January 14, 2021

Greetings from Pittsburgh!

Today’s digest contains lots of microbial ecology articles focused on everything from the impacts of sleep on dental biofilm to the response of soil microbiota to high petroleum pollution. Also included are two articles focused on insect-plant interactions, with the first focusing on gall induction in insects and the second on the intestinal microbiota of the pine defoliator C. chuxiongica.

General microbiome

Novel cyanotoxin-producing Synechococcus in tropical lakes – Yew-Hoong et al. – Water Research

Multi-site human microbiome

Impacts of sleep on the characteristics of dental biofilm – Sotozono et al. – Scientific Reports

Animal experiments

Dysbiosis of rat vagina is efficiently rescued by the vaginal microbiota transplantation or probiotic combination: Vaginal microbiota transplantation rescues dysbiosis in rat vagina – Chen et al. – International Journal of Antimicrobial Agents

Are bacterial symbionts associated with gall induction in insects? – Hammer et al. – Arthropod-Plant Interactions

The diversity and function of intestinal microorganisms in four geographic Cephalcia chuxiongica (a pine defoliator) populations – Yu et al. – Journal of Applied Entomology

Animal microbiome

Linking bacterial communities associated with the environment and the ecosystem engineer Orchestia gammarellus at contrasting salt marsh elevations – Hernández et al. – Microbial Ecology

Plant, root, and soil microbiome

Response of bacterial and fungal communities to high petroleum pollution in different soils – Galitskaya et al. – Scientific Reports

Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing – Hu et al. – AMB Express

First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand – Wongsaroj et al. – Scientific Reports

Water and extremophile microbiome

Coastal bacterial community response to glacier melting in the Western Antarctic Peninsula – Alcamán-Arias et al. – Microorganisms

Microbial necromass formation, enzyme activities and community structure in two alpine elevation gradients with different bedrock types – Bhople et al. – Geoderma

Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases – DeCastro et al. – Scientific Reports

The effect of an adsorbent matrix on recovery of microorganisms from hydrocarbon-contaminated groundwater – Taylor et al. – Microorganisms

Built environment

Electrochemical performance and response of bacterial community during phenanthrene degradation in single-chamber air-cathode microbial fuel cells – Hua et al. – Environmental Science and Pollution Research

Food microbiology

Combination of Flos Sophorae and chili pepper as a nitrite alternative improves the antioxidant, microbial communities and quality traits in Chinese sausages – Tang et al. – Food Research International

December 27, 2020

Joyeuses fêtes from Paris, France ! In today’s digest, you will find great papers looking at various animal and plant microbiomes. In particular, I recommend taking some time to look at a preprint from Brealey and collaborators exploring the impact of human antibiotic use on oral microbiome in wild animals. The authors used shotgun metagenomics to determine the abundance and diversity of antimicrobial resistance genes in the oral microbiome of brown bears from Swedish museum specimens. Importantly, they show a significant increase in antimicrobial resistance genes in correlation with modern human antibiotics use, showing an impact even on wildlife of our antibiotic consumption.

Today’s non-microbiology pick takes a look back at the history of bioinformatics through the data analysis and visualization of papers published between 1998 and 2019. In addition of reading this very interesting paper, you can take a look at the data collected through interactive visualizations available at http://bioinfo.dcc.ufmg.br/history !

Have a great Sunday!

Pregnancy and early life

Preprint: Metabolomic signature of the maternal microbiota in the fetus – Pessa-Morikawa et al. – BioRXiv

Human nearly-sterile sites

Preprint: The urinary microbiome in postmenopausal women with recurrent urinary tract infections – Hiersoux Vaughan et al. – BioRXiv

Preprint: Biofilm development on urinary catheters promotes the appearance of viable but non-culturable (VBNC) bacteria – Wilks et al. – BioRXiv

Animal microbiome

Preprint: Wild animal oral microbiomes reflect the history of human antibiotics use – Brealey et al. – BioRXiV

Plant, root, and soil microbiome

Dissimilarity analysis of microbial communities in the rhizosphere and tissues of diseased and healthy cherry trees (Cerasus pseudocerasus) – Ding et al. – Canadian Journal of Plant Pathology

First Recorded Account of Arbuscular Mycorrhizal Fungi in Sand Dunes in South Eastern Australia: Biogeography and Species Richness – Hanlon et al. – Journal of Coastal Research

Diversity and structural differences of bacterial microbial communities in rhizocompartments of desert leguminous plants – Zhou et al. – PLOS ONE

Preprint: Orchard management and landscape context mediate the floral microbiome of pear – Schaeffer et al. – BioRXiv

Water and extremophile microbiome

Interplay of microbial communities with mineral environments incoralline algae – Valdespino-Castillo et al. – Science of the total environment

Acid Mine Drainage as Energizing Microbial Niches for the Formation of Iron Stromatolites: The Tintillo River in Southwest Spain – Chacon-Baca et al. – Astrobiology


PStrain: An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data – Wang et al. – Bioinformatics

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data – Leung et al. – BMC Genomics

My non-microbiology picks

A Brief History of Bioinformatics Told by Data Visualization – Mariano et al. – Brazilian Symposium on Bioinformatics


December 18, 2020

Greetings from cold and snowy Pittsburgh!

As I type this, my housemate (who is an essential healthcare worker) should be getting the first dose of her COVID-19 vaccine! Although I’m not sure what the distribution of COVID-19 vaccines is expected to look like, today’s digest includes an article mapping routine measles vaccination coverage in low- and middle- income countries. I’ve also highlighted a few interesting environmental microbiology preprints, including one on the role of ecosystem engineers in shaping arid soil bacterial communities.

Happy holidays and happy reading!

Events and jobs

Danone North America Gut Microbiome, Yogurt and Probiotics Fellowship Grant – Applications for the 2020-2021 grant are currently open and are due on February 24, 2021.

General microbiome

Mapping routine measles vaccination in low- and middle-income countries – Local Burden of Disease Vaccine Coverage Collaborators – Nature

The functional proteome landscape of Escherichia coli – Mateus et al. – Nature

Preprint: Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Shaw et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities – Baubin et al. – bioRxiv

Preprint: Environmental interactions with amoebae as drivers of bacterial-fungal endosymbiosis and pathogenicity – Itabangi et al. – bioRxiv

December 9, 2020

In today’s digest read about the selection and microdiversity in glacier-fed streams, Gardnerella vaginalis contribution to the increased rate of group B Streptococcus vaginal colonization, making F1 hybrids in Escherichia coli using MAE (Mass Allelic Exchange), smORFinder (annotation tool to identify small proteins in microbial genomes and metagenomes), and more.
Check out the new Science Friday podcast episode on microbial interactions in cheese rinds and Svetlana’s pick for happy holidays.

Human microbiome

Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver – Holly Lutz – Frontiers in Microbiology

Gut microbiome

Landscapes of bacterial and metabolic signatures and their interaction in major depressive disorders – Jian Yang – Science Advances

Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome – Dylan G. Maghini – Nature Protocols

Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses – Shu Yasuda – iScience

The Healthy Microbiome (What is the definition of a healthy gut microbiome?) – Fergus Shanahan – Gastroenterology

The gut microbiota is associated with immune cell dynamics in humans – Jonas Schluter
– Nature

Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure – Jonel Trebicka – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity – Alexander SF Berry – bioRxiv

Animal experiments

*Gardnerella vaginalis promotes group B Streptococcus vaginal colonization, enabling ascending uteroplacental infection in pregnant mice – Nicole M. Gilbert – American Journal of Obstetrics & Gynecology

Akkermansia muciniphila: A potential novel mechanism of nuciferine to improve hyperlipidemia – Yue Yu – Biomedicine & Pharmacotherapy

Gut microbiota modulation by both Lactobacillus fermentum MSK 408 and ketogenic diet in a murine model of pentylenetetrazole-induced acute seizure – Ju Young Eor – Epilepsy Research

Host-age prediction from fecal microbiome composition in laboratory mice – Adrian Low – bioRxiv

Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling Through The Aryl Hydrocarbon Receptor – Aayushi Uberoi – bioRxiv

Water microbiome

*Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome – Stilianos Fodelianakis – bioRxiv

Phages and viruses

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis – Andrey N. Shkoporov – bioRxiv

Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase – Marike Palmer – Frontiers in Microbiology

Broad Virus Detection and Variant Discovery in Fecal Samples of Hematopoietic Transplant Recipients Using Targeted Sequence Capture Metagenomics – Suze A. Jansen – Frontiers in Microbiology

Antimicrobial Resistance

Review: Multidrug-resistant high-risk Enterococcus faecium clones: can we really define them? – Ana R. Freitas – International Journal of Antimicrobial Agents

Review: Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance – Madangchanok Imchen – Frontiers in Genetics

Predicting clinical resistance prevalence using sewage metagenomic data – Antti Karkman – Communications Biology

Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants – John Leech – mSystems

Uncovering hidden antimicrobial resistance patterns within the hospital microbiome – Bastiaan W. Haak and W. Joost Wiersinga – Nature Medicine

Isolation and characterization of human pathogenic multidrug resistant bacteria associated with plastic litter collected in Zanzibar – Farah N. Rasool – Journal of Hazardous Materials

Integrated metagenomic and metatranscriptomic analyses of ultraviolet disinfection effects on antibiotic resistance genes and bacterial communities during wastewater treatment – Shuyu Jia – Ecotoxicology

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more – Magdalena Skarżyńska – Plos One


*Mass allelic exchange: enabling sexual genetics in Escherichia coli – Varnica Khetrapal – bioRxiv

Review: Microbial model communities: To understand complexity, harness the power of simplicity – Johan Bengtsson-Palme – Computational and Structural Biotechnology Journal

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae – Sivkheng Kann – BMC Microbiology


*Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes – Matthew G. Durrant and Ami S. Bhatt – Cell Host Microbe

Accurate Microbiome Sequencing with Synthetic Long Read Sequencing – Nico Chung – bioRxiv

Species level resolution of female bladder microbiota from marker gene surveys – Carter Hoffman – bioRxiv

Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis – Paul E. Smith – Frontiers in Microbiology


H3ABioNet Seminars and Webinars – H3ABioNet Pan African Bioinformatics Network

Inspiring the next generation of scientists… online – The Young Microbiologists Symposium (YMS) 2020

MLCB 2020 Day 1 and 2 talks – Machine Learning in Computational Biology meeting


Why We’re Giving Thanks To Microbes For Stinky Cheese with Benjamin Wolfe and Casey Cosetta – Katie Feather and Ira Flatow – Science Friday

Svetlana’s pick

Planning Our “Home-mas” this December – MissPond – Emma Pond

Holiday Gift Guide For Microbe Lovers – Justine Dees – Joyful Microbe

The 2020 cookbook giftlist – Fiona Beckett – Matching Food & Wine

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 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


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


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

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

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

November 3, 2020

Greetings Everyone!!

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

October 27, 2020

Greetings from Pittsburgh, PA!

Today’s digest a contains articles focused on the oral microbiome, koala symbionts, soil microbial communities, and more. For those of you who are a bit too tired to digest cutting-edge research, I suggest using the 10 simple steps outlined in the highlighted editorial to colorize your own data visualizations. Finally, if you just need a break, I suggest bookmarking the article on the whale skin microbiome and revisiting the film Star Trek IV: The Voyage Home.

Happy reading (or movie watching)!

General microbiome

Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population – Verma et al. – Archives of Microbiology

Pregnancy and early life

Maternal and cord blood vitamin D level and the infant gut microbiota in a birth cohort study – Kassem et al. – Maternal Health, Neonatology and Perinatology

Human gut microbiome

Review: A review on preventive role of ketogenic diet (KD) in CNS disorders from the gut microbiota perspective – Rawat et al. – Reviews in Neurosciences

Animal experiments

Challenges in microbiological identification of aerobic bacteria isolated from the skin of reptiles – Brockmann et al. – PLOS ONE

Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum – Dahlhausen et al. – Peer J

Vertical transmission of zika virus in Aedes albopictus – Lai et al. – PLOS Neglected Tropical Diseases

Cultured-dependent and cultured-independent study of bacteria associated with Thai commercial stingless bee Lepidotrigona terminata – Suphaphimol et al. – Journal of Apicultural Research

Animal microbiome

**Skin microbiome of beluga whales: spatial, temporal, and health-related dynamics – Van Cise et al. – Animal Microbiome

Diversity of bacterial symbionts associated with Myzus persicae (Sulzer) (Hemiptera: Aphididae: Aphidinae) revealed by 16S rRNA Illumina sequencing – Xu et al. – Microbial Ecology

Plant, root, and soil microbiome

Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer–prey systems – Erktan et al. – Biogeosciences

Responses of soil bacteria and fungi after 36 years fertilizer, straw cover, and irrigation management practices in northwest China – Zhang et al. – Soil Use and Management

Water and extremophile microbiome

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance – Herold et al. – Nature Communications

Islands in the sand: Are all hypolithic microbial communities the same? – Lebre et al. – FEMS Microbiology Ecology

Shifts of sediment bacterial community and respiration along a successional gradient in a typical karst plateau lake wetland (China) – Xia et al. – Journal of Oceanology and Limnology

Salinity controls soil microbial community structure and function in coastal estuarine wetlands – Zhang et al. – Environmental Microbiology

Phages and viruses

Association of host proteins with the broad host range filamentous phage NgoΦ6 of Neisseria gonorrhoeae – Piekarowicz et al. – PLOS ONE


**Editorial: Ten simple rules to colorize biological data visualization – Hattab et al. – PLOS Computational Biology

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy – de Koning et al. – GigaScience

Predicting antimicrobial resistance using conserved genes – Nguyen et al. – PLOS Computational Biology


Review: Innovations to culturing the uncultured microbial majority – Lewis et al. – Nature Reviews Microbiology

Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods – Wang et al. – PeerJ

Science, publishing, and career

Comment: Crowdsourcing virtual summer research opportunities to support minorities in microbiology – Johnson et al. – Nature Microbiology

October 11, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find quite a few exciting reads about ancient microbes!

Duchêne and collaborators review recents efforts in paleopathology leading to the genome sequencing of ancient pathogens of historical interest such as the pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae). In their review, the authors explore this amazing topic that aims to broaden our understanding of the past infectious disease.

On the other hand, Eisenhofer and collaborators examine ancient microbial DNA preserved within dental calculus samples from two major cultural periods in Japan: the Jomon period circa 3000 years ago and the Edo period circa 400–150 ago. In this piece, they explore how human oral microbiomes have changed through time in ancient Japanese populations.

Finally, you’ll find in this digest a non-microbiology pick: a “10 simple rules” paper outlining best practices for annotating and submitting sequencing data! Indeed, metadata accompanying sequence datasets is critical to ensure data longevity and reusability by both human and machine agents, and poor metadata can drastically reduce the value of sequencing experiments by limiting its reuse in integrative analyses!

Have a great Sunday!

General Microbiology

Review: The Recovery, Interpretation and Use of Ancient Pathogen Genomes – Duchêne et al. – Current Biology

Multi-site human microbiome

Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus – Jacobson et al. – Philosphical transactions of the royal society of Biological sciences.

Human respiratory and oral microbiome

Investigating the demographic history of Japan using ancient oral microbiota – Eisenhofer et al. – Philosphical transactions of the royal society of Biological sciences.

Human gut microbiome

Preprint: Distinct human gut microbial taxonomic signatures uncovered with different sample processing and microbial cell disruption methods for metaproteomic analysis – Garcia-Duran et al. – BioRxiv.

Review: Deciphering diet-gut microbiota-host interplay: Investigations of pectin. – Tan and Nie – Trends in Food Science & Technology

Plant, root, and soil microbiome

Book Chapter: Microbes and Environment: Global Warming Reverting the Frozen Zombies. In: Fahad et al. (eds) Environment, Climate, Plant and Vegetation Growth. Springer, Cham.

Taxonomic Diversity of Bacteria and Their Filterable Forms in the Soils of Eastern Antarctica (Larsemann Hills and Bunger Hills) – Kudinova et al. – Microbiology.

Preprint: Long-term warming effects on the microbiome and nitrogen fixation associated with the moss Racomitrium lanuginosum in Icelandic tundra – Klarenberg et al. – bioRxiv

Water and extremophile microbiome

Diversity of Eukaryotic Microorganisms in the Drainage Waters of a Coal Open-Cast Mine – Gruzdev et al. – Microbiology

Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system – Zeng et al. – AMB express.

Comparative diversity analysis of halophiles at two polar saltern systems in Indramayu, West Java, Indonesia – Chasanah et al. – Letters in Applied Microbiology.

Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria – Norris et al. – BioRxiv.

Food microbiology

Review: Microbial diversity of seafood. Parlapani. Current Opinion in Food Science.

Phages and viruses

The first head‐tailed virus, MFTV1, produced by a hyperthermophilic methanogenic deep‐sea archaea – Thiroux et al. – Environmental microbiology.

Review: Single-virus genomics and beyond – Martinez et al. – Nature reviews Microbiology


A Rapid Automated Process for Organizing Bacterial Cluster Segments Using Deep Neural Networks – Elroy Martis et al. – IEEE conference


FACS-iChip: a high-efficiency iChip system for microbial ‘dark matter’ mining – Liu et al. – Marine Life Science and Technology

Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses – Sabatier et al. – Microorganisms

Science, publishing, and career

Preprint: Advancing science or advancing careers? Researchers’ opinions on success indicators – Aubert Bonn and Pinxten – BioRxiv.

My non-microbiology picks

Ten simple rules for annotating sequencing experiments – Stevens et al. – Plos Computational Biology

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.



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