August 14, 2017

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.


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


“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


*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

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