September 30, 2021

Today’s digest includes a quantification of bacterial strains after fecal microbiota transplantation, a network analysis of the strawberry greenhouse soil microbiome after soil amendments, and an article about enhanced copper-resistance genes in Alteromonas macleodii. Also included are multiple preprints on topics such as denitrification pathways present in tunda soil metagenomes as well as the response of Endozoicomonas, a core coral bacterial group, to heat stress and host lysates.

General microbiome

Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature – Achtman et al. – PLOS Genetics

Preprint: Role of the mobilome in the global dissemination of the carbapenem resistance gene blaNDM – Acman et al. – bioRxiv

Preprint: Existence of log-phase Escherichia coli persisters and lasting memory of a starvation pulse – Svenningsen et al. – bioRxiv

Human gut microbiome

Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes – Aggarwala et al. – Nature Microbiology

Animal microbiome

A role for arthropods as vectors of multidrug-resistant Enterobacterales in surgical site infections from South Asia – Hassan et al. – Nature Microbiology

Plant, root, and soil microbiome

Response of soil microbiome structure and its network profiles to four soil amendments in monocropping strawberry greenhouse – Liu et al. – PLOS One

Preprint: Truncated denitrifiers dominate the denitrification pathway in tundra soil metagenomes – Pessi et al. – bioRxiv

Water and extremophile microbiome

Preprint: Response of Endozoicomonas montiporae to heat stress and coral host lysates – Chan et al. – bioRxiv

Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings – Cusick et al. – PLOS One

Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India – Sushmitha et al. – PLOS One

Preprint: Ecological stochasticity and phage induction diversify bacterioplankton communities at the microscale – Szabo et al. – bioRxiv

September 15, 2021

Today’s digest is fairly light. It includes an article focused on the protective role of bacterial endosymbionts on soil fungus, a preprint on the indoor environment as a source for human-associated anaerobes, and work demonstrating how protein biosensors can be used to track the effects osmotic stress on cells.

Happy reading!

General microbiome

Preprint: Comprehensive comparative genomics analysis for the emerging human pathogen Streptococcus dysgalactiae subsp. equisimilis (SDSE): A case study and Pan-subspecies genomic analysis – Saeb & Tayeb – bioRxiv

Preprint: The model arbuscular mycorrhizal fungus Rhizophagus irregularis harbours endosymbiotic bacteria with a highly reduce genome – Savary et al. – bioRxiv

Preprint: A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare? – van Vilet et al. – bioRxiv

Animal microbiome (for animals in the wild)

Differences in gut microbiome composition between sympatric wild and allopatric laboratory populations of omnivorous cockroaches – Tinker et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Bacterial endosymbionts protect beneficial soil fungus from nematode attack – Büttner et al. – Proceedings of the National Academy of Sciences of the United States of America

Built environment

Preprint: The indoor environment – A potential source for intact human-associated anaerobes – Pausan et al. – bioRxiv

Techniques

Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells – Cuevas-Velazquez et al. – Nature Communications

July 23, 2021

Happy Friday!

It’s an exciting day here because I’m packing for fieldwork! In just a few short days I’ll be sampling from a saline aquifer in Illinois. For those of you who aren’t lucky enough to be going into the field, today’s digest is packed with a wide range of articles. Topics covered include the wild spider gut microbiome, the presence of antibiotic resistance genes in an Ohio river, the mosquito virome, the plant rhizosphere, and more.

Happy reading!

Human gut microbiome

Preprint: Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria – Pudlo et al. – bioRxiv

Animal experiments

Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge – Harlow et al. – PLOS ONE

Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation – Velasco et al. – PLOS ONE

Animal microbiome

Preprint: Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys – Craft et al. – bioRxiv

Interspecific variation and functional traits of the gut microbiome in spiders from the wild: The largest effort so far – Tyagi et al. – PLOS ONE

Plant, root, and soil microbiome

Preprint: Tillage intensity and plant rhizosphere selection shape bacterial-archaeal assemblage diversity and nitrogen cycling genes – Cloutier et al. – bioRxiv

Water and extremophile microbiome

Preprint: An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent – Murphy – bioRxiv

Biogeochemistry of the Antrim Shale Natural Gas Reservoir – Stemple et al. – ACS Earth and Space Chemistry

Built environment

Preprint: Novel municipal sewage-associated bacterial genomes and their potential in source tracking – Linder et al. – bioRxiv

Preprint: Structure of bacterial communities in Japanese-style bathrooms: Comparative sequencing of bacteria in shower water and showerhead biofilms using a portable nanopore sequencer – Fujiyoshi et al. – bioRxiv

Phages and viruses

Preprint: Dynamic surveillance of mosquitoes and their viromes in Wuhan during 2020 – Ren et al. – bioRxiv

Techniques

Simple mapping-based quantification of a mock microbial community using total RNA-seq data – Moriya – PLOS ONE

Preprint: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Shibata et al. – bioRxiv

June 23, 2021

Happy Wednesday!

Today’s digest includes a review on the microbial transformations of human bile acids as well as research articles focused on extremophiles including Arthrobacter, Acidithiobacillus, and Atribacteria. Also included are a wide variety of preprints on topics such as CRISPR-Cas, the vaginal microbiome, immunocompetence in pigs, the evaluation of RNAlater for preserving field samples for metaproteomics, and more!

Happy reading!

General microbiome

Preprint: CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids – Pinilla-Redondo et al. – bioRxiv

Human respiratory microbiome

Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China–association with asthma, rhinitis and rhinoconjunctivitis in high school students – Fu et al. – Microbiome

Human vaginal microbiome

Preprint: Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data – France et al. – bioRxiv

Human gut microbiome

Review: Microbial transformations of human bile acids – Guzior & Quinn – Microbiome

Preprint: Targeted high-resolution taxonomic identification of Bifidobacterium longum subsp. infantis using human milk oligosaccharide metabolizing genes – Tso et al. – bioRxiv

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants – Xie et al. – Microbiome

Animal experiments

Preprint: Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs – Ramayo-Caldas et al. – bioRxiv

Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens – Wen et al. – Microbiome

Animal microbiome

Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish – Röthig et al. – Microbiome

Plant, root, and soil microbiome

Preprint: Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments – Glass et al. – bioRxiv

Preprint: Seed microbiota revealed by a large-scale meta-analysis including 50 plant species – Simonin et al. – bioRxiv

Preprint: The activity and functions of subarctic soil microbial communities vary across vegetation types – Viitamäki et al. – bioRxiv

Water and extremophile microbiome

Preprint: Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep – Chen et al. – bioRxiv

Preprint: Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures – Li et al. – bioRxiv

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir – Mo et al. – Microbiome

Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution – Shen et al. – Microbiome

Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs – Sriaporn et al. – Microbiome

Built environment

Preprint: Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking – Suttner et al. – bioRxiv

Phages and viruses

Preprint: Expanding clinical phage microbiology: Simulating phage inhalation for respiratory tract infections – Porat et al. – bioRxiv

Techniques

Ultra-accurate microbial amplicon sequencing with synthetic long reads – Callahan et al. – Microbiome

Preprint: Evaluation of RNAlater as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses – Jensen et al. – bioRxiv

Preprint: Predicting microbiome compositions through deep learning – Michel-Mata et al. – bioRxiv

June 4, 2021

Greetings from Pittsburgh!

Today’s digest includes a review about the digestibility of adult dog diets, several articles about the human gut microbiome, an article about the spinach phyllosphere, and research about the effect of fertilizer and continuous garlic cultivation on the soil microbiome. It also includes topics such as microorganisms in ancient Siberian permafrost, the use of a probiotic consortium as an alternative to chemical remediation of oil spills, and much more!

If you want a lighter read, I’ve also included a fun Smithsonian Magazine article about the use of bacteria in art restoration.

Happy Friday!

General microbiome

Review: An evolving view on biogeochemical cycling of iron – Kappler et al. – Nature Reviews Microbiology

Review: Beyond horizontal gene transfer: the role of plasmids in bacterial evolution – Rodríguez-Beltrán et al. – Nature Reviews Microbiology

Review: Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle – Salje – Nature Reviews Microbiology

Reviews: Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions – Weisskopf et al. – Nature Reviews Microbiology

Human skin microbiome

Apple cider vinegar soaks do not alter the skin bacterial microbiome in atopic dermatitis – Luu et al. – PLOS One

Human gut microbiome

Metabolomic profiling identifies complex lipid species and amino acid analogues associated with response to weight loss interventions – Bihlmeyer et al. – PLOS One

Gut microbiome differences among Mexican Americans with and without type 2 diabetes mellitus – Kitten et al. – PLOS One

Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank – Liu et al. – Microbiome

Gut microbiota profiles of young South Indian children: Child sex-specific relations with growth – Shivakumar et al. – PLOS One

Animal experiments

Review: Soybean meal and poultry offal meal effects on digestibility of adult dogs diets – Vanelli et al. – PLOS One

Animal microbiome

A survey of mosquito-borne and insect-specific viruses in hospitals and livestock markets in western Kenya – Chiuya et al. – PLOS One

Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contact – Émie et al. – Microbiome

Characterization of oral and cloacal microbial communities in cold-stunned Kemp’s ridley sea turtles (Lepidochelys kempii) during the time course of rehabilitation – McNally et al. – PLOS One

Plant, root, and soil microbiome

Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage – Ibekwe et al. – PLOS One

Comparison of bacterial and archaeal communities in two fertilizer doses and soil compartments under continuous cultivation system of garlic – Zhou et al. – PLOS One

Water and extremophile microbiome

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale – Carnevali et al. – Microbiome

Urban wastewater bacterial communities assemble into seasonal steady states – LaMartina et al. – Microbiome

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost – Liang et al. – Microbiome

Genomic and immunogenic changes of Piscine novirhabdovirus (Viral Hemorrhagic Septicemia Virus) over its evolutionary history in the Laurentian Great Lakes – Niner et al. – PLOS One

Built environment

Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites – Silva et al. – Microbiome

Microbes in the news

Italian Art Restorers Used Bacteria to Clean Michelangelo Masterpieces – Davis-Marks – Smithsonian Magazine

May 17, 2021

Good morning from Pittsburgh.

Today’s digest is preprint-heavy and has quite a few articles focused on soil, plants, and agriculture. If you aren’t interested in those areas of research, we also have articles with topics spanning the 1918 pandemic to multi-donor fecal transplants to carbohydrate utilization by marine fungi.

Happy reading!

General microbiome

Fresh extension of Vibrio cholerae competence type IV pili predisposes them for motor-independent retraction – Chlebek et al. – Appl Environ Microbiol

Preprint: Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions – Honda et al. – bioRxiv

Preprint: Archival influenza virus genomes from Europe reveal genomic and phenotypic variability during the 1918 pandemic – Patrono et al. – bioRxiv

Preprint: Fluorescent protein expression as a proxy of bacterial fitness in a high throughput assay – Schlechter et al. – bioRxiv

Preprint: Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units – Viana de Siqueira et al. – bioRxiv

Human skin microbiome

Preprint: Anatomy promotes neutral coexistence of strains in the human skin microbiome – Conwill et al. – bioRxiv

Preprint: Gene- and genome-centric dynamics shape the diversity of oral bacterial populations – Utter et al. – bioRxiv

Human gut microbiome

Preprint: Two microbiota subtypes identified in Irritable Bowel Syndrome with distinct responses to the low-FODMAP diet – Vervier et al. – bioRxiv

Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity – Wilson et al. – Microbiome

Plant, root, and soil microbiome

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula – Brown et al. – Microbiome

Preprint: A novel dual enrichment strategy provides soil- and digestate-competent N2O-respiring bacteria for mitigating climate forcing in agriculture – Jonassen et al. – bioRxiv

Preprint: Temporal dynamics of microbial transcription in wetted hyperarid desert soils – León-Sobrino et al. – bioRxiv

Preprint: Metagenomic sequencing for rapid identification of Xylella fastidiosa from leaf samples – Roman-reyna et al. – BioRxiv

Preprint: Pseudomonas arenae sp. nov., Pseudomonas glycinis sp. nov. and Pseudomonas harudinis sp. nov., three novel bacterial species and plant endophytes – Seaton et al. – bioRxiv

Preprint: Phage-resistant bacteria reveal a role for potassium in root colonization – Tzipilevich & Benfey – bioRxiv

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems – Qian et al. – Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Potential and expression of carbohydrate utilization by marine fungi in the global ocean – Baltar et al. – Microbiome

Preprint: Syntrophic H2 production enhances the performance of primarily acetate-supplemented reactors treating sulphate contaminated solutions – Hessler et al. – bioRxiv

April 26, 2021

Greetings from Pittsburgh! Today’s digest is preprint heavy. Topics include an optimized protocol for cyanobacterial 16S rRNA analysis, a panel of Pseudomonas aeruginosa clinical isolates, and more! Happy reading!

Events and jobs

The National Summer Undergraduate Research Project is looking for microbiology or computational immunology grad trainees, postdocs, staff scientists, and group leaders to serve as mentors for their summer program. Sign up here!


General microbiome

Preprint: A panel of diverse Pseudomonas aeruginosa clinical isolates for research and development – Lebreton et al. – bioRxiv

Pregnancy and early life

Preprint: Diet potentially drives the differentiation of eating behaviours via alterations to the gut microbiome in infants – Yan et al. – bioRxiv

Multi-site human microbiome

An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer – Borchmann – Microbiome

Plant, root, and soil microbiome

Preprint: Transcription of macromolecular N degrading genes provides a window into organic nitrogen decomposition in soil – Sieradzki et al. – bioRxiv

Built environment

Preprint: Microbial biomass, composition, and functions are responsible for the differential removal of trace organic chemicals in biofiltration systems – Cao et al. – bioRxiv
Microbes in space

Food microbiology

Preprint: Fluoroquinolone-resistant Escherichia coli originating on dairy farms are an infrequent cause of bacteriuria in humans living in the same geographical region – Mounsey et al. – bioRxiv

Techniques

Preprint: Optimized protocol for Cyanobacterial 16S rRNA analysis in Danube Delta lakes – Moza & Postolache – bioRxiv

April 2, 2021

Good morning and happy Friday!

In my last blog post I requested reader contributions and many of you reached out! Below are some of the highlights which include a commentary on phylogenetic core groups, a preprint on viral RNA methylation in Wolbachia, a database for the murine oral bacterial community, and a research article on fungal modification in the leaf-cutter ant fungal garden ecosystem.

Events and jobs

Biological Sciences Laboratory Instructor Position at Smith College in Northampton, MA

General microbiome

***Commentary: Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework – Pascual-García – Microbiome

Animal microbiome

***Preprint: Differential viral RNA methylation contributes to pathogen blocking in Wolbachia-colonized arthropod – Bhattacharya et al. – bioRxiv

Preprint: Isolation and characterization of a novel Wolbachia bacteriophage from Allonemobius socius crickets in Missouri – Fischer et al. – bioRxiv

***From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem – Khadempour et al. – mSystems

Plant, root, and soil microbiome

Preprint: Experimental evolution-driven identification of Arabidopsis rhizosphere competence genes in Pseudomonas protegens – Zhang et al. – bioRxiv

Built environment

Metagenomic profile of microbial communities in a drinking water storage tank sediment after sequential exposure to monochloramine, free chlorine, and monochloramine – Gomez-Alvarez et al. – ACS EST Water

Bioinformatics

***A 16S rRNA gene and draft genome database for the murine oral bacterial community – Joesph et al. – mSystems

March 30, 2021

Good morning!

Today’s digest is fairly light, with just a few preprints, so I’d like to do something a bit different today! If you have a recent microbiome-related publication (or have read one that’s particularly exciting) send me a direct message on Twitter (@KaraAnnTinker) or comment on this blog post. If it hasn’t been included on the blog yet, I’ll either update today’s post or cover it on my next blog post later this week.

General microbiome

Preprint: Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration – Carlson et al. – bioRxiv

Preprint: Paraburkholderia edwinii protects Aspergillus sp. from phenazines by acting as a toxin sponge – Dahlstrom and Newman – bioRxiv

Plant, root, and soil microbiome

Preprint: Strain diversity of plant-associated Lactiplantibacillus plantarum – Yu et al. – bioRxiv

Water and extremophile microbiome

Preprint: Microbial helpers allow cyanobacteria to thrive in ferruginous waters – Szeinbaum et al. – bioRxiv

March 18, 2021

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