed a reference-free and alignment-free deep learning tool, called DeepVirFinder, allowing the retrieval of viral sequences in metagenomes.

Today’s non-microbiology digest is a paper announcing the last update of the Genome Online Database (GOLD), a manually curated collection of genome projects and their metadata from around the world, which now contains more than a million entries! Great news for bioinformaticians!

Have a great Saturday!


Human gut microbiome

The bacterial association with oral cavity and intra-abdominal abscess after gastrectomy – Nishikawa et al. – PlosOne


Animal microbiome

Loss of symbiont infectivity following thermal stress can be a factor limiting recovery from bleaching in cnidarians – Kishimoto et al. – ISME Journal

Plant, root, and soil microbiome

A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases – Tian et al. – ISME Journal

Air microbiome

Spatio-temporal variations in bacterial and fungal community associated with dust aerosol in Kuwait – Al Salameen et al. – PlosOne

Water and extremophile microbiome

Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system – Huber et al. – ISME Journal

A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities – Kraemer et al. – ISME Journal

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline – Mara et al. – ISME Journal


Phages and Viruses

Metagenomic Analysis of the Enteric RNA Virome ofInfants from the Oukasie Clinic, North West Province,South Africa, Reveals Diverse Eukaryotic Viruses – Mogotsi et al. – Viruses

Bioinformatics

Identifying viruses from metagenomic data using deep learning – Ren et al. – Quantitative Biology

Review: Reconstructing organisms in silico: genome-scale models and their emerging applications – Fang et al. – Nature Reviews Microbiology

Zero-Inflated gaussian mixed models for analyzing longitudinal microbiome data – Zhang et al. – PlosOne

Evaluating the number of different genomes in a metagenome by means of the compositional spectra approach – Kirzhner et al. – PlosOne

Survey of metaproteomics software tools for functional microbiome analysis – Sajulga et al. – PlosOne

Techniques

Sample pooling methods for efficient pathogen screening: Practical implications – Furstenau et al. – PlosOne


My non-microbiology picks

Genomes OnLine Database (GOLD) v.8: overview and updates – Mukherjee et al. – Nucleic Acids Research