Today’s Digest brings you plenty of articles and news pieces, and highlights include mouse experiments with humanized microbiota, with “wilding” microbiota, and a collection of rumen metagenomes. Enjoy reading!

Event

The Expert Is In: Magnetic bacteria pumping iron! – National Museum of Natural History – August 9, 11am-1pm EDT

Antimicrobial resistance

Random peptide mixtures entrapped within a copper-cuprite matrix: new antimicrobial agent against methicillin-resistant Staphylococcus aureus – Tal Stern Bauer et al. – Scientific Reports

ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes – Mohd Wasi, Nitesh Kumar Khandelwal & Alexander J. Moorhouse et al. – Frontiers in Microbiology

Preprint: Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance – David C. Danko et al. – bioRxiv

Antimicrobial use in an Indonesian community cohort 0-18 months of age – Jarir At Thobari et al. – PLoS One

Erythromycin-resistant lactic acid bacteria in the healthy gut of vegans, ovo-lacto vegetarians and omnivores – Vesna Milanović et al. – PLoS One

Pregnancy and early life

Predictive value of cervical cytokine, antimicrobial and microflora levels for pre-term birth in high-risk women – Rashmi Manning et al. – Scientific Reports

Human multi-site microbiome

A new issue of the Gastroenterology Clinics of North America

Human oral microbiome

Review: Oral microbial biofilms: an update – Seyed Ali Mosaddad et al. – European Journal of Clinical Microbiology & Infectious Diseases

Amplicon-based microbiome study highlights the loss of diversity and the establishment of a set of species in patients with dentin caries – Diana Wolff et al. – PLoS One

Microbiome in maintained periodontitis and its shift over a single maintenance interval of three months – Hongye Lu et al. – Journal of Clinical Periodontology

Human gut microbiome

Review: Role of microbes, metabolites and effector compounds in host–microbiota interaction: a pharmacological outlook – Bharat Bhushan et al. – Environmental Chemistry Letters

Age-Associated Changes in Gut Microbiota and Dietary Components Related with the Immune System in Adulthood and Old Age: A Cross-Sectional Study – Nuria Salazar et al. – Nutrients

Review: Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions – Michael I McBurney et al. – The Journal of Nutrition

Review: Gut Dysbiosis and the Intestinal Microbiome: Streptococcus thermophilus a Key Probiotic for Reducing Uremia – Luis Vitetta et al. – Microorganisms

Animal experiments

** Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host – Aonghus Lavelle et al. – Microbiome

Microbiota of newborn calves and their mothers reveals possible transfer routes for newborn calves’ gastrointestinal microbiota – Daniela Klein-Jöbstl et al. – PLos One

Isoorientin attenuates benzo[a]pyrene-induced colonic injury and gut microbiota disorders in mice – Shenyuan He et al. – Food Research International

** Laboratory mice born to wild mice have natural microbiota and model human immune responses – Stephan P. Rosshart et al. – Science

Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon – Shruti Gupta et al. – Microorganisms

Whole Body Vibration-Induced Omental Macrophage Polarization and Fecal Microbiome Modification in a Murine Model – Jack C. Yu et al. – International Journal of Molecular Sciences

Press: Whole body vibration shakes up microbiome, reduces inflammation in diabetes – EurekAlert

Press: Whole body vibration helps reduce inflammation, thanks to the gut microbiome – Angela Betsaida B. Laguipo – News-Medical

Animal microbiome

Sex-specific linkages between taxonomic and functional profiles of tick gut microbiomes – Dasiel Obregón et al. – Frontiers in Cellular and Infection Microbiology

** Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery – Robert D. Stewart et al. – Nature Biotechnology

Humoral immune responses against gut bacteria in dogs with inflammatory bowel disease – Sirikul Soontararak et al. – PLoS One

Plant, root and soil microbiome

Solarization-based pesticide degradation results in decreased activity and biomass of the soil microbial community – M.Díaz-López et al. – Geoderma

Soil microbial carbon metabolism reveals a disease suppression pattern in continuous ginger mono-cropping fields – Xiaojiao Liu et al. – Applied Soil Ecology

Influence of 2,4-D residues on the soil microbial community and growth of tree species – Luciana Monteiro Aguiar et al. – International Journal of Phytoremediation

A Microbiome Study Reveals Seasonal Variation in Endophytic Bacteria Among different Mulberry Cultivars – Ting Ou et al. – Computational and Structural Biotechnology Journal

Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides – Barbara Cania et al. – Microbial Ecology

Water and extremophile microbiome

A snapshot of microbial community structures in 20 different field-scale anaerobic bioreactors treating food waste – Seung Gu Shin et al. – Journal of Environmental Management

Microbial uptake kinetics of dissolved organic carbon (DOC) compound groups from river water and sediments – Francesca L. Brailsford et al. – Scientific Reports

Biological removal of selenate in saline wastewater by activated sludge under alternating anoxic/oxic conditions – Yuanyuan Zhang et al. – Frontiers of Environmental Science & Engineering

Built environment microbiome

Environmental factors influencing fungal growth on gypsum boards and their structural biodeterioration: A university campus case study – Negin Kazemian et al. – PLoS One

Phages and viruses

Identification of diverse bat alphacoronaviruses and betacoronaviruses in China provides new insights into the evolution and origin of coronavirus-related diseases – Yelin Han et al. – Frontiers in Microbiology

The respiratory microbiota: Associations with influenza symptomatology and viral shedding – Kyu Han Lee et al. – Annals of Epidemiology

Technology

Review: Simultaneous improving nitrogen removal and decreasing greenhouse gas emission with biofilm carriers addition in ecological floating bed – Shanshan Sun et al. – Bioresource Technology

Comparative evaluation of a novel recombinase polymerase amplification-lateral flow dipstick (RPA-LFD) assay, LAMP, conventional PCR, and leaf-disc baiting methods for detection of Phytophthora sojae – Tingting Dai et al. – Frontiers in Microbiology

Review: Emerging molecular techniques for studying microbial community composition and function in microbiologically influenced corrosion – Susmitha Purnima Kotu et al. – International Biodeterioration & Biodegradation

Microbes in the news

Phase Genomics’ Platform Links Viruses and Antibiotic Resistance Genes to the Microbiome in Study of a Highly Complex Microbial Community – Phase Genomics – Globe Newswire

Mouse Genetics Shape the Gut Microbiome More than Their Environment – Nicoletta Lanese – The Scientist

JMM EDITOR’S CHOICE: HOW DOES SMOKING AFFECT THE ORAL MICROBIOME? – Microbiology Society

NEWSProbiotics brand Life Space celebrates the wonder of the human microbiome – Zoe Wilkinson – Mumbrella

Caveats and clinical implications in the connection between the duodenal microbiome, diet and functional gastrointestinal symptoms – Gut Microbiota for Health

The many modes of microbial magic – Giuliana Viglione – Chemical & Engineering News

The secret lives of microbes – ANNEMIEKE VAN ROEKEL – Euro Scientist

IIT develops state-of-art device to detect bacteria – The Pioneer

The Germiest Places in Your Child’s School – Alex Watt – Red Book

Teresa van Dongen’s Mud Well light uses microorganisms to create electricity – Rima Sabina Aouf – De Zeen

Microbes on the market

Shoreline Biome Announces International Distribution Partnerships – Yahoo Finance

What are the prospects for microbiome skin care in Asia? – Simon Pitman – Cosmetics Design – Europe

Biotech startup joins quest to harness microbiome to untether reliance on antibiotics in women’s health – Natalie Grover – Endpoints News

PanTheryx funding will help intensify growth in animal microbiome-focused products – Joseph Harvey – Informa