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 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

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. 

October 16, 2020

In today’s digest read about how food additives affect the intestinal microbiota and induce intestinal inflammation, the role of the gut microbiome in honey bee nestmate recognition, how to use gene-level analysis to identify microbial “genome islands” associated with human health, and more. Check out the list of audiobooks about microbes. Happy Friday!

General microbiome

Time as a microbial resource – Karen G. Lloyd – Environmental Microbiology Reports

Review: The Central Role of Interbacterial Antagonism in Bacterial Life – S. Brook Peterson – Current Biology

Gut microbiome

*Dietary Emulsifiers Directly Impact Adherent-Invasive E. coli Gene Expression to Drive Chronic Intestinal Inflammation – Emilie Viennois – Cell Reports

Microbial Strain Engraftment, Persistence and Replacement after Fecal Microbiota Transplantation – Daniel Podlesny – medRxiv

Characterization of presumptive vancomycin-resistant enterococci recovered during infection control surveillance in Dallas, Texas – Sara Ping – bioRxiv

Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria – Samir Giri – bioRxiv

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria – Mathilde Lebas – Microorganisms

A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within Vibrio cholerae infected patients – Inès Levade – bioRxiv

Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial – Anne-Sophie Alvarez – Scientific Reports

Skin microbiome

Microbial and transcriptional differences elucidate atopic dermatitis heterogeneity across skin sites – Noora Ottman – Allergy

Respiratory microbiome

Multicenter analysis of sputum microbiota in tuberculosis patients – Claudia Sala – PlosOne

Lacticaseibacillus casei AMBR2 modulates the epithelial barrier function and immune response in a donor-derived nasal microbiota manner – Charlotte De Rudder – Scientific Reports

Animal microbiome

*The gut microbiome defines social group membership in honey bee colonies – Cassondra L. Vernier – Science Advances

Early-life gut dysbiosis linked to juvenile mortality in ostriches – Elin Videvall – Microbiome

Animal experiment

The Immune System Fails to Mount a Protective Response to Gram-Positive or Gram-Negative Bacterial Prostatitis – Federico Lupo – Journal of Immunology

The aging mouse microbiome has obesogenic characteristics – Dana Binyamin – Genome Medicine

Tetracycline Antibiotics Induce Host-Dependent Disease Tolerance to Infection – Henrique G. Colaço – Immunity

Water microbiome

Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks – Isabel Douterelo – Water Research

Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria – Ekaterina Y. Gottshall – bioRxiv

Viruses and phages

Culturing novel and abundant pelagiphages in the ocean – Zefeng Zhang – Environmental Microbiology

High-throughput mapping of the phage resistance landscape in E. coli – Vivek K. Mutalik – PlosBiology

Fungi

Minireview: Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance – Brianna Ball – mBio

Technique

Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment – Andrea Sajuthi – bioRxiv

Bioinformatics

*Gene-level metagenomics identifies genome islands associated with immunotherapy response – Samuel S Minot – bioRxiv

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom – Keith Mitchell – Frontiers in Microbiology

Raman2imzML converts Raman imaging data into the standard mass spectrometry imaging format – Stefania Alexandra Iakab – BMC Bioinformatics

Scientific writing

Eight problems with literature reviews and how to fix them – Neal R. Haddaway – Nature Ecology & Evolution

Scientific art

Inktober2020 #PathogenPortraits by Dr Eliza Wolfson

Citizen science

The Human Diets & Microbiome Initiative in the US (THDMI): A unique opportunity to become a citizen scientist. Join for FREE to uncover the secret of the gut microbiome.

Books

11 Audiobooks About Microbes – Justine Dees – Joyful Microbe

October 8, 2020

Greetings!!
Congratulations to the Nobel prize winners in Chemistry : Emmanuelle Charpentier and Jennifer A. Doudna for the discovery of “Genetic scissors: a tool for rewriting the code of life- the CRISPR/Cas9 genetic scissors.” Today’s brief digest covers a wide range of articles on early life microbiome to respiratory microbiome. Happy reading!!!

General microbiome
Electrochemical Investigation of Thiobacillus denitrificans in a Bacterial Composite – Abada et al – Journal of the Electrochemical Society

Pregnancy and early life
Review: Can we prevent allergic disease? Understanding the links between the early life microbiome and allergic diseases of childhood – Petersen and Turvey – Current Opinion in Pediatrics

Multi-site human microbiome
Nutritional Targeting of the Microbiome as Potential Therapy for Malnutrition and Chronic Inflammation – Schröder et al – Nutrients

Human respiratory microbiome
Airway bacterial and fungal microbiome in chronic obstructive pulmonary disease – Liu et al – bioRxiv

Human gut microbiome
Review: Mechanistic insight into the gut microbiome and its interaction with host immunity and inflammation – Xue et al – Animal Nutrition

Ethanol extract of Centella asiatica alleviated dextran sulfate sodium-induced colitis via restoration on mucosa barrier and gut microbiota homeostasis – Li et al – Journal of Ethnopharmacology

Development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communities: SalmoSim – Kazlauskaite et al – bioRxiv

Time-dependent modulation of gut microbiome in response to systemic antifungal agents – Udawatte et al – bioRxiv

Animal microbiome
North American fireflies host low bacterial diversity – Green et al – bioRxiv

Plant, root, and soil microbiome
Anthropogenic Invasion of Micromycetes to Undisturbed Ecosystems of the Larsemann Hills Oasis (East Antarctica) – Vlasov et al – Russian Journal of Biological Invasions

Larch or Mongolian pine? Effects of tree species on soil properties and microbial biomass with the consideration of afforestation time – Teng et al – Ecological Engineering

Water and extremophile microbiome
Understanding the microbial trends in a nitritation reactor fed with primary settled municipal wastewater – Pedrouso et al – Separation and Purification Technology

Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea – Chen et al – Science of The Total Environment

Microbial community structure in the river sediments from upstream of Guanting Reservoir: potential impacts of reclaimed water recharge – Xie et al – Science of The Total Environment

Food microbiology
Next-generation sequencing to enhance the taxonomic resolution of the microbiological analysis of meat and meat-derived products – Reckem et al – Current Opinion in Food Science

Techniques
CRISPR/Cas12a mediated genome engineering in photosynthetic bacteria – Zhang et al – bioRxiv

October 1, 2020

Greetings, friends!

Today’s digest contains a wealth of microbiology articles focused on everything from the dog ear canal microbiome to estuarine methanogen communities. Rather than highlight a specific research article, today I’d like to encourage you to check out this week’s New York Times article profiling the organizers of Black in Micro Week and this commentary published by one of the organizers in mSphere. Black in Micro week began this Monday and programming is scheduled to continue through October 4th. If you missed earlier events, you’re in luck! The organizers have already uploaded videos of all completed events at the Black in Micro youtube channel.

Enjoy!


Events

Black in Micro Week is this week (September 28 – October 4th, 2020) on your favorite social media platforms! Check out the Black in Microbiology website for additional information, including a full programming schedule, and follow @BlackinMicro and #BlackinMicro on Twitter and Instagram.

Human respiratory microbiome

Airway microbiota is associated with the severity of non‐CF bronchiectasis – Li et al. – The Clinical Respiratory Journal

Human gut microbiome

Systematic analysis of gut microbiota in pregnant women and its correlations with individual heterogeneity – Yang et al. – npj Biofilms and Microbiomes

Review: Implication of gut microbiota in cardiovascular diseases – Zhou et al. – Oxidative Medicine and Cellular Longevity

Animal experiments

Changes in the ear canal microbiota of dogs with otitis externa – Kasai et al. – Journal of Applied Microbiology

Plant, root, and soil microbiome

Soil borne Fusarium solani exhibited pathogenic effect on tomato cultivars in Nigeria – Abiala et al. – Archives of Phytopatholgy and Plant Protection

A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus – Nelson et al. – The ISME Journal

Successional change of the fungal microbiome pine seedling roots inoculated with Tricholoma matsutake – Park et al. – Frontiers in Microbiology

Review: Arbuscular mycorrhizal fungi: an ecological accelerator of phytoremediation of metal contaminated soils – Tiwari et al. – Archives of Agronomy and Soil Science

Co‐occurrence history increases ecosystem stability and resilience in experimental plant communities – van Moorsel et al. – Ecology

Quantitative estimation of stochastic and deterministic processes for soil prokaryotic community assembly in the Yellow River floodplain – Yu et al. – European Journal of Soil Science

Water and extremophile microbiome

Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre – Allen et al. – Molecular Ecology

An unexpectedly broad thermal and salinity-tolerant estuarine methanogen community – Blake et al. – Microorganisms

Microbial communities responded to tetracyclines and Cu(II) in constructed wetlands microcosms with Myriophyllum aquaticum – Guo et al. – Ecotoxicology and Environmental Safety

Built environment

Microbial community and function in nitrogen transformation of ectopic fermentation bed system for pig manure composting – Chen et al. – Bioresource Technology

Effect of hydrothermal hot-compression method on the antimicrobial performance of green building materials from heterogeneous cellulose wastes – Echeverria et al. – Journal of Cleaner Production

Nitrous oxide emission and microbial community of full-scale anoxic/aerobic membrane bioreactors at low dissolved oxygen setpoints – Wen et al. – Journal of Water Process Engineering

Response of Cyperus involucratus to sulfamethoxazole and ofloxacin-contaminated environments: Growth physiology, transportation, and microbial community – Xu et al. – Ecotoxicology and Environmental Safety

Microbes in the news

Black microbiologists push for visibility amid a pandemic – Wu – New York Times

Science, publishing, and career

Commentary: mSphere of influence: That’s racist—COVID-19, biological determinism, and the limits of hypotheses – Taylor – mSphere

September 3, 2020

At the beginning of todays post I wanted to highlight some interesting recent articles on COVID-19 and in particular a recent trial demonstrating the utility of BCG for a trained immunity response to protect against respiratory infections in the elderly. Enjoy!

COVID-19 & Vaccines

Tracking the COVID-19 pandemic in Australia using genomics – Seemann et al. Nature Communications. 

A comparison of four serological assays for detecting anti–SARS-CoV-2 antibodies in human serum samples from different populations – Grzelak et al. Science Translational Medicine

Phase 1–2 Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine – Keech et al. New England Journal of Medicine

ACTIVATE: Randomised clinical trial of BCG vaccination against infection in the elderly – Giamarellos-Bourboulis et al. Cell

 

General microbiome

Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease – Bushman et al. Cell Host & Microbe

Gut mycobiome and its interaction with diet, gut bacteria and alzheimer’s disease markers in subjects with mild cognitive impairment: A pilot study – Nagpal et al. EBioMedicine

Relationship between the composition of the intestinal microbiota and the tracheal and intestinal colonization by opportunistic pathogens in intensive care patients – Fontaine et al. PLOS One

Human respiratory microbiome

Respiratory Bacteria Stabilize and Promote Airborne Transmission of Influenza A Virus – Rowe et al. mSystems

Animal microbiome

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia – Shanmuganandam et al. PeerJ

Water and extremophile microbiome

Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters – Marchioro et al. PeerJ

Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth – Miller et al. mBio. 

Phages and viruses

Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts – Fujimoto et al. Cell Host & Microbe

Bioinformatics

BLAST-QC: automated analysis of BLAST results – Torkian et al. Environmental Microbiome

 

September 2, 2020

Greetings for the month of September: the Haervest-monath (Harvest Month). Today’s microbiome digest consists of a cool editorial article on hidden theatre of microbes. The digest also features two interesting reviews; first one detailing the role of skin microbiota in forensic sciences and the second one with focus on association of sponges and their microbiome.

Let’s celebrate the month of September with some fascinating microbiome studies.

There are flowers enough in the summertime,
More flowers than I can remember—
But none with the purple, gold, and red
That dye the flowers of September!

—Mary Howitt (1799-1888)

General microbiome
*Editorial: Unveiling the Hidden Theatre of Microbes – Böttcher T – ChemBioChem

Chitosan-chelated zinc modulates cecal microbiota and attenuates inflammatory response in weaned rats challenged with Escherichia coli – Feng et al – Journal of Microbiology

Multi-site human microbiome
Potential Associations Among Alteration of Salivary miRNAs, Saliva Microbiome Structure, and Cognitive Impairments in Autistic Children – Ragusa et al – Int. J. Mol. Sci.

Human respiratory microbiome
Review: The importance of airway and lung microbiome in the critically ill – Martin-Loeches et al – Critical Care

Human skin microbiome
A Novel Mycovirus Evokes Transcriptional Rewiring in the Fungus Malassezia and Stimulates Beta Interferon Production in Macrophages – Clancey et al – mBio

A Novel Virus Alters Gene Expression and Vacuolar Morphology in Malassezia Cells and Induces a TLR3-Mediated Inflammatory Immune Response – Park et al – mBio

*Review: Challenges in Human Skin Microbial Profiling for Forensic Science: A Review – Neckovic et al – Genes

Human gut microbiome
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics – Martino et al – Nat Biotechnol

Animal microbiome
*The relationship between microbiomes and selective regimes in the sponge genus Ircinia – Kelly et al – bioRxiv

Techniques
Flow cytometry with cell sorting and sequencing as a tool for the study of the Humboldt Current krill stomach microbiota – Henriquez-Castillo et al – bioRxiv

Microbes in the news
EurekAlert News: Researchers receive $3 million NSF grant to ‘understand the rules of life – Zhou J

August 14, 2020

Good morning from Massachusetts! Dr. Elisabeth Bik will be giving a Zoom talk today on research misconduct in biomedical research. You can register at the link under events. Fittingly, today’s digest includes a preprint on the effects of retraction after misconduct on citations. Other highlights today include an entire theme issue on the microbiome and host evolution and a paper on phylogenomic analyses of archaea attempting to elucidate the DPANN lineage. In early life, the placental microbiome debate rages on with a paper demonstrating evidence for contamination rather than an actual placental microbiome. Finally, I have highlighted a paper studying whether soil archives can give us a glimpse into soil microbial communities of the past.

Have a great weekend!

Events

Dr. Bik is discussing “The Dark Side of Science: Misconduct in Biomedical Research” today at 12PM EDT! Register here.

General microbiome

Theme Issue: The role of the microbiome in host evolution – Philosophical Transactions of the Royal Society B

Pregnancy and early life

Evidence for contamination as the origin for bacteria found in human placenta rather than a microbiota – Rémi Gschwind – PloS One

Human milk microbiome

SARS-CoV-2 in human milk is inactivated by Holder pasteurization but not cold storage – Gregory J. Walker – Journal of Paediatrics and Child Health

Human oral microbiome

Review: Oral microbiome geography: Micron-scale habitat and niche – Jessica L. Mark Welch – Cell Host & Microbe

Human gut microbiome

Epidemiology and associated microbiota changes in deployed military personnel at high risk of traveler’s diarrhea – William A. Walters – PloS One

Animal experiments

Differential alteration in gut microbiome profiles during acquisition, extinction, and reinstatement of morphine-induced CPP – Jianbo Zhang – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Modulation of the intestinal microbiota of broilers supplemented with monensin or functional oils in response to challenge by Eimeria spp. – Alexandre Maciel Vieira – PloS One

Herpes simplex virus infection, Acyclovir and IVIG treatment all independently cause gut dysbiosis – Chandran Ramakrishna – PloS One

Animal microbiome

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet – Francesca Albonico – PloS One

Hydrolytic bacteria associated with natural helminth infection in the midgut of Red Sea marbled spinefoot rabbit fish Siganus rivulatus – Ghada Abd-Elmonsef Mahmoud – Microbial Pathogenesis

Plant, root, and soil microbiome

Book: Agriculturally Important Fungi for Sustainable Agriculture Vol 2: Functional Annotation for Crop Protection – Eds. Ajar Nath Yadav et al. – Springer

Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities? – Gian Maria Niccolò Benucci – PloS One

Labile carbon limits late winter microbial activity near Arctic treeline – Patrick F. Sullivan – Nature Communications

Enhanced biodegradation of crude oil by constructed bacterial consortium comprising salt-tolerant petroleum degraders and biosurfactant producers – Weiwei Chen – International Biodeterioration & Biodegradation

Plant–archaea relationships: a potential means to improve crop production in arid and semi-arid regions – Elizabeth Temitope Alori – World Journal of Microbiology and Biotechnology

First report of Fusarium equiseti causing crown rot and damping-off on durum wheat in Algeria – Amor Bencheikh – Archives of Phytopathology and Plant Protection

Soil microbial diversity and composition: Links to soil texture and associated properties – Qing Xia – Soil Biology and Biochemistry

Water, air, and extremophile microbiome

Effects of different habitats on the bacterial community composition in the water and sediments of Lake Taihu, China – Wenjie Chang – Environmental Science and Pollution Research

Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea – Shanshan Yang – Nature Communications

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution – Nina Dombrowski – Nature Communications

Preprint: Occurrence, identification and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa – Fadare Temitope Folake — BioRxiv

Built environment

The microbiome of drinking water biofilters is influenced by environmental factors and engineering decisions but has little influence on the microbiome of the filtrate – Ben Ma – Environmental Science & Technology

In-situ remediation of acid mine drainage from abandoned coal mine by filed pilot-scale passive treatment system: Performance and response of microbial communities to low pH and elevated Fe – Haiyan Chen – Bioresource Technology

Bioinformatics and other techniques

De novo sequence assembly requires bioinformatic checking of chimeric sequences – Laila Sara Arroyo – PloS One

Review on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the rapid screening of microbial species: A promising bioanalytical tool – Suresh Kumar Kailasa – Microchemical Journal

Microbes in the News

Using the infant stool microbiome to predict NEC: New machine learning tool predicts devastating intestinal disease in premature infants – Science Daily

Science Publishing and Career

Preprint: Does retraction after misconduct have an impact on citations? A pre-post study – Cristina Candal-Pedreira – bioRxiv