So it is technically already January 15 most countries, but I have been busy today preparing to transfer Microbiome Digest to an eager group of 20 new contributors. It takes a lot of time to hopefully be able to safe some time – if that makes sense.
My inbox is still full of new alerts, but here is what I have been able to “digest” so far. It’s already a lot!
General human microbiome
Navigating social and ethical challenges of biobanking for human microbiome research –
Kim H. Chuong – BMC Medical Ethics
Editorial: Influence of the microbiota on host physiology – moving beyond the gut
– Kim E. Barrett – The Journal of Physiology
Pregnancy and early life
* Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid – Diogo Antonio Tschoeke – BMC Medical Genomics
Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota – Jasmine C. C. Davis – Scientific Reports
Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research
The Microbiome and Complement Activation A Mechanistic Model for Preterm Birth – Alexis B. Dunn – Biological Research for Nursing
Review: Asthma and the microbiome: defining the critical window in early life – Leah T. Stiemsma – Allergy, Asthma & Clinical Immunology
Human gut microbiome
Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology
Serum Trimethylamine N-oxide, Carnitine, Choline and Betaine in Relation to Colorectal Cancer Risk in the Alpha Tocopherol and Beta Carotene Study – Kristin A. Guertin – Cancer Epidemiology, Biomarkers & Prevention
Laboratory Testing of Donors and Stool for Fecal Microbiota Transplantation for Recurrent C. difficile Infection – Michael H. Woodwort – Journal of Clinical Microbiology
Editorial: Gut microbiota: implications for sports and exercise medicine – Owen Cronin – British Journal of Sports Medicine
Review/Addendum: Pathogen control at the intestinal mucosa – H2O2 to the rescue
Ulla G. Knaus – Gut Microbes
Editorial: Tune into the rhythm of your bugs – Purna Kashyap – Science Translational Medicine
Preview: Are Gut Microbes Responsible for Post-dieting Weight Rebound? – Julien Chilloux – Cell Metabolism
Review: Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease – Dawei Gong – Gastroenterology Research and Practice
Year in Review: Gut microbiota in 2016: A banner year for gut microbiota research – Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology
Review: Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? – Vanina Guernier – BMC Infectious Diseases
Review: An expanding stage for commensal microbes in host immune regulation – Yan Shi – Cellular & Molecular Immunology
Perspective: Decoding host–microbiota communication in the gut – now we’re flying!
– Stephen J. Keely – The Journal of Physiology
Just based on the abstract, this appears a wild hypothesis potentially ignoring economic status, fiber consumption etc: Latitude as a co-driver of human gut microbial diversity? – Emma Dikongué – Ideas that Push the Boundaries
Book: Gut Microbiome and Behavior, Volume 131 – John F. Cryan, Gerard Clarke – Elsevier
Animal experiments
Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice – Jaques Belik – Scientific Reports
Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine
Year in review: Microbiome in 2016: T follicular helper cells and the gut microbiome in arthritis – Veena Taneja – Nature Reviews Rheumatology
Animal microbiome
* Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms – Simon Bahrndorff – PLOS ONE
Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m) – Bettina Glasl – Coral Reefs
Symbiont-induced odorant binding proteins mediate insect host hematopoiesis – Joshua B Benoit – eLIFE
Drivers of variation in species impacts for a multi-host fungal disease of bats –
Kate E. Langwig – Philosophical Transactions of the Royal Society B
Sponges: Evaluating the core microbiota in complex communities: A systematic investigation – Carmen Astudillo-Garcia – Environmental Microbiology
Plant, root, and soil microbiome
Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland – Haggai Wasserstrom – Scientific Reports
Phylogenetic relatedness, phenotypic similarity and plant–soil feedbacks – Connor R. Fitzpatrick
Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology
Water microbiome
Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China – Jingqiu Liao – Limnology and Oceanography
Built environment microbiome
Microbial diversity in different compartments of an aquaponics system – Zala Schmautz – Archives of Microbiology
Food microbiology
The influence of thiamine and riboflavin on various spoilage microorganisms commonly found in beer – Barry Hucker – The Journal of The Institue of Brewing
Waste and pollution microbiology
Microbial flora analysis for the degradation of beta-cypermethrin – Zhang Qi – Environmental Science and Pollution Research
Fungi (also see Animal Microbiome)
Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge – Neil A. R. Gow – Philosophical Transactions of the Royal Society B
Proteomics and metabolomics
MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota – Aitor Blanco-Míguez – Database
Perspective: Progress in the biology and analysis of short chain fatty acids – Roel J. Vonk – The Journal of Physiology
Bioinformatics and biostatistics
Using Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease – Mehrdad Yazdani – IEEE
Microscale Insight into Microbial Seed Banks – Kenneth J. Locey – Frontiers in Microbiology
* EMPeror: Bringing the Dynamic Microbiome to Life with Animations – Yoshiki Vázquez-Baeza – Cell Host & Microbe
Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities – Gongchao Jing – Scientific Reports
Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices – Hua X. – Human Heredity
MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets – Xilin Xu – Biophysics Reports
Techniques
Methodological flaws introduce strong bias into molecular analysis of microbial populations – N. Krakat – Journal of Applied Microbiology
Editorial: Microbial Nanoscopy: Breakthroughs, Challenges, and Opportunities – Yves F. Dufrêne – ACS Nano
More microbes
* Asgard archaea illuminate the origin of eukaryotic cellular complexity – Katarzyna Zaremba-Niedzwiedzka – Nature
* Species-Independent Attraction to Biofilms through Electrical Signaling – Jacqueline Humphries – Cell
A bacterial global regulator forms a prion – Andy H. Yuan – Science
A periplasmic polymer curves Vibrio cholerae and promotes pathogenesis – Thomas M. Bartlett – Cell
Assembly of a nucleus-like structure during viral replication in bacteria – Vorrapon Chaikeeratisak – Science
Microbes in the news
Man’s best friend, bacteria’s worst enemy: dog sniffs out superbug in Canadian hospital – Ashifa Kassam – The Guardian
This article is not as bad as the title suggests but with photoshopped images:
Revealed: The millions of stomach-churning bacteria lurking in YOUR hair, skin, lungs, gut and mouth – and why – Mary Kekatos – Daily Mail
Video: Career profiles: Program Director at National Science Foundation Matthew Kane – American Society for Microbiology
A clear picture of bacteria: A new study has frozen bacteria extremely fast to gain a true-to-nature image of the internal and external structure – Science Daily
Microbiome Digest - Bik's Picks 