Microbiome publications are definitely not taking a winter break, so here is your holiday update. Merry Christmas to those who celebrate!
Human oral microbiome
Serum IgG Antibody Levels to Periodontal Microbiota Are Associated with Incident Alzheimer Disease – James M. Noble – PLOS ONE
Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle – Xuesong He – PNAS USA
Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant
and periodontal sites – Simone Schaumann – BMC Oral Health
Human respiratory microbiome
The Microbial Community of the Cystic Fibrosis Airway Is Disrupted in Early Life – Julie Renwick – PLOS ONE
Human gut or general microbiome
Effects of bowel cleansing on the intestinal microbiota – Jonna Jalanka – Gut
The Microbiome of Aging and Age-Related Disease – 2014 Meeting Abstracts
Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – ArXiv.org
Cancer and the microbiome: potential applications as new tumor biomarker – Khan Shahanavaj – Expert Review of Anticancer Therapy
Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Camila S. Cardinelli – Obesity Surgery
Animal models of microbiome research
Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology
Animal microbiome
Microbiomes, plausible players or not in alteration of host behaviour – David G. Biron – Frontiers in Microbiology
The Howler Monkey as a Model for Exploring Host-Gut Microbiota Interactions in Primates – Katherine R. Amato, Nicoletta Righini – Howler Monkeys
The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra) – Katherine R. Amato – Microbial Ecology
Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota – T.D.J. Bello González – Beneficial Microbes
Effects of dietary supplementation of a commercial prebiotic Previda® on survival, growth, immune responses and gut microbiota of Pacific white shrimp, Litopenaeus vannamei – J.D. Anuta – Aquaculture Nutrition
Metagenomic-Based Study of the Phylogenetic and Functional Gene Diversity in Galápagos Land and Marine Iguanas – Pei-Ying Hong – Microbial Ecology
Plant microbiome
The plant microbiome at work – Klaus Schlaeppi and Davide Bulgarelli – Molecular Plant-Microbe Interactions
Tree communities rapidly alter soil microbial resistance and resilience to drought – David Rivest – Functional Ecology
The Sesquiterpene Biosynthesis and Vessel-Occlusion Formation in Stems of Aquilaria sinensis (Lour.) Gilg Trees Induced by Wounding Treatments without Variation of Microbial Communities – Zheng Zhang – International Journal of Molecular Sciences
Analysis of microbial taxonomical groups present in maize stalks suppressive to colonization by toxigenic Fusarium spp.: A strategy for the identification of potential antagonists – Jürgen Köhl – Biological Control
Soil and sediment microbiome
Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland – Raeid M. M. Abed – PLOS ONE
Do climate factors govern soil microbial community composition and biomass at a regional scale? – L. Ma – Biogeosciences Discuss
Water microbiome
Early succession of micro-periphyton communities in kelp bed and barren ground ecological systems – Roberto A. Uribe – Marine Ecology
Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China – Shang Wang – Scientific Reports
Effects of warming on microbial communities in the coastal waters of temperate and subtropical zones in the Northern Hemisphere, with a focus on Gammaproteobacteria
Dao Thi Anh Tuyet – Journal of Oceanography
Colonization in the photic zone and subsequent changes during sinking determines bacterial community composition in marine snow – Stefan Thiele – Applied and Environmental Microbiology
Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland
Raeid M. M. Abed – PLOS ONE
Bioreactor microbiology
Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures – Shaobo Liang – Bioresource Technology
A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates – Damian E. Helbling – Water Research
Metagenomics
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India – Johan Bengtsson-Palme – Frontiers in Microbiology
Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity – Michelle Davison – Photosynthesis Research
Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms – Martial Marbouty – eLIFE
Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing – Alexander W. Eastman and Ze-Chun Yuan – Frontiers in Microbiology
Metabolomics and transcriptomics
Terpene synthases are widely distributed in bacteria – Yuuki Yamada – PNAS USA
Scaling microbial biomass, metabolism and resource supply – Robert L. Sinsabaugh – Biogeochemistry
Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume – Jason A Hilton – ISME Journal
Mining Soil Metagenomes to Better Understand the Evolution of Natural Product Structural Diversity: Pentangular Polyphenols as a Case Study – Hahk-Soo Kang and Sean F. Brady – Journal of the American Chemical Society
Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale – Darrell W. Cockburn – Molecular Microbiology
Techniques
Deciphering the Prokaryotic Community and Metabolisms in South African Deep-Mine Biofilms through Antibody Microarrays and Graph Theory – Yolanda Blanco – PLOS ONE
Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing – Annette Carola Anderson – BMC Microbiology
Probiotics
Probiotic and technological properties of Lactobacillus spp. strains from the human stomach in the search for potential candidates against gastric microbial dysbiosis – Susana Delgado – Frontiers in Microbiology
Phages and viruses
Effectiveness of bacteriophages in the sputum of cystic fibrosis patients – E. Saussereau – Clinical Microbiology and Infection
More Microbiology
Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology
Bacterial microcompartments and the modular construction of microbial metabolism – Cheryl A. Kerfeldemail, Onur Erbilgin – Trends in Microbiology
The impact of triclosan on the spread of antibiotic resistance in the environment – Daniel E. Carey – Frontiers in Microbiology
Microbes in the news
At Last, I Meet My Microbes – Katherine Harmon Courage – NPR Shots
This Is Your Microbiome: Katherine Harmon Courage at NPR is taking a tour through her microbiome and that of her husband, mother, and dog, as she recounts in a four-part series – Genome Web
Big Idea 2015: Medicine, Wellbeing, and the Microbiome – Deepak Chopra – LinkedIn
When Threatened By Worms, Bacteria Summon Killer Fungi – Ed Yong – National Geographic
Parkinson’s disease linked to gut bacteria – Tim Sandle – Digital Journal
Bacteria in 550-million-year-old fossils provide new clues about fossil formation – Science Codex
Yellowstone Thermal Pools Colored by Pollution – Patrick J Kiger – Discovery
Floating Toilets That Clean Themselves Grow On A Lake – Nsikan Akpan – NPR Goats and Soda
Bettendorf wrestling coach’s invention tackles germs and bacteria on sporting mats and floors – Dennis Moran – QC Online
People on Craigslist Want to Give You Bacteria for Free – Natalie Kitroeff – BusinessWeek
Science, publishing, career
Patterns of text reuse in a scientific corpus – Daniel T. Citron and Paul Ginsparg – PNAS USA
The Anti-Plagiarism Machine: An analysis of hundreds of thousands of scientific papers finds text re-use is rampant, but it isn’t always malicious – Adrienne Lafrance – The Atlantic
“You Are Welcome Here”: Small Stickers Make a Big Difference for LGBTQ Scientists – Kyle Frischkorn – Scientific American
Science and Art
Incredible Bacteria-Laced Fabric Combines Art, Biology And Fashion – Priscilla Frank – Huffington Post
Bik’s Picks
Evolutionary perspectives on human height variation – Gert Stulp and Louise Barrett – Biological Reviews
What the ‘marshmallow test’ can teach you about your kids – Chuck Hadad – CNN
7 of the Ocean’s Strangest Creatures, Including a Fish With a Flashlight – Matt Simon – Wired
Modern genetics confirm ancient relationship between fins and hands – Science Daily
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Microbiome Digest - Bik's Picks 