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 26, 2020

Greetings from Pittsburgh!

Today’s digest is heavy on environmental microbiology work, especially plant, root, and soil microbiome studies. I also want to highlight a fun research paper (and paired Wired article) on the microbiome of da Vinci’s drawings.

Happy reading! And for all of those in the U.S. who are celebrating the Thanksgiving holiday, please be safe and follow all local COVID precautions.


Multi-site human microbiome

Mycobiome changes in the vitreous of post fever retinitis patients – Arunasri et al. – PLOS ONE

Review: Metabolomics analysis of microbiota-gut-brain axis in neurodegenerative and psychiatric diseases – Konjevod et al. – Journal of Pharmaceutical and Biomedical Analysis

Animal experiments

Cerumen microbial community shifts between healthy and otitis affected dogs – Borriello et al. – PLOS ONE

Plant, root, and soil microbiome

The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil types – Evdokimova et al. – PLOS ONE

Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata – Ihua et al. – PLOS ONE

High nitrogen concentration alter microbial community in Allium fistulosum rhizosphere – Zhao et al. – PLOS ONE

Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale – Zhuang et al. – npj Biofilms and Microbiomes

Water and extremophile microbiome

Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient – Euler et al. – PLOS ONE

Built environment

**The microbiome of Leonardo da Vinci’s drawings: A bio-archive of their history – Piñar et al. – Frontiers in Microbiology

Microbes in the news

**Meet the microbes living on Da Vinci’s iconic sketches – Simon – Wired

Science, publishing, and career

Postdocs under pressure: ‘Can I even do this any more?’ – Woolston – Nature

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 24, 2020

Good morning from Western New York! Today’s publication features more interesting associations of the gut microbiome with disease states including Acute Gastritis, Parkinson’s Disease and Stroke. There are 2 other links involving gut dysbiosis playing roles in the development of COPD. Finally, albeit on a bit of a tangential line, I have included an interesting article from the Journal of Cosmology on The Seeding of Life In The Solar System. Enjoy reading and have a great day!

COVID-19

Utilizing microbiome approaches to assist source tracking, treatment and prevention of COVID-19: Review and Assessment -M Han, et al. – Computational and Structural Biotechnology Journal

Severe COVID-19, multisystem inflammatory syndrome in children, and Kawasaki disease: immunological mechanisms, clinical manifestations and management – J Kabeerdoss, et al. – Rheumatology International

Preprint: Universally available herbal teas based on sage and perilla elicit potent antiviral activity against SARS-CoV-2 in vitro– Vu Thuy Khanh Le-Trilling, et al. – bioRxiv

ORAL MICROBIOME

Amoebae in Chronic, Polymicrobial Endodontic Infections Are Associated with Altered Microbial Communities of Increased Virulence – G Koller, et al. – Journal of Clinical Medicine

APPLIED MICROBIOLOGY

Biological approaches practised using genetically engineered microbes for a sustainable environment: A review – G Pant, et al. – Journal of Hazardous Materials

HUMAN GUT MICROBIOME

Autoimmune Gastritis and Gastric Microbiota – L Conti, et al. – Microorganisms

Preprint: Alterations and Association of Fecal Microbiota and Amino Acids in Parkinson’s Patients– Z Yan, et al. – Research Square

The Gut Ecosystem: A Critical Player in Stroke-RD Jiménez, C Benakis – NeuroMolecular Medicine

HUMAN RESPIRATORY MICROBIOME

News Article: Gut-lung axis: Intestinal microbiome and metabolite changes may be linked to COPD, reveals studyFirstpost

News Article:COPD: What role does the microbiome play? Medical News Today

ANIMAL EXPERIMENTS

Perfluorooctanoic acid-induced liver injury is potentially associated with gut microbiota dysbiosis– G Wang, et al. – Chemosphere

MICROBIAL ECOLOGY

The Life Hidden Inside Caves: Ecological and Economic Importance of Bat Guano– S Sakoui, et al. – International Journal of Ecology

WATER AND EXTREMOPHILE MICROBIOME

Harnessing the Genetic Diversity and Metabolic Potential of Extremophilic Microorganisms through the Integration of Metagenomics and Single-Cell Genomics– D Goyal, et al. – Extremophilic Microbes and Metabolites-Diversity …

BUILT ENVIRONMENT

Critical Review: Propensity of Premise Plumbing Pipe Materials to Enhance or Diminish Growth of Legionella and Other Opportunistic Pathogens – AC Cullom, et al. – Pathogens

MICROBES IN SPACE

Seeding the Solar System with Life: Earth, Venus, Mars, Moon, Protoplanets – R Joseph, et al. – Journal of Cosmology

PHAGES AND VIRUSES

Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation– LA Draper, et al. – BMC Biology

TECHNIQUES

Review: Role of the CRISPR Technique in Decoding the Principles of Quorum Sensing – M Salaria, et al. – Quorum Sensing : Microbial Rules of Life

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 17, 2020

Multi-site human microbiome

Microbiome diversity predicts surgical success in patients with rectovaginal fistula – Leach et al. – International Urogynecology Journal

Human oral microbiome

[REVIEW]Oral Microbiota and Cancer Development – Tuominen & Rautava – Pathobiology

Human vaginal/pregnancy microbiome

Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Feehily et al. – npj biofilms and microbiomes

Human gut microbiome

[REVIEW]IBDs and the pediatric age: Their peculiarities and the involvement of the microbiota – Cococcioni et al. – Digestive and Liver Disease

Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers – Byrd et al. – JEM

Species-dependent variation of the gut bacterial communities across Trypanosoma cruzi insect vectors – Arias-Giraldo – PLOS One

Gut Microbiota and Cancer Correlates – Malaviya et al. – Probiotic Research in Therapeutics

Short-Chain Fatty Acids and Lipopolysaccharide as Mediators Between Gut Dysbiosis and Amyloid Pathology in Alzheimer’s Disease – Marizzoni et al. – Journal of Alzheimer’s Disease

Built environment (subways, indoor surfaces)
Unravelling the importance of the eukaryotic and bacterial communities and their relationship with Legionella spp. ecology in cooling towers: a complex network – Paranjape et al. – Microbiome

Techniques
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities – Kleiner et al. – Microbiome

[REVIEW]NMR: Unique Strengths That Enhance Modern Metabolomics Research – Edison et al. – Analytical Chemistry

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Study offers “indisputable” link between Alzheimer’s and gut microbiome – Lavars – New Atlas

November 15, 2020

We’ve got a short digest for you all today. In particular, I’d recommend checking out Glowacki and Martens who’ve written a nice review of the polysaccharide utilization loci observed in bacterial members of the human microbiome (with a special emphasis on Bacteroides). Mhuireach, Wilson, and Johnson’s recent paper on the urban aerobiome is a nice contribution to growing recognition that we need to begin considering our environmental microbiome, not just those microbiota residing on or within us.

General microbiome
Do seasonal microbiome changes affect infection susceptibility, contributing to seasonal disease outbreaks? – Stencel 2020 – BioEssays

Human skin microbiome
Infant skin bacterial communities vary by skin site and infant age across populations in Mexico and the United States – Manus et al. 2020 – mSystems

Human vaginal microbiome
Identification of vaginal microbial communities associated with extreme cervical shortening in pregnant women – Di Paola et a. 2020 – Journal of Clinical Medicine

Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species – Li and Ma 2020 – Computational and Structural Biotechnology Journal

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid – Brandt and Barrangou 2020 – BMC Microbiology

Human gut microbiome
Gut microbiota and metabolic health among overweight and obese individuals – Kim et al. 2020 – Scientific Reports

Developmental differences in the intestinal microbiota of Chinese 1-year-old infants and 4-year-old children – Guo et al. 2020 – Scientific Reports

If you eat it, or secrete it, they will grow: the expanding list of nutrients utilized by human gut bacteria – Glowacki and Martens 2020 – Journal of Bacteriology

Plant, root, and soil microbiome
No apparent effect of invasive alien goldenrod on soil microbial communities or soil fauna feeding activity – Klimek et al. 2020 – Acta Oecologica

The role of secretion systems, effectors, and secondary metabolites of beneficial rhizobacteria in interactions with plants and microbes – Lucke, Correa, and Levy 2020 – Frontiers in Plant Science

Water and extremophile microbiome
Chemical profiling provides insights into the metabolic machinery of hydrocarbon-degrading deep-sea microbes – Moreno-Ulloa et al. 2020 – mSystems

Built environment
Urban aerobiomes are influenced by season, vegetation, and individual site characteristics – Mhuireach, Wilson, and Johnson 2020 – EcoHealth

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