After the US government shutdown, today’s Digest features several human gut microbiome, food microbiology papers and many news pieces. There are some other highlights as well. A large longitudinal experiment in a tropical rain forest examines how soil microbes adapt genetically to nutrient changes in the soil. A synthetic enzyme rescues E. coli in iron-limited medium. Open access from high impact medical journals is still lacking.

Jobs and events

Digital Communications Officer – Microbiology Society – London

Keystone Symposium on Natural Products and Synthetic Biology

General microbiology

Sequence-based classification and identification of Fungi – David Hibbett et al. – Mycologia

Preprint: E. coli translation strategies differ across nutrient conditions – Sophia Hsin-Jung Li et al. – bioRxiv

* A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli – Ann E Donnelly et al. – Nature Chemical Biology

Press: A randomly generated, totally novel enzyme rescues mutant bacteria – Diana Gitig – ArsTechnica

Annotations of Microbacterium foliorum – Debbie Jacobs-Sera – Sea Phages

Human gut microbiome

Reoccurring review (no abstract available): Letter to the Editor: Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Andre Alonso Taco-Masias and Augusto Rafael Fernandez-Aristi – Obesity Surgery

Also see a previous review: Influence of intestinal microbiota on body weight gain: a narrative review of the literature – Camila S. Cardinelli et al. – Obesity Surgery

Impact of intestinal mannitol on hyperammonemia, oxidative stress and severity of hepatic encephalopathy in the ED – Daniel H. Montes-Cortés et al. – The American Journal of Emergency Medicine

Clostridial strain-specific characteristics associated with necrotizing enterocolitis – Sophia Schönherr-Hellec et al. – Applied and Environmental Microbiology

Intestinal dysbiosis and permeability: the yin and yang in alcohol dependence and alcoholic liver disease – Peter Stärkel et al. – Clinical Science

In vitro fermentation of Cookeina speciosa glucans stimulates the growth of the butyrogenic Clostridium cluster XIVa in a targeted way – Thaisa MoroCantu-Jungles et al. – Carbohydrate Polymers

Animal microbiome

In vitro: Rumen bacteria at work: bioaugmentation strategies to enhance biogas production from cow manure – E.G. Ozbayram et al. – Journal of Applied Microbiology

Plant, root and soil microbiome

* Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil – Qiuming Yao et al. – Nature Ecology and Evolution

Press: Researchers reveal how microbes cope in phosphorus-deficient tropical soil – Sara Shoemaker – Phys.org

Water and extremophile microbiome

Bacterial community changes in copper and PEX drinking water pipeline biofilms under extra disinfection and magnetic water treatment – J. Inkinen et al. – Journal of Applied Microbiology

Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber – M. Salomez et al. – Journal of Applied Microbiology

Lead-resistant bacteria from Saint Clair River sediments and Pb removal in aqueous solutions – Nichole Bowman et al. – Applied Microbiology and Biotechnology

Food microbiology

Ultrasound improves antimicrobial effect of sodium dichloroisocyanurate to reduce Salmonella Typhimurium on purple cabbage – Ana Lúcia Almeida Duarte et al – International Journal of Food Microbiology

Characterization of the spoilage potential of pure and mixed cultures of bacterial species isolated from tropical yellowfin tuna (Thunnus albacares) – A. Silbande et al. – Journal of Applied Microbiology

Impact of storage conditions on fungal community composition of green coffee beans Coffea arabica L. stored in jute sacks during 1 year – L.M. Broissin-Vargas et al. – Journal of Applied Microbiology

An assessment of the microbiological quality and safety of raw drinking milk on retail sale in England – C. Willis et al. – Journal of Applied Microbiology

Microbes in the news

Bacteria warning for Kapiti waterways – Newshub

Common salt kills rat fever bacteria? Public health experts say it can – TNN – Times of India

Editorial: Vendors’ ultimatum will save us from cholera, typhoid – The Standard

Why Flesh-Eating Bacteria Can Look Like the Flu – Rachael Rettner – Live Science

Geologists find bacteria that takes traces of gold and turns them into nuggets – Eliza Goetze – ABC News

Shigella Bacteria Diarrhea in Children: Should WHO Guidelines Be Modified? – Julie McShane – Medical News Bulletin

* Chemical ‘aphrodisiac’ jumpstarts the sex life of a single-celled organism – Brianna Abbott – Science Line

Microbiome predicts blood infections in pediatric cancer patients – EurekAlert

Dietary Fiber Protects Against Obesity and Metabolic Syndrome, Study Finds – Georgia State University News Hub

How climate change weakens coral ‘immune systems’ – EurekAlert

* Early changes in brain immunity may underlie sex bias in autism – Nicholette Zeliadt – Spectrum

Detecting Zoonotic Protists In Raw Sewage For Environmental Monitoring – Steven Sullivan – Science Trends

Microbes on the market

Synspira Therapy Eliminates Antibiotic-resistant Lung Bacteria, Study Shows – Marta Figueiredo – Cystic Fibrosis News Today

Microbiome Sequencing Service Market – Baseclear, Clinical-Microbiomics, MR DNA (Molecular Research Lp), Molzym, Zymo Research, Rancho Biosciences, Microbiome Therapeutics, Microbiome Insights, Openbiome, Resphera Biosciences, Shanghai Realbio Technology – Oscar – Hugo Press

VALBIOTIS Announces a Significant Effect of VALEDIA® on Intestinal Microbiota – Business Wire

Publishing and education

* Preprint: Open access policies of high impact medical journals: a cross-sectional study – Time Ellison et al. – bioRxiv