November 15, 2018

Here’s your Thursday Digest. Highlights include a photo competition to showcase your research, Titanium ion enhancing fresh flower longevity, and an update on the UNITE database for fungal classification.


** BMC ‘Research in progress’ photo competition – deadline tomorrow, November 16.

General microbiology

Review: The birth, evolution and death of metabolic gene clusters in fungi – Antonis Rokas et al. – Nature Reviews Microbiology

Considerations When Designing a Microbiome Study: Implications for Nursing Science – Katherine A. Maki et al. – Biological Research For Nursing

Review: Probiotics in human health and disease: from nutribiotics to pharmabiotics – Eun-Sook Lee et al. – Journal of Microbiology

Antimicrobial resistance

Review: Genome-based prediction of bacterial antibiotic resistance – Michelle Su et al. – Journal of Clinical Microbiology

Pregnancy and early life

Colonization of Cutibacterium avidum during infant gut microbiota establishment – Vanesa Natalin Rocha Martin et al. – FEMS Microbiology Ecology

Human skin microbiome

The proteomic and metabolomic characterization of exercise-induced sweat for human performance monitoring: A pilot investigation – Sean W. Harshman et al. – PLoS One

Human oral microbiome

In vitro: The effect of the stress hormone cortisol on the metatranscriptome of the oral microbiome – Ana E. Duran-Pinedo et al. – npj Biofilms and Microbiomes

Human gut microbiome

Alterations of fecal bacterial communities in patients with lung cancer – Wei-Quan Zhang et al. – American Journal of Translational Research

Temporal Variability of Escherichia coli Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics – Taylor K. S. Richter et al. – mSphere

Review: An insight into the intestinal web of mucosal immunity, microbiota, ​and diet and their role in inflammation and infection – Eliana Marino & Yu Anne Yap – Frontiers in Immunology

Human multisite microbiome

Determinants of the urinary and serum metabolome in children from six European populations – Chung-Ho E. Lau et al. – BMC Medicine

Human gut-microbiome-brain axis

Alteration of gut microbiota-associated epitopes in children with autism spectrum disorders – Mingbang Wang et al. – Brain, Behavior, and Immunity


Metabolomic biomarkers and novel dietary factors associated with gestational diabetes in China – Xuyang Chen et al. – Metabolomics

Animal experiments

An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis – Aliia R. Fatkhullina et al. – Immunity

Gut microbiota dysbiosis correlates with a low-dose PCB126-induced dyslipidemia and non-alcoholic fatty liver disease – Yulang Chi et al. – Science of The Total Environment

Animal microbiome

The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status – Sarah M. Hird et al. – mSphere

Milk Metabolomics Data Reveal the Energy Balance of Individual Dairy Cows in Early Lactation – Wei Xu et al. – Scientific Reports

Food microbiome

An integrated metagenomic/metaproteomic investigation of microbiota in dajiang-meju, a traditional fermented soybean product in Northeast China – Mengxi Xie et al. – Food Research International

Plant, root and soil microbiome

The ability of plants to produce strigolactones affects rhizosphere community composition of fungi but not bacteria – Lilia Costa Carvalhais et al. – Rhizosphere

Root exudates induce soil macroaggregation facilitated by fungi in subsoil – Vera L. Baumert et al. – Frontiers in Environmental Science

Long-term combined application of manure and chemical fertilizer sustained higher nutrient status and rhizospheric bacterial diversity in reddish paddy soil of Central South China – Xinwei Cui et al. – Scientific Reports

** Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity – Cai-Xia Li et al. – Microbial Ecology

Ectomycorrhizal fungi inoculation alleviates simulated acid rain effects on soil ammonia oxidizers and denitrifiers in Masson pine forest – Yan Li et al. – Environmental Microbiology

Compounded disturbance chronology modulates the resilience of soil microbial communities and N-cycle related functions – Kadiya Calderón et al. – Frontiers in Microbiology

Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials – Sihang Yang et al. – Science of The Total Environment

Silver Toxicity Thresholds for Multiple Soil Microbial Biomarkers – Sotirios Vasileiadis et al. – Environmental Science & Technology

Ectomycorrhizal fungal communities and their functional traits mediate plant-soil interactions in trace element contaminated soils – Marta Gil-Martínez et al. – Frontiers in Plant Science

Modulation of litter decomposition by the soil microbial food web under influence of land use change – Amber Heijboer et al. – Frontiers in Microbiology

Water and extremophile microbiome

Response and recovery of microbial communities subjected to oxidative and biological treatments of 1,4-dioxane and co-contaminants – Yu Miao et al. – Water Research

In situ real-time quantification of microbial communities: Applications to cold and dry volcanic habitats – Linda S.Powers et al. – Global Ecology and Conservation

Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis – Martin Alexander Fischer et al. – Microbial Biotechnology

Importance of soil texture to the fate of pathogens introduced by irrigation with treated wastewater – Olabiyi Obayomi et al. – Science of The Total Environment

Active pathways of anaerobic methane oxidation across contrasting riverbeds – Li-dong Shen et al. – The ISME Journal

Drying and rainfall shape the structure and functioning of nitrifying microbial communities in riverbed sediments – Maria Isabel Arce et al. – Frontiers in Microbiology

Microbes in space

Inner Workings: Hunting for microbial life throughout the solar system – Adam Mann – PNAS

Confirmation of Microbial Ingress from Space – N. C. Wickramasinghe et al. – Advances in Astrophysics

Phages and viruses

Review: Targeting mechanisms of tailed bacteriophages – Franklin L. Nobrega et al. – Nature Reviews Microbiology

Viral diversity of Rhipicephalus microplus parasitizing cattle in southern Brazil – William Marciel de Souza et al. – Scientific Reports

Review: Respiratory Viral Infection-induced Microbiome Alterations and Secondary Bacterial Pneumonia – Shigeo Hanada et al. – Frontiers in Immunology


Review: Model Microbial Consortia as Tools for Understanding Complex Microbial Communities – Haruta, Shin & Yamamoto, Kyosuke – Current Genomics

Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer – Manasi S. Shah et al. – PLoS One


** The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications – Rolf Henrik Nilsson et al. – Nucleic Acids Research

Bioinformatics tools to assess metagenomic data for applied microbiology – Otávio G. G. Almeida & Elaine C. P. De Martinis – Applied Microbiology and Biotechnology

Pan-genomic analysis provides novel insights into the association of E. coli with human host and its minimal genome – Zhi-Kai Yang et al. – Bioinformatics

Microbes in the news

You Are What Your Bacteria Eat – Patricia Conway & Jorgen Schlundt – Innovation Magazine

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