June 18, 2022

Have a nice weekend! Today, in this Digest: The effect of the gut dysbiosis on prostate cancer, microbial inheritance, bee microbiome, rhizosphere microbiota, a comparison of DNA isolation techniques for deep amplicon sequencing, and more…

Human and General Microbiome

Gut dysbiosis promotes prostate cancer progression and docetaxel resistance via activating NF-κB-IL6-STAT3 axis – Weibo Zhong – Microbiome

On the effect of inheritance of microbes in commensal microbiomes – Román Zapién-Campos – BMC Ecology and Evolution

Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth – Sunwha Park – Scientific Reports

Deep Grouping Analysis of the Altered Cervical Canal Microbiota in Intrauterine Adhesion Patients – Xiangdong Hua – Reproductive Sciences

Intestinal microbiota transplantation: do not forget the metabolites – Benjamin H Mullish – The Lancet. Gastroenterology & Hepatology

Characterization of oral and gut microbiome and plasma metabolomics in COVID-19 patients after 1-year follow-up – Guang-Ying Cui – Military Medical Research

Congenitally underdeveloped intestine drives autism-related gut microbiota and behavior – Jie Li – Brain, Behavior, and Immunity

Beneficial Microbes and Compounds

Lacticaseibacillus rhamnosus HA-114 improves eating behaviors and mood-related factors in adults with overweight during weight loss: a randomized controlled trial – Béatrice S-Y Choi – Nutritional Neuroscience

Model Animal Microbiome

New Strains of Akkermansia muciniphila and Faecalibacterium prausnitzii are Effective for Improving the Muscle Strength of Mice with Immobilization-Induced Muscular Atrophy – Hye Rim Byeon – Journal of Medicinal food

Non-Model Animal Microbiome

Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes – Wyatt A Shell – Communications Biology

Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review – Sonam Dixit – Animal Biotechnology

Plant Microbiome

Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees – Maximilian Fernando Becker – Environmental Microbiome

Identifying plant genes shaping microbiota composition in the barley rhizosphere – Carmen Escudero-Martinez – Nature Communications

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato – Ben O Oyserman – Nature Communications

Environmental Microbiome

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables – Jessica L Gronniger – Environmental Microbiology

Microplastics alter nitrous oxide production and pathways through affecting microbiome in estuarine sediments – Cheng Chen – Water Research

500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China – Lei Zhou – Scientific Data

Food Microbiome

Microbiome and -omics application in food industry – Ilario Ferrocino – International Journal of Food Microbiology

Bioinformatic and Experimental Microbiome Analysis

A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities – Justin P Shaffer – BioTechniques

Review: Machine Learning Advances in Microbiology: A Review of Methods and Applications – Yiru Jiang – Frontiers in Microbiology

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

March 23, 2022

General microbiome

Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance – Yu et al. – Nature Microbiology

Human skin microbiome

Skin microbiota diversity among genetically unrelated individuals of Indian origin – Pothbhare et al. – PeerJ

Human gut microbiome

[REVIEW]Gut microbiota and allergic diseases in children – Akagawa & Kaneko – Allergology International

[REVIEW]Gut microbiome: New biomarkers in early screening of colorectal cancer – Zhou et al. – Journal of Clinical Laboratory Analysis

Can gut microbiota throughout the first 10 years of life predict executive functioning in childhood? – Eckermann et al. – Developmental Psychobiology

[PREPRINT]Meta-analysis of the autism gut microbiome identifies factors influencing study discrepancies and machine learning classification – Chavira, Wang & Mills – bioRxiv

Changes of Intestinal Microflora in Colorectal Cancer Patients after Surgical Resection and Chemotherapy – Huang et al. – Computational and Mathematical Methods in Medicine

Animal microbiome

Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation – Dallas & Warne – Microbial Ecology

Changes in gut microbiota composition with age and correlations with gut inflammation in rats – Meng et al. – PLOS One

[REVIEW]Translational multi-omics microbiome research for strategies to improve cattle production and health – Wang & Guan – Emerging Topics in Lefe Sciences

Multi-omics reveals host metabolism associated with the gut microbiota composition in mice with dietary ε-polylysine – Zhang et al. – Food & Function

Soil causes gut microbiota to flourish and total serum IgE levels to decrease in mice – Zhou et al. – Environmental Microbiology

Microbiome-metabolomics deciphers the effects of Cistanche deserticola polysaccharides on agedconstipated rats – Liu et al. – Food & Function

Plant, root, and soil microbiome

[PREPRINT]Plant Virus Database: a resource for exploring the diversity of plant viruses and their interactions with hosts – Wu et al. – bioRxiv

Waste microbiome

[PREPRINT]Identification of Microbial Flora and Isolation of Functional Strains Related to the Degradation of Domestic Waste – Huang, Liu & Zong – bioRxiv

Food microbiology

Comprehensive characterization of the bacterial community structure and metabolite composition of food waste fermentation products via microbiome and metabolome analyses – Li et al. – PLOS One


MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations – Gregory et al. – Microbiome

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities – Kalmar et al. – PLOS Genetics


[PREPRINT]Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip – Mahajan et al. – bioRxiv

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Florence tomb by Michelangelo restored with aid of bacteria – The Guardian

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

November 15, 2021

Today’s digest contains an article about the effect of shale flowback fluid on the polluted soil microbiome. It also includes multiple preprints on topics such as long-read sequencing on the Oxford Nanopore, arctic marine protists, rapid antibiotic susceptibility testing for mixed infections, and more.

Happy reading!

General microbiome

Preprint: Rapid antibiotic susceptibility testing and species identification for mixed infections – Kandavalli et al. – bioRxiv

Preprint: Bacterial quorum sensing allows graded and bimodal cellular responses to variations in population density – Rattray et al. – bioRxiv

Preprint – Phage-encoded sigma factors alter bacterial dormancy – Schwartz et al. – bioRxiv

Human respiratory microbiome

Preprint: Aspergillus fumigatus drives tissue damage via iterative assaults upon mucosal integrity and immune homeostasis – Okaa et al. – bioRxiv

Human skin microbiome

Preprint: Cobamide sharing drives skin microbiome dynamics – Swaney et al. – bioRxiv

Plant, root, and soil microbiome

Toxic effects of shale gas fracturing flowback fluid on microbial communities in polluted soil – Zudong Mei et al. – Environmental Monitoring and Assessment

Water and extremophile microbiome

Preprint: Colonial choanoflagellate isolated from Mono Lake harbors a microbiome – Hake et al. – bioRxiv

Preprint: Linking extreme seasonality and gene expression in arctic marine protists – Wutkowska et al. – bioRxiv

Preprint: Biosorption potential and molecular characterization of metal resistant autochthonous microbes from tannery solid waste – Younas et al. – bioRxiv


Preprint: Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing – Sereika et al. – bioRxiv

Preprint: Going through phages: A Computational approach to Revealing the role of prophage in Staphylococcus aureus – Sweet et al. – bioRxiv

October 22, 2021

Happy Friday!

Today’s digest includes an article on the role of age in the human intestinal microbiome, research on the role of a novel Acidobacteriota in seafloor sulfur cycling, work demonstrating the use of machine learning to predict camplyobacter source data, and much more! I also included the link to a page on “The Secret World Inside You”, a science exhibit focused on the human microbiome that is at the Witte Museum in San Antonio, Texas from now until April 10, 2022. If anyone ends up checking it out, I’d love to hear about it!


A microbiome science exhibit, “The Secret World Inside You,” is at The Witte Museum in San Antonio, Texas from October 16, 2021 to April 10, 2022 .

Human gut microbiome

Bile acid-independent protection against Clostridioides difficile infection – Aguirre et al. – PLOS PATHOGENS

The importance of age in compositional and functional profiling of the human intestinal microbiome – Herzog et al. – PLOS ONE

Plant, root, and soil microbiome

The chosen few—variations in common and rare soil bacteria across biomes – Bickel & Or – The ISME Journal

The fungus Kalmusia longispora is able to cause vascular necrosis on Vitis vinifera – Karácsony et al. – PLOS ONE

Water and extremophile microbiome

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling – Flieder et al. – The ISME Journal

Beach sand oil spills select for generalist microbial populations – Heritier-Robbins et al. – The ISME Journal

Preprint: Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA – Matsuoka et al. – bioRxiv

Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake – Reboul et al. – The ISME Journal

Phages and viruses

Review: Community context matters for bacteria-phage ecology and evolution – Blazanin & Turner – The ISME Journal


Machine learning to predict the source of campylobacteriosis using whole genome data – Arning et al. – PLOS GENETICS

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 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


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


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