November 28, 2020

Greetings from Santiago, Chile! Today, in this brief Digest, we have a preprint with interesting results obtained by the Dutch Microbiome Project. We have as well a couple of papers exploring the relationship between microbiome and COVID-19, and more other papers. Have a nice weekend!

Human and General Microbiome

Preprint: The Dutch Microbiome Project defines factors that shape the healthy gut microbiome – Ranko Gacesa – BioRxiv

Viral Infection-Induced Gut Dysbiosis, Neuroinflammation, and α-Synuclein Aggregation: Updates and Perspectives on COVID-19 and Neurodegenerative Disorders – Cristian Follmer – ACS Chemical Neuroscience

Dual and mutual interaction between microbiota and viral infections: a possible treat for COVID-19 – Taha Baghbani – Microbial Cell Factories

Gut microbiome is more stable in males than in females during the development of colorectal cancer – Haijun Liao – Journal of Applied Microbiology

Expression of toll-like and adhesive receptors on epithelial cells of the oral mucosa in periodontitis – O.A. Lukova – Russian Clinical Laboratory Diagnostics

The Microbiome in Hidradenitis Suppurativa: A Review – Kirsty J. L. Wark – Dermatology and Therapy 

Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes – Meghan H. Shilts – Scientific Reports 

Emotional well-being and gut microbiome profiles by enterotype – Sung-Ha Lee – Scientific Reports 

Vitamin D metabolites and the gut microbiome in older men – Robert L. Thomas – Nature Communications

Animal Microbiome

Reduced rotavirus vaccine efficacy in protein malnourished human-faecal-microbiota-transplanted gnotobiotic pig model is in part attributed to the gut microbiota – V. Srivastava – Beneficial Microbes

Clinical efficacy of spray-based heat-treated lactobacilli in canine atopic dermatitis: a preliminary, open-label, uncontrolled study – Domenico Santoro – Veterinary Dermatology

Extremophiles

Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern – Varun Paul – Scientific Reports 

Microbiome Methods and Analysis

The application potential of machine learning and genomics for understanding natural product diversity, chemistry, and therapeutic translatability – David Prihoda – Natural Product Reports

Other

Efficient protection of microorganisms for delivery to the intestinal tract by cellulose sulphate encapsulation – Walter H. Gunzburg – Microbial Cell Factories

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 19, 2020

Today, in this (late) Digest:  a set of reviews about the role of microbiota in neurodegeneration, psoriasis and stroke; different studies about the microbiome genital/urinary tracts, and microbiome studies in pandas, salmon and pigeons.

Human and General Microbiome

Review: Complex Interaction between Resident Microbiota and Misfolded Proteins: Role in Neuroinflammation and Neurodegeneration – Juliana González-Sanmiguel – Cells (MDPI)

Review: Gut-Brain-Skin Axis in Psoriasis: A Review – Guang Chen – Dermatology and Therapy

Minireview: The Gut Ecosystem: A Critical Player in Stroke – Rosa Delgado Jiménez – NeuroMolecular Medicine

Meta-analysis: A meta-analysis of the effect of binge drinking on the oral microbiome and its relation to Alzheimer’s disease – Ayuni Yussof – Scientific Reports

Associations between Pro- and Anti-Inflammatory Gastro-Intestinal Microbiota, Diet, and Cognitive Functioning in Dutch Healthy Older Adults: The NU-AGE Study – Annick P. M. van Soest – Nutrients (MDPI)

Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery – Marina Muñoz – Microbial Genomics

Exogenous infusion of short-chain fatty acids can improve intestinal functions independently of the gut microbiota – Hua Zhou – Journal of Animal Science

The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study – N. V. Patin – mBio

Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota – Nesreen H Aljahdali – BMC Microbiology

Fusobacterium nucleatum in biopsied tissues from colorectal cancer patients and alcohol consumption in Korea – Myungsook Kim – Scientific Reports

The Gut Microbiome in Polycystic Ovary Syndrome and its Association with Metabolic Traits – Kreete Lüll – The Journal of Clinical Endocrinology & Metabolism

Genito-Urinary Tract Microbiome

The discovery of bacterial biofilm in patients with muscle invasive bladder cancer – Naomi Nadler – APMIS

Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection – Bi Qingqing – Microbial Pathogenesis

Ureteral Stent Microbiota Is Associated with Patient Comorbidities but Not Antibiotic Exposure – Kait F. Al – Cell Reports Medicine

Beneficial Microbes and Compounds

Review: Living Therapeutics: The Next Frontier of Precision Medicine – Vince W. Kelly – ACS Synthetic Biology

Interplay between dietary phenolic compound intake and the human gut microbiome in hypertension: A cross-sectional study – Lorena Calderón-Pérez – Food Chemistry 

Blueberry Consumption Challenges Hepatic Mitochondrial Bioenergetics and Elicits Transcriptomics Reprogramming in Healthy Wistar Rats – Sara Nunes – Pharmaceutics (MDPI)

Lactobacillus reuteri DSM 17938 alleviates d-galactosamine-induced liver failure in rats – Huiyong Jiang – Biomedicine & Pharmacotherapy

Animal Microbiome

Effect of long-term methylene blue treatment on the composition of mouse gut microbiome and its relationship with the cognitive abilities of mice – Artem P. Gureev – PLoS One

Changes in the diversity and composition of gut microbiota in pigeon squabs infected with Trichomonas gallinae – Feng Ji – Scientific Reports

Analysis of the vaginal microbiome of giant pandas using metagenomics sequencing – Lan Zhang – Microbiology Open

Association of gut microbiota with metabolism in juvenile Atlantic salmon – H. Dvergedal – Microbiome 

Food Microbiome

Differentiation of Milk and Whey Protein Concentrates by Microbiome Profiling Using 16S Metagenomics – Christopher M Thompson – Journal of AOAC international

Microbiome analysis methods and tools

Mediation effect selection in high-dimensional and compositional microbiome data – Haixiang Zhang – Statistics in Medicine

Evaluation of Sampling Methods for the Study of Avian Respiratory Microbiota – Michael Edward C. Abundo – Avian Diseases

MHSNMF: multi-view hessian regularization based symmetric nonnegative matrix factorization for microbiome data analysis – Yuanyuan Ma – BMC Bioinformatics

November 12, 2020

Good morning! There’s a really exciting collection of papers to share with you this morning. Among them, a study of gut archaea across multiple host domains, a link between F. nucleatum and esophageal cancer, and two new databases of shotgun metagenomic data. (There’s also a fun paper about environmental transmission of microbes aboard the International Space Station.)

General microbiome

Preprint – Strong influence of vertebrate host phylogeny on gut archaeal diversity, Nicholas D Youngblut et al., bioRxiv

A genomic catalog of Earth’s microbiomes, Stephen Nayfach et al., Nature Biotechnology

Human vaginal microbiome

Review – Vaginal microbiota and the potential of Lactobacillus derivatives in maintaining vaginal health, Wallace Jeng Yang Chee, Microbial Cell Factories

Human gut microbiome

Preprint – Fusobacterium Nucleatum Predicts a Risk for Esophageal Squamous Cell Carcinoma, Chao Shi et al., Research Square

Preprint – Human reference gut microbiome comprising 5,414 prokaryotic species, including newly assembled genomes from under-represented Asian metagenomes, Kim and Lee et al., bioRxiv

Preprint – Genetic Evidence for Selective Transfer of Microbes Between the International Space Station and an Astronaut, David C. Danko et al., bioRxiv

Review: An infectious diseases perspective on the microbiome and allogeneic stem cell transplant, Olivia C. Smibert et al., Current Opinion in Infectious Diseases

Animal experiments

Preprint – Longitudinal effects of antibiotics and fecal transplant on lemur gut microbiota structure, associations, and resistomes, Sally L. Bornbusch et al., bioRxiv

Pinto beans modulate the gut microbiome, augment MHC II protein, and antimicrobial peptide gene expression in mice fed a normal or western-style diet, Babajide A. Ojo et al., Journal of Nutritional Biochemistry

Preprint – Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents of the Zebrafish Gut, Wesley Loftie-Eaton et al., bioRxiv

Animal microbiome

Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys, Anna J. Jasinska et al., Microbiome

A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo, Narat and Amato et al., Scientific Reports

Bioinformatics

Preprint – AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities, Almut Heinken et al., bioRxiv

Techniques

Preprint – Benchmarking DNA isolation kits used in analyses of the urinary microbiome, Lisa Karstens et al., bioRxiv

November 9, 2020

Happy Monday morning from San Francisco, California! Hope everyone had a restful weekend. For those who aren’t quite ready for the working week, how about easing in to things with a warm beverage and some great microbiome reads?

Today’s digest includes two papers that blew my mind. The first is a paper by van Tatenhove-Pel et al. which looks at how cell-to-cell distance in 3D space impacts the metabolic interactions between bacteria. The second, by Nowosad et al., examines the role of the gut microbiota on B cell selection and antibody affinity maturation in gut-associated germinal centers. Other fascinating papers include: a pilot study profiling the gut microbiomes of South Africans in an urban cohort and a transitioning rural cohort which was designed collaboratively with community leaders (Oduaran et al.); a review paper about using brachyuran crabs as a model for studying how animal-microbiome symbioses evolve when aquatic organisms transition to land (Cannicci et al.); and a paper that used shotgun metagenomics to identify current and historical microbiomes in lake sediment which could help our understanding of how humans impact lake ecosystems over time (Garner et al.). Happy reading, y’all!

General Microbiome
Microbial competition reduces metabolic interaction distances to the low µm-range. – van Tatenhove-Pel, R.J. et al., The ISME Journal

Human Respiratory Microbiome
Developmental patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk. – Tang, H.H.F, et al., Journal of Allergy and Clinical Immunology

Human Gut Microbiome
Distinct Fecal and Plasma Metabolites in Children with Autism Spectrum Disorders and Their Modulation after Microbiota Transfer Therapy. – Kang, D-W et al., mSphere

Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes. – Sánchez-Quinto, A. et al., Microorganisms

Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition. – Oduaran, O.H. et al., BMC Microbiology

Maturation of the gut microbiome during the first year of life contributes to the protective farm effect on childhood asthma. – Depber, M. et al., Nature Medicine

Fecal Microbiota Changes in Patients With Postpartum Depressive Disorder. – Zhou, Y. et al., Frontiers in Cellular and Infection Microbiology

Animal Experiments
Tunable dynamics of B cell selection in gut germinal centres. – Nowosad, C.R. et al., Nature

Acute liver failure is regulated by MYC- and microbiome-dependent programs. – Kolodziejczyk, A.A. et al., Nature Medicine

Epithelial TLR4 signaling activates DUOX2 to induce microbiota-driven tumorigenesis. – Burgueño, J.F. et al., Gastroenterology

Gut Microbiome Alters the Activity of Liver Cytochromes P450 in Mice With Sex-Dependent Differences. – Jourová, L. et al., Frontiers in Pharmacology

Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp. – Gálvez, E.J.C. et al., Cell Host & Microbe

FXR in the dorsal vagal complex is sufficient and necessary for upper small intestinal microbiome-mediated changes of TCDCA to alter insulin action in rats. – Zhang, S-Y et al., Gut

Animal Microbiome
Review: To the Land and Beyond: Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization. – Cannicci, S. et al., Frontiers in Microbiology

Insect Microbiome
The direct and indirect effects of environmental toxicants on the health of bumblebees and their microbiomes. – Rothman, J.A. et al., Proceedings of the Royal Society B, Biological Sciences

A Very Hungry Caterpillar: Polyethylene Metabolism and Lipid Homeostasis in Larvae of the Greater Wax Moth ( Galleria mellonella). – LeMoine, C.M. et al., Environmental Science and Technology

Plant, Root, and Soil Microbiome
Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds. – Liao, S. et al., mSystems

Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems. – Allard, S.M. et al., mSystems

Water and Extremophile Microbiome
The water chemistry and microbiome of household wells in Medawachchiya, Sri Lanka, an area with high prevalence of chronic kidney disease of unknown origin (CKDu). McDonough, L.K. et al., Scientific Reports

Sediment Metagenomes as Time Capsules of Lake Microbiomes. – Garner, R.E. et al., mSphere

Built Environment
Bioaerosols in the Athens Metro: Metagenetic insights into the PM 10 microbiome in a naturally ventilated subway station. – Grydaki, N. et al., Environment International

Probiotics
Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions. – Albright, M.B.N. et al., mBio

Microbiological, immunological, and histological changes in the gut of Salmonella Enteritidis-challenged rats fed goat cheese containing Lactobacillus rhamnosus EM1107. – Rolim, F.R.L. et al., Journal of Dairy Science

Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics. – Duar, R.M. et al., Nutrients

Persistence of Suspected Probiotic Organisms in Preterm Infant Gut Microbiota Weeks After Probiotic Supplementation in the NICU. – Yousuf, E.I. et al., Frontiers in Microbiology

Bioinformatics
Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. – Lam, T.J. et al., PLoS Computational Biology

Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes. – Berglund, F. et al., Microbial Genomics

Review: Naught all zeros in sequence count data are the same. – Silverman, J.S. et al., Computational and Structural Biotechnology Journal

Techniques
Microbiomic Analysis on Low Abundant Respiratory Biomass Samples; Improved Recovery of Microbial DNA From Bronchoalveolar Lavage Fluid. – Saladié, M. et al., Frontiers in Microbiology

Jumping the green wall: The use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research. – Víquez-R, L. et al., Ecology and Evolution

November 5, 2020

Hello, friends!

I’m an American who grew up in North Carolina, lived in Georgia for many years, and now counts Pennsylvania as home. All of this is to say, I’ve been especially consumed by the US election this morning and so today’s digest is tailor made to distract me for a few hours. It contains a heavy dose of general microbiome, environmental microbiology, and microbial ecology articles. If you need a bigger distraction than usual, I’ve highlighted a few articles that I am particularly looking forward to reading and am using this space as an opportunity to reintroduce myself and share why these articles have peaked my interest.

I completed my PhD research on the cockroach gut microbiome and through this work, I realized how complex microbiome-host-environmental interactions can be. Because of this, my first highlighted article is a review about cockroach-associated microbes. Currently, I work in a national lab studying environmental-associated microbes (and their functional capacity!) in a variety of different energy-associated environments. It’s no wonder I’m excited to read the second highlighted article focused on novel soil microbes found in an abandoned coal mine! I’m also very hungry at the moment, so as soon I read the phrase “smoked cow cheese” I was motivated to explore my cheese drawer as well as think more about microbial food safety and the microbial production of favor compounds. Finally, I love musical theater and science outreach, so I’m delighted to share a mouldy article that combines both passions.

Happy reading, everyone!


General microbiome

Review: The pneumococcal social network – Aggarawal et al. – PLOS Pathogens

Expanding magnetic organelle biogenesis in the domain Bacteria – Lin et al. – Microbiome

Gene duplication drives genome expansion in a major lineage of Thaumarchaeota – Sheridan et al. – Nature Communications

Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress – Yu et al. – Ecotoxicology

Effects of heavy ion particle irradiation on spore germination of Bacillus spp. from extremely hot and cold environments – Zammuto et al. – Life
Human gut microbiome

Gut microbiome

Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging – Sala et al. – PLOS ONE

Implication of gut microbiota in the physiology of rats intermittently exposed to cold and hypobaric hypoxia – Ramos-Romero et al. – PLOS ONE

Animal microbiome

Exploring the resident gut microbiota of stranded odontocetes: high similarities between two dolphin species Tursiops truncatus and Stenella coeruleoalba – Abdelrhman et al. – Journal of the Marine Biological Association of the UK

**Review: Bacteria associated with cockroaches: health risk or biotechnological opportunity? – Guzman & Vilcinskas – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Impact of land uses, drought, flood, wildfire, and cascading events on water quality and microbial communities: A review and analysis – Mishra et al. – Journal of Hydrology

Dams shift microbial community assembly and imprint nitrogen transformation along the Yangtze River – Gao et al. – Water Research

Built environment

**Isolation and characterization of soil bacteria from an abandoned coal mine in southeast Kansas – Bechtold et al. – BioOne Complete

Review: Understanding building-occupant-microbiome interactions toward healthy built environments – Li et al. – Frontiers of Environmental Science & Engineering

Food microbiology

**Microbial quality of smoked cow cheese “Parencia” – Kačániová et al. – Scientific Papers: Animal Science and Biotechnologies

Phages and viruses

Virome of bat guano from nine northern California roosts – Li et al. – Journal of Virology

Bioinformatics

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities – Chen et al. – Nucleic Acids Research

PhANNs, a fast and accurate tool and web server to classify phage structural proteins – Cantu et al. – PLOS Computational Biology

Techniques

Low-cost biofuel-powered autoclaving machine for use in rural health care centres – Ahmed et al. – Journal of Medical Engineering & Technology

**‘The Mould that Changed the World’: Quantitative and qualitative evaluation of children’s knowledge and motivation for behavioural change following participation in an antimicrobial resistance musical – Hall et al. – PLOS ONE

Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes – McClenaghan et al. – PLOS ONE

November 4, 2020

Some very nice articles in todays digest including a probiotic study in Science Translation Medicine and a non-microbiome pick for dog lovers at the end. Enjoy!

COVID-19 & Vaccines

SARS-CoV-2 viral load is associated with increased disease severity and mortality – Fajnzylber et al. Nature Communications

Gut microbiome

Multi-omics analyses of radiation survivors identify radioprotective microbes and metabolites – Guo et al. Science

Dietary simple sugars alter microbial ecology in the gut and promote colitis in mice – Khan et al. Science Translational Medicine

Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions – Bojar et al. Cell Host & Microbe

Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations – Pruss et al. ISME

Microbiota-Derived Short-Chain Fatty Acids Promote LAMTOR2-Mediated Immune Responses in Macrophages – Wu et al. mSystems

Probiotics

A probiotic yeast-based immunotherapy against Clostridioides difficile infection – Chen et al. Science Translational Medicine

Water and extremophile microbiome

Host specificity of microbiome assembly and its fitness effects in phytoplankton – Jackrel et al. ISME

Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge) – Lecoeuvre et al. ISME

Phages and viruses

Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics – Arbas et al. Nature Microbiology

Bioinformatics

Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons – Wei et al. Bioinformatics

phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes – Gruber-Vodicka et al. mSystems

Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity – Youngblut et al. mSystems

Non-microbiome pick 

Origins and genetic legacy of prehistoric dogs – Berstrom et al. 

November 3, 2020

Greetings Everyone!!

Happy reading of an interesting digest for November 3, 2020.

General microbiome
The perfect condition for the rising of superbugs: person-to-person contagion and antibiotic use are the key factors responsible for the positive correlation between antibiotic resistance gene diversity and virulence gene diversity in human metagenomes -Domingues et al – bioRxiv

Human gut microbiome
Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish – Härer et al – Microbiome

Exploring the resident gut microbiota of stranded odontocetes: high similarities between two dolphin species Tursiops truncatus and Stenella coeruleoalba – Abdelrhman et al – Journal of the Marine Biological Association of the United Kingdom

Animal experiments
Investigating the cow skin and teat canal microbiomes of the bovine udder using different sampling and sequencing approaches – Dean et al – Journal of Dairy Science

Animal microbiome
Review: Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont – Boilard et al – microorganisms

Plant, root, and soil microbiome
Free Iron and Iron-Reducing Microorganisms in Permafrost and Permafrost-Affected Soils of Northeastern Siberia – Rivkina et al – Eurasian

Soil Science
Behaviors of cadmium in rhizosphere soils and its interaction with microbiome communities in phytoremediation – Niu et al – Chemosphere

Water and extremophile microbiome
Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter – Santos-Júnior et al – Microbiome

Microbiome variability across the native and invasive range of the ascidian Clavelina oblonga – Goddard-Dwyer et al – Applied and Environmental Biology

Microbiome of the Black Sea water column analyzed by genome centric metagenomics – Cabello-Yeves et al – bioRxiv

Built environment
Review: Understanding building-occupant-microbiome interactions toward healthy built environments: A review – Li et al – Frontiers of Environmental Science & Engineering

Microbes in space
Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission – Ott et al – Microbiome

Bioinformatics
NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis – Zhang and Yi – BMC Bioinformatics

Techniques
MASI: microbiota—active substance interactions database – Zeng et al – Nucleic Acids Research