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 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

August 4, 2020

Greetings Everyone. Today’s Microbiome Digest comprises of a wide variety of topics covering soil microbiota, tumor to water to extremophile microbiome. The digest has some reviews, books, as well as interesting articles on how synthetic microbial communities facilitate sustainable growth and the role of microbial communities in balancing the environment. A terrific news article covering the isolation of microbes buried beneath the sea floor for more than 100 million years. Today’s digest can be summarized by a quote by Julie Morley.

“Every being devotes and dedicates itself to some innate purpose. Single cells, microbes, plants, insects, animals – every being makes it own unique contribution” – Julie J. Morley

General microbiome

*Shifts in the microbiota associated with male mosquitoes (Aedes aegypti) exposed to an obligate gut fungal symbiont (Zancudomyces culisetae) – Jonas Frankel-Bricker – Scientific Reports

Microbiome-derived metabolites reproduce the mitochondrial dysfunction and decreased insulin sensitivity observed in type 2 diabetes – Ormsby et al – bioRxiv

*Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth – Zuñiga et al – Nature Communications

Multi-site human microbiome

Microbiome harbored within tumors: a new chance to revisit our understanding of cancer pathogenesis and treatment – Zhao et al – Signal Transduction and Targeted Therapy

Human skin microbiome
Paradigms and Perspectives: The skin microbiome as a clinical biomarker in atopic eczema: Promises, navigation, and pitfalls – Reiger et al – The journal of Allergy and Clinical Immunology

Human gut microbiome
Review: Gut microbiota and atherosclerosis: role of B cell for atherosclerosis focusing on the gut-immune-B2 cell axis – Chen et al – Journal of Molecular Medicine

Gut microbiome a promising target for management of respiratory diseases – Trivedi et al – Biochemical Journal

*A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota – Aakko et al – Scientific Reports

Effects of antibiotic treatment on gut microbiota and how to overcome its negative impacts on human health – Ribeiro et al – ACS Infect. Dis

Animal experiments
Dynamics of uterine microbiota in postpartum dairy cows with clinical or subclinical endometritis – Pascottini et al – Scientific Reports

Plant, root, and soil microbiome
Book chapter: The Extended Microbiota: How Microbes Shape Plant-Insect Interactions – Mayoral-Peña et al – Evolutionary Ecology of Plant-Herbivore Interaction

Response of Soil Microbial Community to C:N:P Stoichiometry along a Caragana korshinskii Restoration Gradient on the Loess Plateau, China – Zhang et al – forests

Review: The endosphere microbial communities, a great promise in agriculture – Adeleke et al – International Microbiology

Water and extremophile microbiome
Influence of microorganisms on initial soil formation along a glacier forefield on King George Island, maritime Antarctica – Krauze et al – Biogeosciences

Review: Microbial communities of soda lakes and pans in the Carpathian Basin: a review – Tamás Felföldi – Biologia Futura

Fungal Community in Antarctic Soil Along the Retreating Collins Glacier (Fildes Peninsula, King George Island) – dos Santos et al – microorganims

Culture Independent Diversity of Bacterial Communities Indigenous to Lower Altitude at Laohugou Glacial Environment – Ali et al – Geomicrobiology Journal

Review: Methanosarcina acetivorans: A Model for Mechanistic Understanding of Aceticlastic and Reverse Methanogenesis – James G. Ferry – Front.Microbiol

The Composition of Microbial Communities in Six Streams, and Its Association With Environmental Conditions, and Foodborne Pathogen Isolation – Chung et al – Front.Microbiol

Food microbiology
FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation – Vaccalluzzo et al – Food Microbiology


Bioinformatics
Book: A Bioinformatics Primer for the Analysis of Illumina MiSeq Data of Litter-Associated Fungi and Bacteria – Seena et al – Methods to Study Litter Decomposition

Techniques
Review: Method development for cross-study microbiome data mining: challenges and opportunities – Su et al – Computational and Structural Biotechnology Journal

Microbes in the news
*Scientists pull living microbes, possibly 100 million years old, from beneath the sea – Elizabeth Pennnisi – Science

June 20th, 2020

Glad midsommar!

Happy midsummer to everyone from Sweden. Today’s digest is heavy on the preprints with a couple of thought-provoking editorials from the journal Nature. You will notice a lot of articles related to COVID-19. There is an interesting study that proposes the use of dogs and their sensory powers to detect CoV infections. More importantly, a preprint discusses the use of a tyrosine kinase as a potential drug and another preprint discusses the results of a massive FDA-approved drug repurposing screen for COVID. Also in the digest is an article where the researchers have shown that the gut microbiome produces neurotransmitters and another article that explains how Streptomyces spores hitchhike. Another article, although not related to our general theme, is super interesting as well. A group of scientists have proposed that the first egg of the dinosaurs was probably soft-shelled and not like the hard eggs we imagined all this time!

I am sorry for doing a lousy job today at providing a proper context and some informative introduction to today’s digest as it is the most awaited Midsommar holiday and the barbecue is calling! I hope everyone is enjoying the summer. Make sure to follow social distancing guidelines!

COVID-19

Preprint: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 – Nirmitee Sanjay Mulgaonkar, et al.

Preprint: Variant analysis of SARS-CoV-2 strains in Middle Eastern countries – Khalid M Bindayna and Shane Crinion

Preprint: Polymorphism and selection pressure of SARS-CoV-2 vaccine and diagnostic antigens: implications for immune evasion and serologic diagnostic performance – Eric Dumonteil and Claudia Herrera

Preprint: Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2 Infected Syrian Hamsters – Rebecca Brocato, et al.

Preprint: High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States – Ryan P McNamara, et al.

Preprint: Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window – Duarte Gouveia, et al.

Preprint: A single dose of recombinant VSV-∆G-spike vaccine provides protection against SARS-CoV-2 challenge – Yfat Yahalom-Ronen, et al.

Preprint: Antiviral treatment of SARS-CoV-2-infected hamsters reveals a weak effect of favipiravir and a complete lack of effect for hydroxychloroquine – Suzanne JF Kaptein, et al.

Preprint: Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2 – Mark Dittmar, et al.

Preprint: Dog Savior: Immediate Scent-Detection of SARS-COV-2 by Trained Dogs – Omar Vesga, et al.

Preprint: Evaluation of the performance of SARS-CoV-2 serological tools and their positioning in COVID-19 diagnostic strategies. – Aurélie Velay, et al.

General Microbiome

Preprint: Exploring the Stony Coral Tissue Loss Disease Bacterial Pathobiome – Deborah Iwanowicz, et al.

Preprint: Hi-C deconvolution of a textile-dye degrader microbiome reveals novel taxonomic landscapes and link phenotypic potential to individual genomes – Ayixon Sanchez-Reyes, et al.

A metabolic pathway for bile acid dehydroxylation by the gut microbiome – Masanori Funabashi, et al. – Nature

A neurotransmitter produced by gut bacteria modulates host sensory behaviour – Michael P. O’Donnell, et al. – Nature

Proteome

Preprint: Novel functional insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies – Lisette Meerstein-Kessel, et al.

Bacteria

Preprint: Conjugal DNA transfer in the maternally inherited symbiont of tsetse flies Sodalis glossinidius – Christopher G Kendra, et al.

Preprint: Systematic analysis of REBASE identifies numerous Type I restriction-modification systems that contain duplicated, variable hsdS specificity genes that randomly switch methyltransferase specificity by recombination. – John M. Atack, et al.

Preprint: The role of LmeA, a mycobacterial periplasmic protein, in stabilizing the mannosyltransferase MptA and its product lipomannan under stress – Kathryn C Rahlwes, et al.

Preprint: Microbial piggy-back: how Streptomyces spores are transported by motile soil bacteria – Alise R. Muok, et al.

Viruses

Preprint: Herbivore-induced activation of viral phosphatase disarms plant antiviral immunities for pathogen transmission – Pingzhi Zhao, et al.

Preprint: Quantifying the acquisition and retention of lumpy skin disease virus by haematophagus insects and the implications for transmission and control – Beatriz Sanz-Bernardo, et al.

Preprint: Identification of a critical horseshoe-shaped region in the nsp5 (Mpro, 3CLpro) protease interdomain loop (IDL) of coronavirus mouse hepatitis virus (MHV) – Benjamin C. Nick, et al.

Preprint: A sweep of earth’s virome reveals host-guided viral protein structural mimicry; with implications for human disease – Gorka Lasso, et al.

Others

The first dinosaur egg was soft – Mark A. Norell, et al. – Nature

Junior researchers hit by coronavirus-triggered hiring freezes – Chris Woolston – Nature

Peer review should be an honest, but collegial, conversation Nature

May 20, 2020

Greetings from Pittsburgh, PA!

Television and movies are a welcome distraction from the current global pandemic. For this digest, I’d like to highlight two articles. The article by Sajjad et al. investigates the possibility of resurrection of ancient microbes present in the natural frozen world and is a perfect pair for the monster-of-the-week X-Files episode “Ice.” The second highlighted article focuses on the microbiome present on two ancient Slavonic parchment codices and how this data can be used to provide additional historical context. Maybe Harrison Ford can team up with Piñar et al. to create a fourth movie in the Indiana Jones Franchise based on their work?

Happy reading, everyone!

General microbiome

Effect of a novel synbiotic on Streptococcus mutans – Bijle et al. – Nature Scientific Reports

Culturomics‐based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis – Durán‐Viseras et al. – Environmental Microbiology

Review: Ecological features of the persistence of Vibrio cholerae: retrospective analysis and actual state of the problem – Menshikova et al. – Jounral of microbiology, epidemiology, and immunobiology

Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage – Reji and Francis – ISME Journal

Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis – Tantivitayakul et al. – Nature Scientific Reports

Plant, root, and soil microbiome

Impacts of forest conversion to plantations on the soil carbon and nitrogen dynamics, and microbial communities – Wang et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Novel yeast taxa from the cold: description of Cryolevonia giraudoae sp. nov. and Camptobasidium gelus sp. nov. – de Garcia et al. – International Journal of Systematic and Evolutionary Microbiology

Remote sensing reveals Antarctic green snow algae as important terrestrial carbon sink – Gray et al. – Nature Communications

Review: Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? – Sajjad et al. – Science of the Total Environment

Built environment

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value – Piñar et al. – Environmental Microbiology

Bioinformatics

Preprint: Efficiently processing amplicon sequencing data for microbial ecology with dadasnake, a DADA2 implementation in Snakemake – Weißbecker et al. – bioRxiv

Techniques

Editorial: Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes – McGenity et al. – Microbial Biotechnology

Discovery of thermophilic Bacillales using reduced-representation genotyping for identification – Talamantes-Becerra et al. – BMC Microbiology

May 8, 2020.

The highlighted paper of the day looked at the relationship between statins and gut microbiome / enterotype prevalence, mined from data collected from the MetaCardis study which looked at over 2000 participants all across the EU and collected over 1,400 parameters.

If you’re looking for a review/news article of the paper head to: Statin drugs might boost healthy gut microbes

If you’re looking for the paper: Statin therapy is associated with lower prevalence of gut microbiota dysbiosis – Sara Silva – Nature

COVID-19


Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids – Xiaohua Duan – bioRxiv

Whose coronavirus strategy worked best? Scientists hunt most effective policies – Elizabeth Gibney – Nature

Coronavirus activates a stem cell-mediated defense mechanism that accelerates the activation of dormant tuberculosis: implications for the COVID-19 pandemic – Lekhika Pathak – bioRxiv

General Microbiome

Multi ‘Omics Profiling of the HIV Airway Epithelium: Integration of the Microbiome, Methylome, and Transcriptome – MS Jude – Am J Respir Crit Care Med

Intracellular Staphylococcus aureus persisters upon antibiotic exposure – Frederuc Peyrusson – Nature Communications

Isolation and characterization of bacteriophages that infect Citrobacter rodentium, a model pathogen for investigating human intestinal diseases – Carolina Mizuno – bioRxiv

MiniReview: A toxic environment: a growing understanding of how microbial communities affect Shiga toxin expression by E. coli O157:H7 – Erin M. Nawrocki – American Society for Microbiology, Applied and Environmental Microbiology

Pregnancy and early life

Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to- weaning transition – Martin Beaumont – Gut Microbes

Gut Microbiome Derived 12,13 Dihome Promotes Antigen Presenting Cell Dysfunction In Vitro and Airway Allergic Inflammation In Vivo – S Levan – Atsjournal


Multi-site human microbiome

The Microbiome and the Gut‐Liver‐Brain Axis for CNS Clinical Pharmacology: Challenges in Specifying and Integrating In Vitro and In Silico Models – Kyle Hawkins – Clinical Pharmacology and Therapeutics

Gut Check: The Intestinal Microbiome Does Not Predict or Protect from Vancomycin- Resistant Enterococcus Acquisition Among Critically Ill Patients – Chanderraj – Atsjournal

The Tumour-Resident Microbiome Is Associated with Cancer Hypomethylation Status in Lung Adenocarcinoma – Marshall – atsjournal

An association between the gut microbiota and immune cell dynamics in humans. – Jonas Schluter – bioRxiv

Metabolomics

Analyzing the impact of Mycobacterium tuberculosis infection on primary human macrophages by combined exploratory and targeted metabolomics – Vrieling Frank

Review: Metabolome–Microbiome Crosstalk and Human Disease – Kathleen Lee-Sarwar – metabolites

Animal Microbiome

Review – Mycobacterium bovis: From Genotyping to Genome Sequencing – Ana Guimaraeas – Microorganism

Animal experiments

Staphylococcus aureus-induced proteomic changes in the mammary tissue of rats: A TMT-based study – Lirong Cai – Plos One

Plant, root, and soil microbiome


Effects of earthworms on the microbiomes and antibiotic resistomes of detritus fauna and phyllosphere – Dong Zhu – Environmental Science and Technology

Surface runoff alters cave microbial community structure and function – Madison Davis – Plos One

Water and extremophile microbiome

Culturing of ‘Unculturable’ Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater – Xiaoqin Wu – bioRxiv

Bioinformatics & Techniques

Sequence count data are poorly fit by the negative binomial distribution – Stjin Hawinkel – Plos One

Book Chappter: Meta-Pangenome: At the Crossroad of Pangenomics and Metagenomics – Bing MA – The Pangenome, Springer.

Snipe: Highly sensitive pathogen detection from metagenomic sequencing data – Lihong Huang – bioRxiv

Validated Method for the Study of Human Lung Microbiota from Excised Tissue – Dumont-Leblond – atsjounal

Microbes in the news

Bad to the Bone – Matthew Greseth- MUSC Health

Meet the ‘psychobiome’: the gut bacteria that may alter how you think, feel, and act – Elizabeth Pennisi – ScienceMag

Decoding the Microbiome: Essential to Advancing Precision Medicine – Heather Hall – rdworldonline

Harithaa’s non-microbiology picks!

Mass spectrometry for future atomic clocks – Marianna Safrova – Nature (news & views)

May 1, 2020

Greetings from Durham, NC!

Hope everyone is doing well and staying healthy. Today’s digest includes several host-microbiome studies, environmental microbiome studies, and an intriguing EurekAlert news article.
In this light digest of today, I wanted to highlight a cool review about correlation of the oral microbiome with children’s health and a very interesting article on cell wall architecture of the gram-positive bacteria.
COVID-19 pandemic has opened a sort of Pandora’s box filled with great science along with pseudoscience. So, the digest has these two great articles from Nature: one about chloroquine and other about the race for coronavirus vaccines.
Staying at home is difficult for everyone, here is a fun activity to do: coloring space microbes book.

Stay Safe and entertained at home!!!!

COVID-19 news articles

The race for coronavirus vaccines: a graphical guide – Callaway – Nature

Chloroquine hype is derailing the search for coronavirus treatments – Ledford – Nature

General microbiome
*The architecture of the Gram-positive bacterial cell wall– Pasquina-Lemonche et al. – Nature

Pregnancy and early life
Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery – Hernandez et al. – Scientific Reports

Metabolic Effects of Bovine Milk Oligosaccharides on Selected Commensals of the Infant Microbiome—Commensalism and Postbiotic Effects – Jakobsen et al. – Metabolites

Multi-site human microbiome
*Review: Oral microbiome: possible harbinger for children’s health – Xiao et al. – Nature International Journal of Oral Science

Animal microbiome
Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen et al. – PLOS ONE

Plant, root, and soil microbiome
Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean – Han et al. – The ISME Journal

Water and extremophile microbiome
Review: Exopolysaccharides from marine bacteria: production, recovery and applications – Dave et al. – Environmental Sustainability

Stromatolitic digitate sinters form under wide‐ranging physicochemical conditions with diverse hot spring microbial communities – Sriaporn et al. – gebiology

Built environment
Comparative analysis of bacterial community and functional species in oil reservoirs with different in situ temperatures – Tian et al. – International Microbiology

Bioinformatics
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions – Medlock et al. – PLOS Computational Biology

Review: The National Microbiome Data Collaborative: enabling microbiome science – Wood-Charlson et al. – Nature Reviews Microbiology

Probiotics / prebiotics
Lactobacillus plantarum NA136 ameliorates nonalcoholic fatty liver disease by modulating gut microbiota, improving intestinal barrier integrity, and attenuating inflammation – Zhao et al. -Applied Microbiology and Biotechnology

Microbes in the news
Scientists explore links between genetics, gut microbiome and memory – DOE/PACIFIC NORTHWEST NATIONAL LABORATORY

April 26, 2020

Greetings from Pittsburgh, PA!

Today’s digest includes several reviews, numerous host-microbiome studies, a wide variety of environmental microbiome studies, and a new book focused on Emerging Technologies in Environmental Bioremediation.

I also wanted to highlight the virtual Fermentation Mini-Seminars offered by the Applied Ecology Department at my alma mater, NC State University. During the first seminar of the series I learned about the Wild Sourdough Project, which is a community-science/citizen-science project where participants can submit observational data about their sourdough culture. If you’re missing the lab, this might be the perfect project for you!

Virtual Events

NCSU Fermentation Mini-Seminars offered every Thursday at 4pm EST from April through August

General microbiome

Special Issue: Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals – De Vrieze et al. – Microbial Biotechnology

Review: Biofilm matrixome: Extracellular components in structured microbial communities – Karygianni et al. – Trends in Microbiology

Review: Microbial symbiosis: A network towards biomethanation – Saha et al. – Trends in Microbiology

Multi-site human microbiome

Microbiota in cerebrovascular disease: A key player and future therapeutic target – Tonomura et al. – Journal of Cerebral Blood Flow & Metabolism

Review: Role of microbiome and antibiotics in autoimmune diseases – Vangoitsenhoven and Cresci – Nutrition in Clinical Practice

Human skin microbiome

Isolation and characterization of diverse microbial representatives from the human skin microbiome – Timm et al. – BMC Microbiology

Human gut microbiome

Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder – Dan et al. – Gut Microbes

Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population – Koliada et al. – BMC Microbiology

Gut microbiome reveals specific dysbiosis in primary osteoporosis – Xu et al. – Frontiers in Cellular and Infection Microbiology

Animal experiments

The clinical drug Ebselen attenuates inflammation and promotes microbiome recovery in mice after antibiotic treatment for CDI – Garland et al. – Cell Reports Medicine

Effect of oxytetracycline treatment on the gastrointestinal microbiome of critically endangered white abalone (Haliotis sorenseni) treated for withering syndrome – Parker-Graham et al. – Aquaculture

Effects of hydrolyzed fish protein and autolyzed yeast as substitutes of fishmeal in the gilthead sea bream (Sparus aurata) diet, on fish intestinal microbiome – Rimoldi et al. – BMC Veterinary Research

Animal microbiome

(My microbiome) would walk 10,000 miles: Maintenance and turnover of microbial communities in introduced dung beetles – Parker et al. – Invertebrate Microbiology

Plant, root, and soil microbiome

Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil – Asem et al. – International Journal of Systemic and Evolutionary Microbiology

Steel slag amendment impacts on soil microbial communities and activities of rice (Oryza sativa L.) – Das et al. – Scientific Reports

Peat properties, dominant vegetation type and microbial community structure in a tropical peatland – Girkin et al. – Wetlands

Integrating transcriptomics and metabolomics to studies key metabolism, pathways and candidate genes associated with drought-tolerance in Carthamus tinctorius L. under drought stress – Wei et al. – Industrial Crops and Products

Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China – Yang et al. – PeerJ

Water and extremophile microbiome

Impacts of an eruption on cold-seep microbial and faunal dynamics at a mud volcano – Girard et al. – Frontiers in Marine Science

Unraveling heterogeneity of coral microbiome assemblages in tropical and subtropical corals in the South China Sea – Gong et al. – Microorganisms

Anode potential-dependent protection of electroactive biofilms against metal ion shock via regulating extracellular polymeric substances – Hou et al. – Water Research

Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin – Nigro et al. – PLOS One

Near streambed flow shapes microbial guilds within and across trophic levels in fluvial biofilms – Risse-Buhl et al. – Limnology and Oceanography

Heterotrophic sulfide-oxidizing nitrate-reducing bacteria enables the high performance of integrated autotrophic-heterotrophic denitrification (IAHD) process under high sulfide loading – Zhang et al. – Water Research

Built environment (subways, indoor surfaces)

Ecological processes affecting long-term eukaryote and prokaryote biofilm persistence in nitrogen removal from sewage – Angell et al. – Genes

Long-term microbial community dynamics in a pilot-scale gas sparged anaerobic membrane bioreactor treating municipal wastewater under seasonal variations – Kannan et al. – Bioresource Technology

Book: Emerging Technologies in Environmental Bioremediation – Edited by Shah et al.

Food microbiology

How processing methods affect the microbial community composition in a cereal-based fermented beverage – Phiri et al. – LWT – Food Science and Technology

High-throughput sequencing and metabolomics reveal differences in bacterial diversity and metabolites between red and white sufu – Tang et al. – Frontiers in Microbiology

April 11, 2020

Happy Saturday morning, y’all! I’m excited for my first contribution to the digest, and hope you enjoy my picks over a luxurious weekend meal. Today’s digest starts with some preprints about COVID including research on a drug that may inhibit viral replication. Other research highlights include an examination of the relationship between the vaginal microbiome and pre-term birth, a preprint on the oral microbiome in space, and a potential new technique for low cost, high-throughput metagenome profiling. Scroll all the way to the end for information about a fun project by a University of Wyoming student called The Microbestiary.

COVID-19
Preprint: Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Auslander, N. et al.

Preprint: Nelfinavir inhibits replication of severe acute respiratory syndrome coronavirus 2 in vitro. Yamamoto, N. et al.

Preprint: Understanding the B and T cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: A computational way to predict the immunogens. Vashi, Y. et al.

General Microbiome
Preprint: From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners. Pierce, EC. et al.

Human Gut Microbiome
Review: Unraveling Host-Gut Microbiota Dialogue and Its Impact on Cholesterol Levels. Villette R. et al. Frontiers in Pharmacology.

Metagenomics analysis reveals features unique to Indian distal gut microbiota. Kaur, K. et al. PLOS ONE.

Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis. Yu, A.I. et al. Cell Reports.

Human Oral Microbiome
Preprint: Characterization of the oral microbiome of medically controlled type-2 diabetes patients. Santos, A. et al.

Human Vaginal Microbiome
Cervicovaginal microbiome and natural history of HPV in a longitudinal study. Usyk, M. et al. PLOS Pathogens.

Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Kosti, I. et al. Frontiers in Microbiology.

Water and Extremophile Microbiome
Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef. Hartman, L.M. et al. Animal Microbiome.

Microbial Diversity and Metabolic Potential in the Stratified Sansha Yongle Blue Hole in the South China Sea. He, P. et al. Scientific Reports.

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources. Compte-Port, S. et al. PLOS ONE.

Animal Experiments and Animal Microbiome
The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts. Vaelli, P.M. et al. eLife.

Metatranscriptomic virome assessment of Rhipicephalus microplus from Colombia. Gomez, G.F. et al. Ticks and Tick-borne Diseases.

Preprint: Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila. Hinzke, T. et al.

Preprint: Similar gut bacterial microbiota in two fruit-feeding moth pests collected from different host species and locations. Gong, Q et al.

Plant, Root, and Soil Microbiome
The preceding root system drives the composition and function of the rhizosphere microbiome. Zhou, Y. et al. Genome Biology.

Microbial Co-Occurrence in Floral Nectar Affects Metabolites and Attractiveness to a Generalist Pollinator. Rering, C.C. et al. Journal of Chemical Ecology.

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. Braga, L.P.P. et al. Microbiome.

A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community. Ye, X. et al. Microbiome.

A plant genetic network for preventing dysbiosis in the phyllosphere. Chen, T. et al. Nature.

Fungal communities differentially respond to warming and drought in tropical grassland soil. de Oliveira, T.B. et al. Molecular Ecology.

Built Environment
An in-depth survey of the microbial landscape of the walls of a neonatal operating room. Derilus, D. et al. PLOS ONE.

Microbes in Space
Preprint: Defining the resilience of the human salivary microbiota by a 520 days longitudinal study in confined environment: the Mars500 mission. Bacci, G. et al.

Phages and Viruses
Phage cocktail containing Podoviridae and Myoviridae bacteriophages inhibits the growth of Pectobacterium spp. under in vitro and in vivo conditions. Zaczek-Moczydłowska, M.A. et al. PLOS ONE.

Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Moniruzzaman M., et al. Nature Communications.

Preprint: Infection with novel Bacteroides phage BV01 alters host transcriptome and bile acid metabolism in a common human gut microbe. Campbell, D.E. et al.

Bioinformatics
Preprint: Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera. Kaufman, J. et al.

Techniques
A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling. Hess, M.K. et al. PLOS ONE.

Industrial Microbiome
Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate. Huang, S. et al. Applied Microbiology and Biotechnology.

Fun with Microbes
University of Wyoming masters student Erin Bentley was selected for an Arctic Circle Expedition in 2021 where she will characterize microbes and share her discoveries on The Microbestiary.
“The Microbestiary strives to show the public, in welcoming and memorable ways, that the microbial world is populated by strange and beautiful characters,” says Bentley in an article published on the UW website.