Microbiota-mitochondria crosstalk in Crohn’s Disease, is there a brain microbiome, Akkermansia proteins, Koala retroviruses, New York City park soil microbiomes, gift-giving insects, mud volcanos, 2.5 billion-year-old microbial fossils.
Events
The Gut Institute Microbiome Event in Berkeley, 10/11 December– Gut Institute
General microbiome
Microbial Ecology: Where are we now? – Lisa A. Boughner – Journal of Postdoctoral Research
Human respiratory microbiome
Common Lung Microbiome Identified among Mechanically Ventilated Surgical Patients – Ashley D. Smith – PLOS ONE
Human skin microbiome
Towards a bacterial treatment for armpit malodour – Chris Callewaert – Experimental Dermatology
Review: Establishing Tolerance to Commensal Skin Bacteria: Timing Is Everything – Tiffany C. Scharschmidt – Dermatologic Clinics
Human microbes in (nearly) sterile sites
* Lots of extraction controls in this study, but they were not sequenced, and hard to accept there are thriving bacterial communities in our brain: Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis – W. G. Branton – Scientific Reports
Human gut microbiome
* Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease – Walid Mottawea – Nature Communications
Changes in Intestinal Microbiota Following Combination Therapy with Fecal Microbial Transplantation and Antibiotics for Ulcerative Colitis – Dai Ishikawa – Inflammatory Bowel Diseases
Urinary metabolomics of young Italian autistic children supports abnormal tryptophan and purine metabolism – Federica Gevi – Molecular Autism
Review: Interaction of gut microbiota with bile acid metabolism and its influence on disease states – Christopher Staley – Applied Microbiology and Biotechnology
Animal and in vitro models
* A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice – Hubert Plovier – Nature Medicine
Stable Host Gene Expression in the Gut of Adult Drosophila melanogaster with Different Bacterial Mono-Associations – Carolyn Elya – PLOS ONE
Checks and balances – microbiota shifts in immunosuppressed mice – W. Florian Fricke – Transplantation
Dual-specificity phosphatase 6 deficiency regulates gut microbiome and transcriptome response against diet-induced obesity in mice – Jhen-Wei Ruan – Nature Microbiology
Short Chain Fatty Acids Prevent High-fat-diet-induced Obesity in Mice by Regulating G Protein-coupled Receptors and Gut Microbiota – Yuanyuan Lu – Scientific Reports
Effect of antibiotic pre-treatment and pathogen challenge on the intestinal microbiota in mice – Tadasu Iizumi – Gut Pathogens
Fecal microbiota manipulation prevents dysbiosis and alcohol-induced liver injury in mice – Gladys Ferrere – Journal of Hematology
Impact of red meat consumption on the metabolome of rats – Louise M. A. Jakobsen – Molecular Nutrition & Food Research
11β-hydroxysteroid dehydrogenase-1 deficiency alters the gut microbiome response to western diet – Jethro S Johnson – Journal of Endocrinology
Microbiota induces expression of tumor necrosis factor in postnatal mouse skin – D. V. Yuzhakova – Biochemistry (Moscow)
Animal microbiome
* Phylogenetic diversity of Koala Retrovirus within a Wild Koala Population – K.J. Chappell – Journal of Virology
* Partitioning the effects of mating and nuptial feeding on the microbiome in gift-giving insects – Chad C. Smith – Environmental Microbiology Reports
The stable microbiome of inter and sub-tidal anemone species under increasing pCO2 – Erinn M. Muller – Scientific Reports
Plant, root, and soil microbiome
* Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity – Zachary Charlop-Powers – PNAS
News: Metagenomics Hints at Natural Product Potential of Microbes in New York City Parks – Genome Web
Study: New York City Dirt Rich in Bacteria Related to Medical Treatments – Robert Lee Hotz
* Sulfur-oxidizing bacteria prior to the Great Oxidation Event from the 2.52 Ga Gamohaan Formation of South Africa -Andrew D. Czaja – Geology
Geologist uncovers 2.5 billion-year-old fossils of bacteria that predate the formation of oxygen – Phys.org
Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls – Cynthia M. Kallenbach – Nature Communications
Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium – Alexander B. Chase – Frontiers in Microbiology
Molecular phylogeny, diversity, community structure, and plant growth promoting properties of fungal endophytes associated with the corms of saffron plant: An insight into the microbiome of Crocus sativus Linn. – Zahoor Ahmed Wani – Fungal Biology
Host and tissue variation overshadow the response of boreal moss-associated fungal communities to increased nitrogen load – Marie L. Davey – Molecular Ecology
Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO2 and Temperature in a Paddy Field – Yuan Liu – Frontiers in Microbiology
Microbial community structure of surface sediments from a tropical estuarine environment using next generation sequencing – Lidita Khandeparker – Ecological Indicators
Fungal endophytic communities associated to the phyllosphere of grapevine cultivars under different types of management – Carla Marisa Reis Varanda – Fungal Biology
Shifting patterns of microbial N-metabolism across seasons in upland Alaskan tundra soils – Shawna McMahon – Soil Biology and Biochemistry
Disruption of plant-soil-microbial relationships influences plant growth – Daniel P. Keymer – Journal of Ecology
Review: Rhizobial diversity and function in rooibos (Aspalathus linearis) and honeybush (Cyclopia spp.) plants: A review – C. Brink – South African Journal of Botany
Water and extremophile microbiome
Landscape-scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton – Juan Pablo Niño-García – Ecology Letters
Diversity and Distribution of Phenol Oxidase Producing Fungi from Soda Lake and Description of Curvularia lonarensis sp. nov. – Rahul Sharma – Frontiers in Microbiology
Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments – Sizhong Yang – Scientific Reports
* Comparative study of Dushanzi and Baiyanggou mud volcano microbial communities in Junggar Basin in Xinjiang, China – Zhiyong Huang – International Research Journal of Public and Environmental Health
Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient – C. Monard – Scientific Reports
Review: Sources of Antibiotics: Hot springs – Girish B. Mahajan – Biochemical Pharmacology
Metagenomics and bioinformatics
Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes – Jonsson Viktor – Journal of Computational Biology
Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains – Weinan Liao – Scientific Reports
Techniques
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community – Miten Jain – Genome Biology
Microbes in the news
The “Internet Of Food,” DNA Testing, And The Quest For The Perfect Diet – Fastcompany
Geologist uncovers 2.5 billion-year-old fossils of bacteria that predate the formation of oxygen – Phys.org
Major finding identifies nitrogen as key driver for gut health – Knowridge
Each animal species hosts a unique microbial community and benefits from it – David Salisbury – Vanderbilt University News
In Brazil, prestigious scientific journal “Nature Communications” focuses on Adventist lifestyle – Felipe Lemos – Adventist
Genes, early environment sculpt the gut microbiome – Science Daily
OpenBiome Now Stores Your Stool In Case of C. difficile Infection – Gastroenterology and Endoscopy News
Microbiome Digest - Bik's Picks 