November 25, 2016

Human multisite microbiome (of dead bodies)

Thesis: Understanding the relationship between the human microbiome and urban decay/recovery among autopsied adults in Detroit, Michigan – Amanda T. Rzotkiewicz – Michigan State University

Human oral microbiome

The autoimmunity–oral microbiome connection – NG Nikitakis – Oral Diseases

Human reproductive and urinary tract microbiome

Potential contribution of the uterine microbiome in the development of endometrial cancer – Marina R. S. Walther-António – Genome Medicine

Proinflammatory Cytokines as Regulators of Vaginal Microbiota – E. A. Kremleva – Bulletin of Experimental Biology and Medicine

Seven Bacteriophages Isolated from the Female Urinary Microbiota – Kema Malkia – Genome Announcements

Human gut microbiome

Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease – Walid Mottawea – Scientific Reports

Metagenomics of two severe foodborne outbreaks provides diagnostic signatures and signs of co-infection not attainable by traditional methods – Andrew D. Huang – Applied and Environmental Microbiology

Review: Gut Microbiota and Autism: Key Concepts and Findings – Helen T. Din – Journal of Autism and Developmental Disorders

Review: Intestinal Microbiota as an Alternative Therapeutic Target for Epilepsy – Jiaying Wu – Canadian Journal of Infectious Diseases and Medical Microbiology

Review: Irritable Bowel Syndrome: A gut microbiota-related disorder? – Yogesh Bhattarai – American Journal of Physiology – Gastrointestinal and Liver Physiology

Review: Gut Microbiota, Bacterial Translocation, and Interactions with Diet: Pathophysiological Links between Major Depressive Disorder and Non-Communicable Medical Comorbidities – Slyepchenko A. – Psychotherapy and Psychosomatics

Review: Microbiome, metabolites and host immunity – Maayan Levy – Current Opinion in Microbiology

Animal and in vitro models

* Persistent microbiome alterations modulate the rate of post-dieting weight regain – Christoph A. Thaiss – Nature

Press: Yo-yo weight gain driven by gut bacteria’s ‘memory’ of obesity, says study – Hannah Devlin – The Guardian
Breakthrough in Dieting Science: Gut Bacteria Are Behind Relapsing Obesity – Ido Efrati and Ruth Schuster – Haaretz

Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition – Vitas E. Wagner – Science Translational Medicine

Antibiotics impair murine hematopoiesis by depleting intestinal microbiota – Kamilla S. Josefsdottir – Blood

Pre- and post-weaning diet alters the faecal metagenome in the cat with differences vitamin and carbohydrate metabolism gene abundances – Wayne Young – Scientific Reports

Mucosa-associated biohydrogenating microbes protect the simulated colon microbiome from stress associated with high concentrations of poly-unsaturated fat – Rosemarie De Weirdt – Environmental Microbiology

Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits – Qiangchuan Hou – Scientific Reports

Evolutionary biologic changes of gut microbiota in an ‘adenoma-carcinoma sequence’ mouse colorectal cancer model induced by 1, 2-Dimethylhydrazine – Teng Sun – Oncotarget

Mini review: All Together Now: Experimental Multispecies Biofilm Model Systems – Chuan Hao Tan – Environmental Microbiology

Animal microbiome

The stable microbiome of inter and sub-tidal anemone species under increasing pCO2 – Erinn M. Muller – Scientific Reports

An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes – Hannes Horn – Frontiers in Microbiology

Plant, root, and soil microbiome

Soil Bacterial Community Response to Short-Term Manipulation of the Nitrogen Deposition Form and Dose in a Chinese Fir Plantation in Southern China – Caixia Liu – Water, Air, & Soil Pollution

Microbial community composition but not diversity changes along succession in arctic sand dunes – Anbu Poosakkannu – Environmental Microbiology

Soil-covered strategy for ecological restoration alters the bacterial community structure and predictive energy metabolic functions in mine tailings profiles – Yang Li – Applied Microbiology and Biotechnology

Contrasting effects of two mammalian soil engineers on microbial communities – David J. Eldridge – Austral Ecology

Habitat-driven variation in mycorrhizal communities in the terrestrial orchid genus Dactylorhiza – Hans Jacquemyn – Scientific Reports

 * Are there keystone mycorrhizal fungi associated to tropical epiphytic orchids? – Stefania Cevallos – Mycorrhiza

Water and extremophile microbiome

Stromatolites from the Aptian Crato Formation, a hypersaline lake system in the Araripe Basin, northeastern Brazil – Lucas Veríssimo Warren – Facies

Diversity, abundance, and possible sources of fecal bacteria in the Yangtze River – Haohao Sun – Applied Microbiology and Biotechnology

Climate-related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes – Carina Rofner – Global Change Biology

Viruses and phages

Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture – Lavinia Gambelli – Frontiers in Microbiology

Seven Bacteriophages Isolated from the Female Urinary Microbiota – Kema Malkia – Genome Announcements


The role of metabolism (and the microbiome) in defining the clinical efficacy of dietary flavonoids – Aedín Cassidy – The American Journal of Clinical Nutrition

Metagenomics and bioinformatics

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains – Weinan Liao – Scientific Reports


ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities
Anders Bjørnsgaard Aas – Molecular Ecology Resources

Microbes in the news

Stockholmers’ poop wanted in fight against drug-resistant bacteria – RT

The modern microbiome: Are we undoing evolution? – Maria Gloria Dominguez-Bello – ASM Cultures

PhD student finds surprising secret to detecting staph infections earlier – Breanne Grady – USC News

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