June 8, 2022

Happy Friday! Today’s digest includes articles about Gardnerella vaginalis clades in pregnancy, how a Japanese herbal medicine may alleviate a leaky gut, and a feasibility study of the impact of oral activated charcoal on healthy volunteers.

General microbiome

Clinical Burkholderia pseudomallei isolates from north Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains – Burnard et al. – PLOS Neglected Tropical Diseases

Preprint: The energy requirements of ion homeostasis determine the lifespan of starving bacteria – Schink et al. – bioRxiv

Preprint: A novel bacterial speciation process observed in a symbiotic marine population – Wang et al. – bioRxiv

Human vaginal microbiome

Gardnerella vaginalis clades in pregnancy: New insights into the interactions with the vaginal microbiome – Severgnini et al. – PLOS One

Human gut microbiome

Saireito, a Japanese herbal medicine, alleviates leaky gut associated with antibiotic-induced dysbiosis in mice – Ozaka et al. – PLOS One

A dose-finding safety and feasibility study of oral activated charcoal and its effects on the gut microbiota in healthy volunteers not receiving antibiotics – Rashidi et al. – PLOS One

Water and extremophile microbiome

The microbial community and functional potential in the Midland Basin reveal a community dominated by both thiosulfate and sulfate-reducing microorganisms – Tinker et al. – Microbiology Spectrum


Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations – Ganz et al.- PLOS One

June 3, 2022

Happy Friday!

Today’s digest has articles on COVID-19 vaccine hesitancy, a new R package to extract network backbones, and a class of novel antibiotics that targets a Mycobacterium tuberculosis PE-PGRS protein. There also preprints on biofilm winkling in Bacillus subtilis, the dental calculus microbiome, and the relationship between eukaryotic genomes and ocean plankton in a global metagenomic dataset.


Next week is ASM Microbe! I’ll be there, wearing a KN-95 and clutching a box of rapid tests. Feel free to comment or reach out if you’re also attending.


Oro-facial mucocutaneous manifestations of Coronavirus Disease-2019 (COVID-19): A systematic review – Fakhruddin et al. – PLOS ONE

Preprint: The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity – Kim et al. – bioRxiv

Determinants of the COVID-19 vaccine hesitancy spectrum – Piltch-Loeb et al. – PLOS ONE

General microbiome

Preprint: Fatty acid synthesis knockdown promotes biofilm wrinkling and inhibits sporulation in Bacillus subtilis – Arjes et al. – bioRxiv

Association of Strongyloides stercoralis infection and type 2 diabetes mellitus in northeastern Thailand: Impact on diabetic complication-related renal biochemical parameters – Yingklang et al. – PLOS ONE

Analysis of secondary metabolite gene clusters and chitin biosynthesis pathways of Monascus purpureus with high production of pigment and citrinin based on whole-genome sequencing – Zhang et al. – PLOS ONE

Human respiratory microbiome

A novel class of antimicrobial drugs selectively targets a Mycobacterium tuberculosis PE-PGRS protein – Seo et al. – PLOS Biology

Human oral microbiome

Preprint: Assessing the influence of the Mediterranean diet on dental calculus microbiome composition: a pilot study – Innocenti et al. – bioRxiv

Human gut microbiome

Lactobacillus plantarum improves LPS-induced Caco2 cell line intestinal barrier damage via cyclic AMP-PKA signaling – Wei et al. – PLOS ONE

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

Preprint: Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton – Alexander et al. – bioRxiv


backbone: An R package to extract network backbones – Neal – PLOS ONE

March 3, 2022

Today’s digest is heavy on studies focused on the gut and soil microbiomes. It also includes articles focused on microbial indoor air quality as well as bacterial vaginosis and aerobic vaginitis among pregnant women. If you’d still like more, I’ve also included several preprints.

Happy reading!

Human vaginal microbiome

Prevalence of bacterial vaginosis and aerobic vaginitis and their associated risk factors among pregnant women from northern Ethiopia: A cross-sectional study – Yalew et al. – PLOS One

Human gut microbiome

Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research – Tierney et al. – PLOS Biology

Preprint: Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation – Venzon et al. – bioRxiv

Hydrogen-producing small intestinal bacterial overgrowth is associated with hepatic encephalopathy and liver function – Yokoyama et al. – PLOS One

Plant, root, and soil microbiome

Preprint: Deciphering the potential niche of two novel black yeast fungi from a biological soil crust based on their genomes, phenotypes, and melanin regulation – Carr et al. – bioRxiv

Bacterial age distribution in soil—Generational gaps in adjacent hot and cold spots – Borer & Or – PLOS Computational Biology

Deciphering the influence of Bacillus subtilis strain Ydj3 colonization on the vitamin C contents and rhizosphere microbiomes of sweet peppers – Liang et al. – PLOS One

Antimicrobial effect and mechanism of bovine lactoferrin against the potato common scab pathogen Streptomyces scabiei – Nakamura et al. – PLOS One

Preprint: Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum – Xi et al. – bioRxiv

Built environment

Comprehensive health risk assessment of microbial indoor air quality in microenvironments – Kumar et al. – PLOS One

Phages and viruses

Preprint: Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: killers and drivers of resistance evolution – Leclerc et al. -bioRxiv


Preprint: Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution – Kiefl et al. – bioRxiv

January 7, 2022

Today’s digest covers a range of topics including a duplex qPCR assay to detect lung infections, an investigation into sand fly symbionts, and a characterization of a fermented soybean food (Pe poke). If you want to end the week on a good note, I’d suggest reading the two articles I’ve highlighted below. One demonstrates that flooding and ecological restoration of former cranberry farmland also restores wetland microbial communities and soil function. The second provides a new barcoding strategy for the phenotypic screening of mosquitos that can be applied towards malaria research.

Happy reading!

General microbiome

Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation – Anbumani et al. – npj Biofilms and Microbiomes

Bacteria can be selected to help beneficial plasmids spread – Dimitriu et al. – PLOS Biology

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network – Urchueguía et al. – PLOS Biology

Human respiratory microbiome

Detection of Pneumocystis jirovecii and Toxoplasma gondii in patients with lung infections by a duplex qPCR assay – Wu et al. – PLOS Neglected Tropical Diseases

Animal experiments

***Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission – Sturm et al. – PLOS Biology

Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia – Vivero-Gomez – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar – Tamang et al. – PLOS One

***Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland – Rubin et al. – PLOS One

Water and extremophile microbiome

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment – Remple et al. – npj Biofilms and Microbiomes

December 20, 2021

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


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

December 2, 2021

Happy December from Pittsburgh!

Today’s digest includes original research on the impacts of fungal entomopathogens on Wolbacia infections and the influence of nutrient status on the response of a diatom to oil and dispersant. I have also included a study protocol for oral microbiome transplant for the treatment of dental caries and periodontal disease as well as preprints on a variety of topics. Finally, I want to highlight two articles I included that are little different from my usual content: the first is on predictors of willingness to receive the COVID-19 vaccination and the second is focused on transparency in peer review.



***To vaccinate or not to vaccinate!? Predictors of willingness to receive Covid-19 vaccination in Europe, the U.S., and China – Brailovskaia et al. – PLOS One

General microbiome

Preprint: Copper nanoparticles as modulator of active bacterial population and their physiology in ecosphere – Alboloushi et al. – bioRxiv

Preprint: Metabolite Damage and Damage-Control in a Minimal Genome – Haas et al. – bioRxiv

Development and characterization of an oral microbiome transplant among Australians for the treatment of dental caries and periodontal disease: A study protocol – Nath et al. – PLOS One

Preprint: Heat activation and inactivation of bacterial spores. Is there an overlap? – Wen et al. – bioRxiv

Animal experiments

Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial – van Tonder et al. – PLOS Pathogens

Animal microbiome

Impacts of fungal entomopathogens on survival and immune responses of Aedes albopictus and Culex pipiens mosquitoes in the context of native Wolbachia infections – Ramirez et al. – PLOS Neglected Tropical Diseases

Water and extremophile microbiome

Influence of nutrient status on the response of the diatom Phaeodactylum tricornutum to oil and dispersant – Kamalanathan et al. – PLOS One

Preprint: Community-wide epigenetics provides novel perspectives on the ecology and evolution of marine microbiome – Seong et al. – bioRxiv

Preprint: Microbial cysteine degradation is a source of hydrogen sulfide in oxic freshwater lakes – Tran et al. – bioRxiv


When and why direct transmission models can be used for environmentally persistent pathogens – Benson – PLOS Computational Biology


Preprint: The processing of staphylococcal biofilm images from Fluorescence and Confocal Microscopy to assess in vitro efficacy of antiseptic molecules – Krasowski et al. – bioRxiv

Science, publishing, and career

***Transparency in peer review: Exploring the content and tone of reviewers’ confidential comments to editors – O’Brien et al. – PLOS One

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

July 16, 2021

Today’s digest features studies on environmental contamination of carbapenem-resistant Klebsiella pneumoniae in China (spoiler: extensive contamination, but has negligible impact on patient colonisation), the dynamic change and correlation of microbiome from different body sites to the treatment response as well as immune-related adverse events of immunotherapy in lung cancer patients, and more.

Also, check out a regularly-updated collection of FREE, ONLINE microbiome events. Happy Friday!

Human microbiome

*Prospective correlation between the patient microbiome with response to and development of immune-mediated adverse effects to immunotherapy in lung cancer – Justin Chau – BMC Cancer

Gut microbiome

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner – Emmanuel Montassier – Nature Microbiology

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Sandeep Verma – PlosOne

Differences in the individual curative effect of acupuncture for obese women with polycystic ovary syndrome based on metagenomic analysis: study protocol for a randomized controlled trial – Huaying Fan – Trials

Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes – Danielle Peterson – Frontiers in Microbiology


*Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study – Li Wei – Microbiology Spectrum

*Linezolid- and multidrug-resistant enterococci in raw commercial dog food, Europe, 2019–2020 – Ana R. Freitas – Emerging Infectious Diseases

Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study – Huan Chen – PeerJ

Predicting antibiotic resistance gene abundance in activated sludge using shotgun metagenomics and machine learning – Yuepeng Sun – Water Research

Animal microbiome

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers – Déborah Romaskevis Gomes Lopes – Journal of Animal Science and Biotechnology

Animal experiment

An osmotic laxative renders mice susceptible to prolonged Clostridioides difficile colonization and hinders clearance – Sarah Tomkovich – bioRxiv


Critical Assessment of Metagenome Interpretation – the second round of challenges – F. Meyer – bioRxiv

Disentangling environmental effects in microbial association networks – Maria Deutschmann – bioRxiv

Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

July 14, 2021

General microbiome

Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals – Kirsch et al. – Annual Review of Virology

Helicobacter pylori infection has a detrimental impact on the efficacy of cancer immunotherapies – Oster et al. – Gut

Pregnancy and early life

Cervicovaginal microbiota and metabolome predict preterm birth risk in an ethnically diverse cohort – Flaviani et al. – JCI Insight

[REVIEW][Early-life gut microbiota and its connection to metabolic health in children: Perspective on ecological drivers and need for quantitative approach – Jian et al. – EBBioMedicine

Associations of air pollution and greenness with the nasal microbiota of healthy infants: A longitudinal study – Gisler et al. – Environmental Research

Human respiratory microbiome

Multi-omics profiling predicts allograft function after lung transplantation – Watzenböck et al. – European Respiratory Journal

Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis – Liu et al. – Genomics, Proteomics & Bioinformatics

Human skin microbiome

[REVIEW]Novel mechanisms of microbial crosstalk with skin innate immunity – Chinnappan & Harris-Tyron – Experimental Dermatology

Shifts in the skin bacterial and fungal communities of healthy children transitioning through puberty – Park et al. – Journal of Investigative Dermatology

Human gut microbiome

Gut-microbiota-targeted diets modulate human immune status – Wastyk et al. – Cell

[REVIEW]Silent hypoxia in COVID-19: a gut microbiota connection – Gopal et al. – Current Opinion in Physiology

[REVIEW]The Athlete and Gut Microbiome: Short-chain Fatty Acids as Potential Ergogenic Aids for Exercise and Training – Bongiovanni, Yin & Heaney

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Verma et al. – PLOS One

Kefir Ameliorates Specific Microbiota-Gut-Brain Axis Impairments in a Mouse Model Relevant to Autism Spectrum Disorder – van de Wouw et al. – Brain, Behavior, and Immunity

Animal microbiome

Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand – Sawaswong et al. – Scientific Reports

Impact of the dietary inclusion of dried food residues on the apparent nutrient digestibility and the intestinal microbiota of dogs – Paßlack et al. – Archives of Animal Nutrition

Triphenyltin exposure causes changes in health-associated gut microbiome and metabolites in marine medaka – He et al. – Environmental Pollution

The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota – Bermudez-Martin et al. – Microbiome

Microbes in space

Seven years of Progress in Determining Fungal Diversity and Characterization of Fungi Isolated from the Japanese Experiment Module KIBO, International Space Station – Satoh et al. – Microbiology and Immunology

Food microbiology

[REVIEW]Virome studies of food production systems: time for ‘farm to fork’ analyses – Mahony & van Sinderen – Current Opinion in Biotechnology


D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies – Chen & Zhang – Bioinformatics

Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model – Hosoda, Fukunaga & Hamada – Bioinformatics

[PREPRINT]Stool Studies Don’t Pass the Sniff Test: A Systematic Review of Human Gut Microbiome Research Suggests Widespread Misuse of Machine Learning – Quinn – arXiv


Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost – Harrison, Randolph & Buerkle – mSystems

Two-Target Quantitative PCR To Predict Library Composition for Shallow Shotgun Sequencing – Cho et al. – mSystems

Statistical approaches for differential expression analysis in metatranscriptomics – Zhang et al. – Bioinformatics

Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets – Kameoka et al. – BMC Genomics

In vitro models of gut digestion across childhood: current developments, challenges and future trends – Fournier et al. – Biotechnology Advances

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