July 8, 2022

Happy Wednesday! Today’s digest includes two gut-brain axis papers from Sarkis Mazmanian’s lab at CalTech. The first article, published in Nature, found that 4-ethylphenol (4EPS) produced by gut microbes from dietary tyrosine was capable of entering the brain and changing gene expression, brain cell interactions, and brain functions. In the second study, published in Nature Medicine, oral administration of the adsorbent AB-2004–which can bind and sequester phenolic compounds–led to reduced levels of gut 4EPS and decreased anxiety in human adolescents with autism spectrum disorder.

I have also included an article published by my thesis lab in The Journal of Allergy and Clinical Immunology looking at the impact of seasons on the respiratory microbiome and asthma exacerbations in children.

Finally, there is an interesting paper by Baranova et al. in which the authors identify a bacterial species ubiquitous across multiple wild animals that appears to have novel functions for pathogen control or microbiome remodeling. Happy reading!

General Microbiome
Scale-dependent tipping points of bacterial colonization resistance. – Karita, Y. et al., PNAS.

Microbial protection favors parasite tolerance and alters host-parasite coevolutionary dynamics. – Rafaluk-Mohr, C. et al., Current Biology.

Human Respiratory Microbiome
Seasonal Airway Microbiome and Transcriptome Interactions Promote Childhood Asthma Exacerbations. – McCauley, K.E. et al., The Journal of Allergy and Clinical Immunology.

Human Skin Microbiome
Secreted Toxins From Staphylococcus aureus Strains Isolated From Keratinocyte Skin Cancers Mediate Pro-tumorigenic Inflammatory Responses in the Skin. – Krueger, A. et al., Frontiers in Microbiology.

Aged related human skin microbiome and mycobiome in Korean women. – Kim, H-J. et al., Scientific Reports.

Human Vaginal Microbiome
Extracellular Vesicles Generated by Gram-Positive Bacteria Protect Human Tissues Ex Vivo From HIV-1 Infection. – Costantini, P.E. et al., Frontiers in Cellular and Infection Microbiology.

Gut-Brain Axis
A gut-derived metabolite alters brain activity and anxiety behavior in mice. – Needham, B.D. et al., Nature.

Safety and target engagement of an oral small-molecule sequestrant in adolescents with autism spectrum disorder: an open-label phase 1b/2a trial. – Campbell, A.S., Needham, B.D., Meyers, C.R. et al., Nature Medicine.

Animal Experiments
Tryptophan-derived microbial metabolites activate the aryl hydrocarbon receptor in tumor-associated macrophages to suppress anti-tumor immunity. – Hezaveh, K. et al., Immunity.

Stochastic microbiome assembly depends on context. – Jones, E.W. et al., PNAS.

IBD-Associated Atg16L1T300A Polymorphism Regulates Commensal Microbiota of the Intestine. – Liu, H. et al., Frontiers in Immunology.

A homeostatic interferon-lambda response to bacterial microbiota stimulates preemptive antiviral defense within discrete pockets of intestinal epithelium. – Van Winkle, J.A. et al. eLife.

Enteric nervous system modulation of luminal pH modifies the microbial environment to promote intestinal health. – Hamilton, M.K. et al., PLoS Pathogens.

Animal Microbiome
Characterization of the Gut Microbiome and Resistomes of Wild and Zoo-Captive Macaques. – Jia, T. et al., Frontiers in Veterinary Science.

Deep Functional Profiling of Wild Animal Microbiomes Reveals Probiotic Bacillus pumilus Strains with a Common Biosynthetic Fingerprint. – Baranova, M.N. et al., International Journal of Molecular Sciences.

Plant, Root, and Soil Microbiome
Plant immunity suppression via PHR1-RALF-FERONIA shapes the root microbiome to alleviate phosphate starvation. – Tang, J. et al., The EMBO Journal.

Extracts from Environmental Strains of Pseudomonas spp. Effectively Control Fungal Plant Diseases. – Librizzi, V. et al., Plants.

Mega-fire in Redwood Tanoak Forest Reduces Bacterial and Fungal Richness and Selects for Pyrophilous Taxa that are Phylogenetically Conserved. – Enright, D.J. et al., Molecular Ecology.

Water and Extremophile Microbiome
Analysis of antibiotic resistance genes reveals its important role in influencing the community structure of ocean microbiome. – Yang, P. et al., The Science of the Total Environment.

Seaweeds influence oyster microbiota and disease susceptibility. – Dugeny, E. et al., The Journal of Animal Ecology.

Air Microbiome
Vertical stratification of the air microbiome in the lower troposphere. – Drautz-Moses, D.I. et al., PNAS.

Bioinformatics
Evaluating supervised and unsupervised background noise correction in human gut microbiome data. – Briscoe, L. et al., PLoS Computational Biology.

December 20, 2021

Posted on December 20, 2021 by Kara

Today’s digest is a grab bag that includes research articles on the vaginal microbiota, the gut microbiota of dairy calves, microbial loads in medical waste, and more! I’ve also highlighted a non-microbiology article that found that pet dog owners were significantly less depressed than non-pet owners during the pandemic. So if you’re looking for more reasons to adopt a new furry friend, you can add this one to the list!

General microbiome

Genomic comparison and phenotypic profiling of small colony variants of Burkholderia pseudomallei – Zulkefli et al. – PLOS One

Human vaginal microbiome

Vaginal microbiota of American Indian women and associations with measures of psychosocial stress – Borgogna et al. – PLOS One

Human gut microbiome

Gut microbiota features associated with Clostridioides difficile colonization in dairy calves – Redding et al. – PLOS One

Animal microbiome

Culicoides Latreille (Diptera: Ceratopogonidae) as potential vectors for Leishmania martiniquensis and Trypanosoma sp. in northern Thailand – Sunantaraporn et al. – PLOS Neglected Tropical Diseases

Migratory wild birds carrying multidrug-resistant Escherichia coli as potential transmitters of antimicrobial resistance in China – Yuan et al. – PLOS One

Plant, root, and soil microbiome

Characterization of soils conducive and non-conducive to Prunus replant disease – Khan et al. – Plos One

Built environment

Disposal habits and microbial load of solid medical waste in sub-district healthcare facilities and households in Yilo-Krobo municipality, Ghana – Egbenyah et al. – PLOS One

Phages and viruses

A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus – Celone et al. – PLOS Neglected Tropical Diseases

Bioinformatics

Genomic prediction using low-coverage portable Nanopore sequencing – Lamb et al. – PLOS One

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations – Lim et al. – PLOS One

Kara’s non-microbiology pick

***Depression, anxiety, and happiness in dog owners and potential dog owners during the COVID-19 pandemic in the United States – Martin et al. – PLOS One

May 3, 2021

Posted on May 2, 2021 by Aleksi Husso

Water microbiome

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea – Płaza et al. – PLoS ONE

From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru – Romero et al. – PLoS ONE

Distribution and diversity of eukaryotic microalgae in Kuwait waters assessed using 18S rRNA gene sequencing – Kumar et al. – PLoS ONE

Plant microbiome

Toward understanding microbiota homeostasis in the plant kingdom – Paasch & He – PLoS Pathogens

Animal microbiome

Seasonal dynamics of diet–gut microbiota interaction in adaptation of yaks to life at high altitude – Guo et al. – npj Biofilms and Microbiomes

Low biomass microbiome

Experimental parameters defining ultra-low biomass bioaerosol analysis – Luhung et al. – npj Biofilms and Microbiomes

Human gut microbiome

A rich meconium metabolome in human infants is associated with early-life gut microbiota composition and reduced allergic sensitization – Petersen et al. – Cell Reports Medicine

March 18, 2021

Posted on March 19, 2021 by Kara

Greetings from Pittsburgh!

Today’s digest has a lot of food and agriculture associated articles. Several articles focus on the effects of various pathogens on dairy cows, beef steers, and poultry breeds! For those of us who are more interested in plants, there is an article on biogas production from tomato waste and a preprint on how the microbial community of food waste changes during the composting process. Finally, I included a research article about social media during the pandemic since I’m sure I’m not the only one who has relied on it a little too heavily over the last year…

Happy reading!

General microbiome

Preprint: Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations – Conrad et al. – bioRxiv

BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE – Demo et al. – PLOS ONE

Review: The gut microbiota–brain axis in behaviour and brain disorders – Morais et al. – Nature Reviews Microbiology

Preprint: Cross-species evolutionary rewiring in the enteric bacterium Campylobacter – Taylor et al. – bioRxiv

Human gut microbiome

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis – Vega et al. – PLOS ONE

Animal experiments

Preprint: Low pathogenic avian influenza virus infection retards colon microbiome diversification in two different chicken lines – Chrzastek et al. – bioRxiv

Preprint: Borrelia infection in rodent host has dramatic effects on the microbiome of ticks – Hamilton et al. – bioRxiv

Animal microbiome

Preprint: The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe – Wallace et al. – bioRxiv

Plant, root, and soil microbiome

Effects of precipitation change and nitrogen addition on the composition, diversity, and molecular ecological network of soil bacterial communities in a desert steppe – Jia et al. – PLOS ONE

Preprint: Changes and composition of microbial community during aerobic composting of household food waste – Jin et al. – bioRxiv

Preprint: What’s under the Christmas tree? Soil acidification alters fir tree rhizosphere bacterial and eukaryotic communities, their interactions, and functional traits – Steven et al. – bioRxiv

A comparative analysis of biogas production from tomato bio-waste in mesophilic batch and continuous anaerobic digestion systems – Szilágyi et al. – PLOS ONE

Food microbiology

Red seaweed (Asparagopsis taxiformis) supplementation reduces enteric methane by over 80 percent in beef steers – Roque et al. – PLOS ONE

Prevalence and distribution of multilocus sequence types of Staphylococcus aureus isolated from bulk tank milk and cows with mastitis in Pennsylvania – Thomas et al. – PLOS ONE

Multidrug-resistant enterobacteria in newborn dairy calves in Germany – Waade et al. – PLOS ONE

Phages and viruses

Review: Viral and host heterogeneity and their effects on the viral life cycle – Jones et al. – Nature Review Microbiology

Bioinformatics

Dcmd: Distance-based classification using mixture distributions on microbiome data – Shestopaloff et al. – PLOS Computational Biology

Kara’s non-microbiology pick

Don’t put all social network sites in one basket: Facebook, Instagram, Twitter, TikTok, and their relations with well-being during the COVID-19 pandemic – Masciantonio et al. – PLOS ONE

December 7, 2020

Posted on December 7, 2020 by Feargal

Today we have some excellent review articles in Science, and Gut as well as several interesting research articles.

COVID-19

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms – Gordon et al. Science

Robust neutralizing antibodies to SARS-CoV-2 infection persist for months – Wajnberg et al. Science

General Microbiome

[REVIEW] The role of the microbiota in human genetic adaptation – Suzuki and Ley – Science

Gut microbiome

Investigating the Role of Diet and Exercise in Gut Microbe-Host Cometabolism – Penney et al. mSystems

[REVIEW] Gut microbiota-derived metabolites as central regulators in metabolic disorders – Agus et al. Gut

Human respiratory microbiome

[REVIEW] Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways. Khanolkar et al. mSystems

Animal microbiome

Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen – Gharechahi et al. ISME

Altitude influences microbial diversity and herbage fermentation in the rumen of yaks – Fan et al. BMC Microbiology

Bioinformatics

[REVIEW] Analysis of microbial compositions: a review of normalization and differential abundance analysis – Lin and Peddada. Npj Biofilms and Microbiomes.

Non-microbiome pick

A comparative genomics multitool for scientific discovery and conservation – Zoonomia Consortium. Nature

November 27, 2020

Posted on November 27, 2020 by Axel Künstner

Hello from Luebeck!

Today’s digest covers the connection between human diseases and gut microbiome, the gut feeling, secrets about plant growth and vertical stratification in urban spaces. Happy reading and happy black Friday!

General microbiome

Human microbiome and allergy – Montecchiani & Fanos – Pediatric Allergy and Immunology

Early life and childhood

Early Gut Fungal and Bacterial Microbiota and Childhood Growth – Schei et al. – Frontiers in Pediatrics

Oral human microbiome

Characterization of Lactobacilli isolated from carious dentin after selective caries removal and cavity sealing – Damé-Teixeira et al. – Archives of Oral Biology

Human gut microbiome

A Pilot Study: Changes of Intestinal Microbiota of Patients With Non-small Cell Lung Cancer in Response to Osimertinib Therapy – Cong et al. – Frontiers in Microbiology

What connection is there between intestinal microbiota and heart disease? – Poli – European Heart Journal Supplements

The Student-Centered Classroom: The New Gut Feeling – Lyles & Oli – FEMS Microbiology Letters

Animal microbiome

Comparison of the fecal microbiota composition between the blue Sheep (Pseudois nayaur) fed with Lolium perenne and Sorghum sudanense – Wu, Yuan & Pan – Canadian Journal of Microbiology

Plant, root, and soil microbiome

[REVIEW]The plant microbiome: The dark and dirty secrets of plant growth – Tkacz & Poole – Pants People Plant

Water and extremophile microbiome

[PREPRINT]Rapid shift in microbial community structure in a neutral hydrothermal hot spring from Costa Rica – Rojas-Gätjens et al. – bioRxiv

Environment

Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al. – Environmental Health Perspectives

Techniques

Power calculations for detecting differences in efficacy of fecal microbiota donors – Olesen – Contemporary Clinical Trials Communications

November 14, 2020

Posted on November 14, 2020 by Alise Ponsero

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