This may be our last edition of the Microbiome Digest before the holidays kick in. A rich and dynamic Digest brings you all things microbiome (apologies for the tight formatting). An encouraging report on how we can reduce antimicrobial resistance organically, an amazing recovery of a human genome and an oral microbiome from chewed birch pitch thousands of years ago, and a network analysis reveals four levels of hierarchical trophic interactions in the human gut microbiome. Enjoy Reading and Happy Holidays!
Events
BMC Medicine’s upcoming collection, New Frontiers in Diagnosis, Treatment and Management of Neuromuscular Disorders, is soliciting submissions.
Danone North America Announces 2019-2020 Gut Microbiome, Yogurt and Probiotics Fellowship Grant – Danone North America
Current Issue of The ISME Journal
The 9th Gut Microbiota for Health World Summit – March 7 and 8 2020 in Madrid, Spain
General microbiology
Depletion of microbiome-derived molecules in the host using Clostridium genetics – Chun-Jun Guo et al. – Science
Microbial carbon limitation ‐ the need for integrating microorganisms into our understanding of ecosystem carbon cycling – Jennifer L. Soong et al. – Global Change Biology
High-order interactions distort the functional landscape of microbial consortia – Sanchez-Gorostiaga & Bajić et al. – PLoS Biology
Antimicrobial resistance
** Significant reduction of vancomycin resistant E. faecium in the Norwegian broiler population coincided with measures taken by the broiler industry to reduce antimicrobial resistant bacteria – Roger Simm et al. – PLoS One
Preprint: Genomic analysis of carbapenemase-encoding plasmids from Klebsiella pneumoniae across Europe highlights three major patterns of dissemination – Sophia David et al. – bioRxiv
Human skin microbiome
The diversity and abundance of fungi and bacteria on the healthy and dandruff affected human scalp – Sally G. Grimshaw et al. – PLoS One
Human oral microbiome
** A 5700 year-old human genome and oral microbiome from chewed birch pitch – Theis Z. T. Jensen et al. – Nature Communications
Press: Ancient “Chewing Gum” Reveals a 5,700-Year-Old Microbiome – Jim Daley – Scientific American
Human respiratory microbiome
The upper-airway microbiota and loss of asthma control among asthmatic children – Yanjiao Zhou et al. – Nature Communications
Press: Child asthma flare-ups coincide with microbiome changes – JULIA EVANGELOU STRAIT-WUSTL – Futurity
Press: Asthma severity linked to microbiome of upper airway – MedicalXpress
Human gut microbiome
Differences in the intestinal microbiome of healthy children and patients with newly diagnosed Crohn’s disease – Kinga Kowalska-Duplaga et al. – Scientific Reports
Obesity and disease severity magnify disturbed microbiome-immune interactions in asthma patients – David Michalovich et al. – Nature Communications
Functional Associations between Gut Microbiome and Bone Health Status in Post-Menopausal Women: A Cross-Sectional Study – Bolaji Lilian Ilesanmi-Oyelere et al. – Proceedings
The microbiota composition of the offspring of patients with gestational diabetes mellitus (GDM) – Valentina Ponzo et al. – PLoS One
Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption – Jeffery& Das et al. – Gastroenterology
Human vaginal microbiome
Characterization of vaginal microbiota in women with preterm labor with intra-amniotic inflammation – Teresa Cobo et al. – Scientific Reports
Human gut-microbiota-brain axis
Review: Tryptophan Metabolism: A Link Between the Gut Microbiota and Brain – Kan Gao et al. – Advances in Nutrition
Cancer microbiome
Preprint: Growth rate alterations of human colorectal cancer cells by 157 gut bacteria – Rahwa Taddese et al. – bioRxiv
Metabolomics
Metabolomics analysis of human acute graft-versus-host disease reveals changes in host and microbiota-derived metabolites – David Michonneau et al. – Nature Communications
** Integrated univariate, multivariate and correlation-based network analyses reveal metabolite-specific effects on bacterial growth and biofilm formation in necrotizing soft tissue infections – MUHAMMAD AFZAL et al. – Journal of Proteome Research
The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics
Animal experiments
Circadian misalignment alters insulin sensitivity during the light phase and shifts glucose tolerance rhythms in female mice – Li-Xin Zhong et al. – PLoS One
Polysaccharide from Rosa roxburghii Tratt fruit attenuates hyperglycemia, hyperlipidemia and regulates colon microbiota in diabetic db/db mice – Lei Wang et al. – Journal of Agricultural and Food Chemistry
Animal microbiome
Review: Beneath the surface: community assembly and functions of the coral skeleton microbiome – Francesco Ricci et al. – Microbiome
Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysis – Qifan Zeng et al. – Microbiome
Microbial diversity within the digestive tract contents of Dezhou donkeys – Guiqin Liu et al. – PLoS One
An inter-island comparison of Darwin’s finches reveals the impact of habitat, host phylogeny, and island on the gut microbiome – Wesley T. Loo et al. – PLoS One
Plant, root and soil microbiome
Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients – Chao-Li Huang et al. – Microbial Ecology
Short-term nitrogen fertilization affects microbial community composition and nitrogen mineralization function in an agricultural soil – Ouyang & Norton – Applied and Environmental Microbiology
Root microbiomes as indicators of seagrass health – Belinda C Martin et al. – FEMS Microbiology Ecology
Water and extremophile microbiome
Microbial chemolithotrophy mediates oxidative weathering of granitic bedrock – Stephanie A. Napieralski et al. – PNAS
Integrating high-throughput sequencing and metagenome analysis to reveal the characteristic and resistance mechanism of microbial community in metal contaminated sediments – Changchun Yan et al. – Science of the Total Environment
Seasonal Variability of Conditionally Rare Taxa in the Water Column Bacterioplankton Community of Subtropical Reservoirs in China – Pascaline Nyirabuhoro et al. – Microbial Ecology
Phages and viruses
Diversity, evolution, and classification of virophages uncovered through global metagenomics – David Paez-Espino et al. – Microbiome
Discordant transmission of bacteria and viruses from mothers to babies at birth – Rabia Maqsood et al. – Microbiome
Technology
Applying indirect open-circuit calorimetry to study energy expenditure in gnotobiotic mice harboring different human gut microbial communities – Ilia G. Halatchev et al. – Microbiome
Manipulating rod-shaped bacteria with optical tweezers – Zheng Zhang et al. – Scientific Reports
** A metagenomic strategy for harnessing the chemical repertoire of the human microbiome – Sugimoto et al. – Science
Enrichment of specific microbial communities by optimum applied voltages for enhanced methane production by microbial electrosynthesis in anaerobic digestion – Flores-Rodriguez & Min – Bioresource Technology
Bioinformatics
Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools – Xiaofang Jiang et al. – PLoS One
** Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang et al. – PLoS Computational Biology
Microbes in the news
Exposure to UVB light may lead to beneficial changes in the human gut microbiome: Study – Danielle Masterson – Nutraingredients
In mice, a high-fat, high-sugar diet remodels the microbiome and endocannabinoid system – ASM – EurekAlert
Prescient Metabiomics and CoreBiome collaborating to develop breakthrough colon cancer screening test – P&T Community
The microbiome is fundamental to both health and disease – Fabian Brockotter – Poultry World
Low FODMAP Diet Helps IDB Patients – Kenny Walter – MDMAG
Coculturing of Mosquito‐Microbiome Bacteria Promotes Heme Degradation in Elizabethkingia anophelis – Jack Ganley et al. – ChemBioChem
** Mining metagenomics: A faster and more efficient method to compare metagenomes – Chinese Academy of Sciences – Phys.org
Oral Health: Caring for the Other Microbiome – Julia Peterman – Whole Foods Magazine
Is There a Link Between Migraine and the Gut Microbiome? – Sally Robertson – News Medical
Non-microbiology pick
Preprint: Grant reviewer perceptions of the quality and effectiveness of panel discussion – Stephen A Gallo et al. – bioRxiv
Microbiome Digest - Bik's Picks 