A burst of articles for your Monday digest. Quite a few highlights emerge from this Digest. There can be racial disparity in gastrointestinal cancer risk. The stress we experience now might influence our children’s aging in the future. And you might want to think twice about choosing between 16S and metagenomic sequencing, depending on the type of samples you have.
Jobs
Research Technician – Molecular Biology and Microbiology Department – Tufts University
General microbiology
*Letter: Pilot study to determine whether microbial contamination levels in hospital washrooms are associated with hand-drying method – M.H. Wilcox et al. – Journal of Hospital Infection
History matters: heterotrophic microbial community structure and function adapt to multiple stressors – Alexander Feckler et al. – Global Change Biology
Pregnancy and early life
Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates – Alicja Nogacka et al. – Microbiome
Pregnancy-induced changes in metabolome and proteome in ovine uterine flushings – Jared J. Romero – Biology of Reproduction
Evolution of newborns urinary metabolomic profiles according to age and growth – Aurélien Scalabre et al. – Journal of Proteome Research
Human oral microbiome
Effect of fermented milk containing Lactobacillus rhamnosus SD11 on oral microbiota of healthy volunteers: A randomized clinical trial – P. Rungsri et al. – Journal of Dairy Science
Human lung microbiome
Microbiome in lung explants of idiopathic pulmonary fibrosis: a case-control study in patients with end-stage fibrosis – Kitsios GD – Thorax
Human gut microbiome
**Racial Disparity in Gastrointestinal Cancer Risk – Hassan Ashktorab et al. – Gastroenterology
Master Thesis: A study of the effects of diet on human gut microbial community structure and mercury metabolism – Ria Saha – University of Ottawa
*Investigation into the stability and culturability of Chinese enterotypes – Yeshi Yin
et al. – Scientific Reports
Bangladesh Environmental Enteric Dysfunction (BEED) study: protocol for a community-based intervention study to validate non-invasive biomarkers of environmental enteric dysfunction – Mahfuz M – BMJ Open
Metabolomics
“Omics” in Human Colostrum and Mature Milk: Looking to Old Data with New Eyes – Flaminia Bardanzellu et al. – Nutrients
Animal experiments
Stability and efficacy of frozen and lyophilized fecal microbiota transplant (FMT) product in a mouse model of Clostridium difficile infection (CDI) – Zhi-Dong Jiang et al. – Anaerobe
Rat: The activity of Hou-Po-Da-Huang-Tang is improved through intestinal bacterial metabolism and Hou-Po-Da-Huang-Tang selectively stimulate the growth of intestinal bacteria associated with health – Xing-Yan Liu et al. – Biomedicine & Pharmacotherapy
Mouse: Navy and black bean supplementation primes the colonic mucosal microenvironment to improve gut health – Jennifer M. Monk et al. – The Journal of Nutritional Biochemistry
Mouse: Human Gut-Derived Commensal Bacteria Suppress CNS Inflammatory and Demyelinating Disease – Ashutosh Mangalam et al. – Cell Reports
Mouse: Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition – Michail Mamantopoulos et al. – Immunity
Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice – Koji Yasuda et al. – mSystems
The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome – Timothy A. Johnson et al. – mBio
Animal microbiome
*The Effects of Captivity on the Mammalian Gut Microbiome – Valerie J. McKenzie et al. – Integrative and Comparative Biology
Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep – Janine Kamke et al. – BMC Research Notes
High diversity and unique composition of gut microbiomes in pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales – Patrick M. Erwin et al. – Scientific Reports
Virome comparisons in wild-diseased and healthy captive giant pandas – Wen Zhang and Shixing Yang et al. – Microbiome
Gut microbiomes of free-ranging and captive Namibian cheetahs: diversity, putative functions, and occurrence of potential pathogens – Wasim uddin et al. – Molecular Ecology
Plant, root and soil microbiome
Ecological and functional effects of fungal endophytes on wood decomposition – Lauren C. Cline et al. – Functional Ecology
Spatial Distribution Patterns of Root-Associated Bacterial Communities Mediated by Root Exudates in Different Aged Ratooning Tea Monoculture Systems – Yasir Arafat et al. – International Journal of Molecular Sciences
Book chapter: The Rhizosphere and Plant Nutrition Under Climate Change – Tarek Alshaal et al. – Essential Plant Nutrients
Fungal Diversity in Tomato Rhizosphere Soil under Conventional and Desert Farming Systems – Elham A. Kazerooni et al. – Frontiers in Microbiology
Banana Fusarium Wilt Disease Incidence Is Influenced by Shifts of Soil Microbial Communities Under Different Monoculture Spans – Zongzhuan Shen et al. – Microbial Ecology
*Characterisation and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in soils and plants around e-waste dismantling sites in southern China – Yujie Wang et al. – Environmental Science and Pollution Research
Water and extremophile microbiome
**Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing – Michael Tessler et al. – Scientific Reports
Interplay of hydrology, community ecology and pollutant attenuation in the hyporheic zone – Ignacio Peralta-Maraver et al. – Science of The Total Environment
Responses of coral-associated bacterial communities to local and global stressors – Jamie McDevitt-Irwin et al. – Frontiers in Marine Science
Built environment microbiome
Variability of indoor fungal microbiome of green and non-green low-income homes in Cincinnati, Ohio – Kanistha Coombs et al. – Science of The Total Environment
Food microbiome
Bacterial diversity of the Colombian fermented milk “Suero Costeño” assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons – Karina Edith Motato – Food Microbiology
Bioinformatics
*Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes – Nathan D. Olson et al. – Briefings in Bioinformatics
Big data management challenges in health research—a literature review – Xiaoming Wang et al. – Briefings in Bioinformatics
Microbes in the news
*FDA: Don’t use these liquid drug or dietary supplement products for infants – Sara Nealeigh – Bradenton Herald
Core bacteria in the gut of horses showed some stability over time in study – HorseTalk
Are Doctors Wrong About Finishing Your Antibiotics? – Paul A. Offit – Daily Beast
*Bacteria at the beach: High levels found at nearly a dozen locations in past two weeks – Sarah Reese – NWI Times
Microbes on the market
OptiBiotix Health PLC (OPTI) Rating Reiterated by FinnCap – Anthony Sawyer – Week Herald
Non-microbiology picks
**Review: Transgenerational Effects of Early Environmental Insults on Aging and Disease Incidence – Mirela Ambeskovic et al. – Neuroscience & Biobehavioral Reviews
Air-quality implications of widespread adoption of cool roofs on ozone and particulate matter in southern California – Scott A. Epstein et al. – PNAS
Microbiome Digest - Bik's Picks 