January 23, 2026

Animal microbiome

Bacterial-archaeal co-occurrence in honey bee gut microbiomes across host species and management regimes -Jian-Ping Ying –PLOS ONE

Bacterial community associated with the surface and inside of centipede forcipules: Identification and characterization -Yasutaka Tanaka – PLOS ONE


Human reproductive & urinary microbiome

Vaginal chlorhexidine gluconate versus fluconazole for recurrent vulvovaginal candidiasis: A randomized noninferiority trial – Cathrin Alvendal – PLOS ONE


Infection and transplantation / Host–microbe interactions

DnaK supports intracellular persistence of Staphylococcus xylosus and confers mechanical resilience to a human breast cancer cell line – Lei Ye – PLOS ONE

Investigation of a viable but non-culturable state in Porphyromonas gingivalis and host cell invasionAdenrele Oludiran – PLOS ONE


Microbial ecology & symbiosis

Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis – Sunnyjoy Dupuis – PLOS ONE


Oral microbiome & animal experiments

Effects of glycyrrhizin on healing and prevention of recurrent aphthous stomatitis in hamster models – Fumie Shiba – PLOS ONE


Plant, soil & ecological microbiome

Tree species-specific strategies of soil aggregation driven by SOC–GRSP coupling under nitrogen addition and precipitation reduction -Mingxin Zhou – PLOS ONE


Microbial genomics & bioremediation

Genomic analysis of Acinetobacter baumannii DUEMBL6 reveals diesel bioremediation potential and biosafety concerns – Nizam Uddin – PLOS ONE


Human gut & inflammatory disease

Identification of hypoxia- and mitophagy-related diagnostic biomarkers for ulcerative colitis based on bioinformatic analysis and machine learning – Zewei Sheng – PLOS ONE


Oral & dental archaeology / Ancient microbiome

Paleo-proteomic analysis of Iron Age dental calculus provides direct evidence of Scythian reliance on ruminant dairy – Jaruschka Pecnik – PLOS ONE


Cancer & clinical oncology

Radiomics profiling combined with clinical risk factors for preoperative lymphatic metastasis prediction in colorectal cancer: A multicenter study – Fangda Guo – PLOS ONE


Toxicology & respiratory health

Potential mechanisms and effects of AFB1-induced asthma: A comprehensive analysis based on network toxicology and molecular docking – Zhiyue Yu – PLOS ONE


Human development & diet (archaeology / isotopes)

Fed the same way? Exploring the influence of breastfeeding, weaning, and childhood diet on adult sex ratios through stable isotope analysis of incremental dentine in Medieval Tuscany – Alessio Amaro – PLOS ONE

13 July, 2019

Good morning everyone!

Today’s digest is kind of diverse (as always), with great papers about women microbiome, sardines gut microbiome, a great review about soil aggregates and, corals microbiomes and much more. Be sure to read the first paper right down here- The Conceptual Ecology of the Human Microbiome. Have a great weekend!

Human microbiome

**From June 2019, but a must-read nonetheless: The Conceptual Ecology of the Human Microbiome, Morar and Bohannan, Q. R. Biology

Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine, Wouter A. A. de Steenhuijsen Piters, Nature Communications

Selected Immunological Mediators and Cervical Microbial Signatures in Women with Chlamydia trachomatis Infection, Simone Filardo, mSystems

Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli, Chunhua Zhao, MPMI

Secondary bile acid ursodeoxycholic acid (UDCA) alters weight, the gut microbiota, and the bile acid pool in conventional mice, Jenessa A. Winston, bioRxiv

Microbiota supplementation with Bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome, Cristina Alcon-Giner, bioRxiv

Animal microbiome

A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians, Lu Wu, mSystems

Contribution of gut microbiota to metabolism of dietary glycine betaine in mice and in vitro colonic fermentation, Ville M. Koistinen, Microbiome

Coral bacterial community structure responds to environmental change in a host-specific manner, Maren Ziegler, Nature Communications

Soil microbiome

**Mini-review: Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales, Regina L. Wilpiszeski , AEM

Continuous monoculture shapes root and rhizosphere fungal communities of corn and soybean in soybean cyst nematode-infested soil, Noah Strom, Phytobiomes

Engineered root bacteria release plant-available phosphate from phytate, Christine N. Shulse, AEM

Diversity and Characterization of Oomycetes Associated with Corn Seedlings in Michigan, J. A. Rojas, Phytobiomes

Environmental microbiome

Diverse, abundant and novel viruses infecting “unculturable” but abundant marine bacteria, Zefeng Zhang, bioRxiv

Biocide resistance and transmission of Clostridium difficile spores spiked onto clinical surfaces from an American healthcare facility, Calie Dyer, AEM

Microbiome in the news

Lab Startup uBiome Laying Off About Half of Global Workforce

Microbiome Repairing Food for Malnourished Children Beats Current Therapy

May 14, 2019

Good morning microbe lovers! This digest presents papers for everyone taste, plus some really nice general microbiology and science papers. Check out cool snow algae microbiome in Antarctica, soil aggregates microbiome, DNA extraction methods in studying animal microbiomes and more.

Don’t forget to spread MD with friends, colleges and others- it really helps us knowing our hard work is actually being read.

General microbiology

Into the wild: microbiome transplant studies need broader ecological reality , Christopher J. Greyson-Gaito, EcoEcoRxiv

Predicting the decision making chemicals used for bacterial growth, Kazuha Ashino, Scientific Reports

A longitudinal big data approach for precision health, Sophia Miryam Schussler-Fiorenza Rose, Nature Medicine

Human Microbiome

Mammographic breast density and its association with urinary estrogens and the fecal microbiota in postmenopausal women, Gieira S. Jones, PLOS One

Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis, K. Erikkson, Journal of Clinical Medicine

Animal Microbiome

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats, Melissa R. Ingala, Ecology and Evolution

Fungal disease and temperature alter skin microbiome structure in an experimental salamander system, CR Muletz-Wolz, Molecular Ecology

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish, A.N Parshukov, Journal of Applied Microbiology

Responses of microbial community structure in turbot (Scophthalmus maximus) larval intestine to the regulation of probiotic introduced through live feed, Yan Jiang, PLOS One

Assessment of microbial communities on freshly killed wild boar meat by MALDI-TOF MS and 16S rRNA amplicon sequencing, M.F. Peruzy, Int. Food Microbiology

**Methods Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, Boyun Jiang, FEMS Microbiology Letters

Air Microbiome

** Snow algae communities in Antarctica: metabolic and taxonomic composition, Matthew P. Davey, The New Phytologist

Soil and Plants Microbiome

**Minireview Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales, Regina L. Wilpiszeski, App. Env. Microbiology

Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities, Raj Kumar Regar, Science of the Total Environment

Interpreting distance‐decay pattern of soil bacteria via quantifying the assembly processes at multiple spatial scales, Maomao Feng, MicrobiologyOpen

Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments, J. Buongiorno, App. Env. Microbiology

Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection, Antonio Jose Fernandez-Gonzales, bioRxiv

Microbiome in the news

Human gut microbiome physiology can now be studied in vitro using Organ Chip technology, Phys.org

Inspirotec Inc and Argonne National Laboratory Collaborate on Largest Study to Date of Airborne Allergens and Microbiome in Same Homes, Globenewswire