September 22, 2022

Happy almost Friday! Today’s digest includes a time series tracking changes after fecal transplant, biofilm-formation analysis from isolations from swine slaughterhouses as well as techniques to improve computational notebooks, rapid genotyping, and more.


Human gut microbiome

Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains – Koo & Morrow – PLOS One

Animal experiments

Microbiome complexity shapes metabolism – Litichevskiy & Thaiss – PLOS Biology

Minimal overall divergence of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes despite potential adaptive enrichment for scale-eating – Heras & Martin – PLOS One

Molecular characterization and biofilm-formation analysis of Listeria monocytogenes, Salmonella spp., and Escherichia coli isolated from Brazilian swine slaughterhouses – Santos et al. – PLOS One

Animal microbiome

Ecology and distribution of Leptospira spp., reservoir hosts and environmental interaction in Sri Lanka, with identification of a new strain – Sluydts et al. – PLOS Neglected Tropical Diseases


A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research – Figueiredo et al. – PLOS Computational Biology

Bacterial concentration and Campylobacter spp. quantification differ when fresh or ultra-frozen samples are analysed over time using molecular biology and culture-based methods – Khattak et al. – Plos One

Robust inference of population size histories from genomic sequencing data – Upadhya & Steinrücken – PLOS Computational Biology

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data – Váradi et al. – PLOS One

Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods – Xue & Marco – PLOS ONE

September 8, 2022

Today’s microbiome digest includes ten rules for teaching yourself R, food safety profiles of ready-to-eat raw minced meat, teaching that addresses eco-anxiety, as well as both pathogenic and entomopathogenic fungi!

Human gut microbiome

Meals, Microbiota and Mental Health in Children and Adolescents (MMM-Study): A protocol for an observational longitudinal case-control study – Asbjornsdottir et al. – PLOS One

Strongyloides stercoralis infection induces gut dysbiosis in chronic kidney disease patients – Hai et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Mycoparasitism capability and growth inhibition activity of Clonostachys rosea isolates against fungal pathogens of grapevine trunk diseases suggest potential for biocontrol – Geiger et al. – PLOS One

Impact of endophytic colonization by entomopathogenic fungi on the behavior and life history of the tobacco peach aphid Myzus persicae var. nicotianae – Wilberts et al. – PLOS One

Food microbiology

Bacteriological quality and antimicrobial susceptibility profiles of isolates of ready-to-eat raw minced meat from hotels and restaurants in Arba Minch, Ethiopia – Tonjo et al. – PLOS One


Ten simple rules for teaching yourself R – Lawlor et al. – PLOS Computational Biology


Laboratory evaluation of RealStar Yellow Fever Virus RT-PCR kit 1.0 for potential use in the global yellow fever laboratory network – Basile et al. – PLOS Neglected Tropical Diseases

Science, publishing, and career )

Insufficient yet improving involvement of the global south in top sustainability science publications – Dangles et al. – PLOS One

Adapt conservation biology teaching to address eco-anxiety in students – São Pedro et al. – PLOS Biology

August 19, 2022

Today’s digest is short and sweet! We have articles on the gut microbiota in rats, the influence of host genetics on the leaf fungal microbiome, and biofilm fouling in drinking water. There are also two manuscripts which provide tips for pathway enrichment analysis and biomarker discovery.

Happy reading! Also, if you’re in Scotland, consider checking out the enormous E. coli in Edinburgh this weekend!

Animal experiments

Effects of sea salt intake on metabolites, steroid hormones, and gut microbiota in rats – Chanmuang et al. – PLOS One

Plant, root, and soil microbiome

The changing influence of host genetics on the leaf fungal microbiome throughout plant development – Karasov & Lundberg – PLOS Biology

Water and extremophile microbiome

Impacts of temperature and hydraulic regime on discolouration and biofilm fouling in drinking water distribution systems – Fish et al. – PLOS Water


Nine quick tips for pathway enrichment analysis – Chicco & Agapito – PLOS Computational Biology

Ten quick tips for biomarker discovery and validation analyses using machine learning – Diaz-Uriarte et al. – PLOS Computational Biology

August 5, 2022

Today’s digest is brief and includes research examining the association between the gut microbiota and Gulf War illness, determining the distribution of psychrophilic microorganisms in a beef slaughterhouse, measuring the quality of DNA sequences via degradation, and more.

Happy Friday!

General microbiome

Measuring quality of DNA sequence data via degradation – Karr et al. – PLOS One

Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis – Nonaka et al. – PLOS One

Human vaginal microbiome

Association of key species of vaginal bacteria of recurrent bacterial vaginosis patients before and after oral metronidazole therapy with short- and long-term clinical outcomes – Mollin et al. – PLOS One

Human gut microbiome

Examining the association between the gastrointestinal microbiota and Gulf War illness: A prospective cohort study – Kates et al. – PLOS One

Food microbiology

Distribution of psychrophilic microorganisms in a beef slaughterhouse in Japan after cleaning – Nakamura et al. – PLOS One

Science, publishing, and career

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses – Bacon et al. – PLOS Computational Biology

July 28, 2022

Today’s digest includes research on the gut microbiome of infants, ruminants, and sand flies! There is also a preprint about sewage microbiomes as well as a research article about photosynthetic bacterial communities in crop fields.

Happy reading!

Human skin microbiome

Lichen Planopilaris: The first biopsy layer microbiota inspection – Pinto et al. – PLOS One

Human gut microbiome

Adaptation of the infant gut microbiome during the complementary feeding transition – McKeen et al. – PLOS One

Animal microbiome

Metagenomic insights into the microbe-mediated B and K2 vitamin biosynthesis in the gastrointestinal microbiome of ruminants – Jiang et al. – Microbiome

Comparative analysis of the gut microbiota of sand fly vectors of zoonotic visceral leishmaniasis (ZVL) in Iran; host-environment interplay shapes diversity – Karimian et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods – Cheng et al. – PLOS One

Built environment

Preprint: A metagenomic investigation of spatial and temporal changes in sewage microbiomes across a university campus – Fierer et al. – bioRxiv

July 1, 2022

We made it to the end of the week, we made it through the end of June. To celebrate, check out the two (!) articles about the pig gut microbiome, try out a new tool for network analysis (MicNet Toolbox), or enjoy an NPR Short Waves podcast episode about Agar Art. Or maybe you’re spending the afternoon preparing a research talk or fieldwork event? If that’s the case, check out the article presenting 10 rules for improving communication among scientists or the one on the hidden labor of managing threats to safety by women in fieldwork.

General microbiome

Assessment of disinfectant efficacy in reducing microbial growth – Alajlan et al. – PLOS One

Animal experiments

Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses – Apiwatsiri et al. – PLOS One

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig – Gaio et al. – PLOS One

Preprint: Using axenic and gnotobiotic insects to examine the role of different microbes on the development and reproduction of the kissing bug Rhodnius prolixus (Hemiptera: Reduviidae) – Gilliland et al. – bioRxiv


MicNet toolbox: Visualizing and unraveling a microbial network – Favila et al. – PLOS One

Evaluating the impact of sample storage, handling, and technical ability on the decay and recovery of SARS-CoV-2 in wastewater – Beattie et al. – PLOS One

Microbes in the news

NPR’s Short Wave Podcast: Let’s Get Crafty With Agar Art (11 minute episode)!

Science, publishing, and career

Ten simple rules for improving communication among scientists – Bautista et al. – PLOS Computational Biology

You can’t report your feelings: The hidden labor of managing threats to safety by women in global public health fieldwork – McAuliffe et al. – PLOS Global Public Health

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

May 6, 2022

Happy Friday! Today’s microbiome digest is a grab bag of articles on topics such as antibiotic cycling and bacterial contamination in surgery, phage isolated from diseased seafood, and microbial communities in snuff. I was particularly interested to see the article focused on degradation genes found in steel industrial soil communities. Finally, I enjoyed checking out two preprints on oral microbiota in Agta, a group of hunter-gatherers from the Philippines.

General microbiome

Preprint: The making of the oral microbiome in Agta hunter-gatherers – Dobon et al. – bioRxiv

Preprint: Microbial population dynamics decouple nutrient affinity from environmental concentration – Fink et al. – bioRxiv

Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand – Huang et al. – PLOS Pathogens

Preprint: Hunter-gatherer oral microbiomes are shaped by contact network structure – Muscitto et al. – bioRxiv

Which vaccine attributes foster vaccine uptake? A cross-country conjoint experiment – Stöckli et al. – PLOS ONE

Associations between microbial communities and key chemical constituents in U.S. domestic moist snuff – Tyxobert et al. – PLOS ONE

Multi-site human microbiome

Mycobacterium tuberculosis infection, immune activation, and risk of HIV acquisition – Bender Ignacio et al. – PLOS ONE

The effects of antibiotic cycling and mixing on acquisition of antibiotic resistant bacteria in the ICU: A post-hoc individual patient analysis of a prospective cluster-randomized crossover study – van Duijin et al. – PLOS ONE

Human gut microbiome

Efficacy of laparotomy sponges to reduce bacterial contamination using an in vitro gastrointestinal surgery model – Bezhentseva et al. – PLOS ONE

Animal experiments

Virulence and antimicrobial resistance gene profiles of Staphylococcus aureus associated with clinical mastitis in cattle – Neelam et al. – PLOS ONE

Preexisting Trichinella spiralis infection attenuates the severity of Pseudomonas aeruginosa-induced pneumonia – Rong Long et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil – Sandhu et al. – PLOS ONE

Water and extremophile microbiome

Transcriptomic analysis of chloride tolerance in Leptospirillum ferriphilum DSM 14647 adapted to NaCl – Rivera-Araya et al. – PLOS ONE

Food microbiology

Sole and combined effect of foliar zinc and arbuscular mycorrhizae inoculation on basmati rice growth, productivity and grains nutrient – Mehmood et al. – PLOS ONE

Characterization and complete genome sequence analysis of a newly isolated phage against Vibrio parahaemolyticus from sick shrimp in Qingdao, China – Tian et al. – PLOS ONE


Financial incentives to increase stool collection rates for microbiome studies in adult bone marrow transplant patients – Thompson et al. – PLOS ONE

April 8, 2022

Good morning! Today’s microbiome digest is brought to you by mild insomnia induced by a mid-afternoon coffee. It includes two food related studies, one on pathogenic E. coli found in ready-to-eat foods and the other focused on a antifungal lipopeptide produced by B. velezensis isolated from honey, and an an article focused on a new approach for processing frozen lung and lavage samples for use in microbiome studies. Also included are several articles focused on the gut microbiome, and several preprints focused on soil microbiome studies. Finally, I want to highlight a piece that details the positive outcomes associated with the National Summer Undergraduate Research Project (NSURP). Registration for this year’s program is still open until April 15th, and the organizers are looking for both mentors, mentees, and donors!

Pregnancy and early life

Group B Streptococcus colonization at delivery is associated with maternal peripartum infection – Brigtsen et al. – PLOS ONE

Human gut microbiome

Mycobacterium avium subsp. paratuberculosis and microbiome profile of patients in a referral gastrointestinal diseases centre in the Sudan – Elmagzoub et al. – PLOS ONE

Animal experiments

Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life – Brand et al. – PLOS ONE

Sex differences in the fecal microbiome and hippocampal glial morphology following diet and antibiotic treatment – Saxena et al. – PLOS ONE

Animal microbiome

Preprint: Anthropogenic disturbance impacts gut microbiome homeostasis in a Malagasy primate – Wasimuddin et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago – Schoenborn et al. bioRxiv

Preprint: The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types – Vitamaki et al. – bioRxiv

Preprint: Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil – Wilhelm et al. – bioRxiv

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

Preprint: Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments – Kohtz et al. – bioRxiv

Food microbiology

Processed ready-to-eat (RTE) foods sold in Yenagoa Nigeria were colonized by diarrheagenic Escherichia coli which constitute a probable hazard to human health – Beshiru et al. – PLOS ONE

Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey – Ziong et al. – PLOS ONE


An optimized approach for processing of frozen lung and lavage samples for microbiome studies – Wiscovitch-Russo et al. – PLOS ONE

Science, publishing, and career

***National Summer Undergraduate Research Project (NSURP): A Virtual Research Experience to Deliver REAL (Retention, Equity, Access, and Life-Changing) Outcomes for Underrepresented Minorities in STEM – Johnson & Knox – JMBE

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