May 23, 2018

Today’s digest is packed full of awesome gut microbiome studies, a bunch of plant/soil studies, new features to QIIME and other bioinformatics, as well as a good serving of interesting pre-prints, editorials, and doctoral theses. Enjoy!

General microbiome

Microbial micropatches within microbial hotspots – Lisa M. Dann – PLOS ONE

Pregnancy and early life

The matter of the reproductive microbiome – Sam Schoenmakers – Obstetric Medicine

Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum – Mie Korslund Wiinblad Crusell – Microbiome

The importance of appropriate initial bacterial colonization of the intestine in newborn, child, and adult health – W Allan Walker – Pediatric Research

Human oral microbiome

Oral health status in historic population: Macroscopic and metagenomic evidence – Claire Willmann – PLOS ONE

The Subgingival Microbiome of Periodontal Pockets With Different Probing Depths in Chronic and Aggressive Periodontitis: A Pilot Study – Meng Shi – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

[Pre-print] Gut microbiota markers in obese adolescent and adult patients: age-dependent differential patterns – Federica Del Chierico – Frontiers in Microbiology

Clinical applications of gut microbiota in cancer biology – Sunny H. Wong – Seminars in Cancer Biology

* Microbiome-Mediated Effects of the Mediterranean Diet on Inflammation – Melisa A Bailey – Advances in Nutrition

** Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury – Benjamin M Howard – Trauma Surgery & Acute Care Open

Hypoxia induces senescence of bone marrow mesenchymal stem cells via altered gut microbiota – Junyue Xing – Nature Communications

Animal experiments

The bacterial and archaeal community structures and methanogenic potential of the cecal microbiota of goats fed with hay and high-grain diets – Wei Jin – Antonie van Leeuwenhoek

Effects of whole-grain rice and wheat on composition of gut microbiota and short-chain fatty acids in rats – Fei Han – Journal of Agriculture and Food Chemistry

Animal microbiome

Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles – Chelsea L. Blankenchip – PeerJ

Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – World Journal of Microbiology and Biotechnology

The gut microbiome is associated with behavioural task in honey bees – J. C. Jones – Insectes Sociaux

The role of the gut microbiome in health and disease of adult honey bee workers – Kasie Raymann – Current Opinion in Insect Science

Plant, root, and soil microbiome

Microbial communities in soil profile are more responsive to legacy effects of wheat-cover crop rotations than tillage systems – Anil Somenahally – Soil Biology and Biochemistry

New insights into the effects of support matrix on the removal of organic micro-pollutants and the microbial community in constructed wetlands – Liang Zhang – Environmental Pollution

[Doctoral thesis] Imprint of management on microbial communities in arable soil – Putz, Martina

Study of microbial diversity in plant–microbe interaction system with oil sludge contamination – Dhote, Monika – International Journal of Phytoremediation

Effect of different potassium levels on nitrogen metabolism, nitrogen bacteria and nitrogen archaea bacteria communities in rhizosphere of tobacco plant – WENG Zebin – Acta Tabacaria Sinica

Canola Root–Associated Microbiomes in the Canadian Prairies – Chih-Ying Lay – Frontiers in Microbiology

Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves – Leandro Pio de Sousa – Genetics and Molecular Biology

[Review] Organic Amendments, Beneficial Microbes, and Soil Microbiota: Toward a Unified Framework for Disease Suppression – Giuliano Bonanomi – Annual Review of Phytopathology

[Pre-print] Metagenomic sequencing provides insights into the location of microbial detoxification in the gut of a small mammalian herbivore – Kevin D. Kohl – bioRxiv

[Pre-print] Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California – Sabah Ul-Hasan – bioRxiv

Water and extremophile microbiome 

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community – M.Peces – Water Research

Built environment

[Editorial] Microbiome Yarns: microbiome of the built environment, paranormal microbiology, and the power of single cell genomics – Kenneth Timmis – microbial biotechnology

New Techniques for the Generation and Analysis of Tailored Microbial Systems on Surfaces – Ariel L. Furst – Biochemistry

* [Pre-print] Strain­level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes – Matthew R. Olm – bioRxiv

Probiotics / prebiotics

The effects of probiotics supplementation on metabolic health in pregnant women: An evidence based meta-analysis – Jia Zheng – PLOS ONE

Bioinformatics

[Pre-print / doctoral thesis] Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binning – Alneberg, Johannes – DiVA

** Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin – Nicholas A. Bokulich – Microbiome

Techniques

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia – Martina Lardi – High-Throughput

VSITA, an Improved Approach of Target Amplification in the Identification of Viral Pathogens – Yi Zhang – Europe PMC

Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol – Ankur Naqib – Gene Expression Analysis

Ed’s non-microbiology picks 

The Environmental Protection Agency in the Early Trump Administration: Prelude to Regulatory Capture

Perspectives on the Great Amazon Reef: Extension, Biodiversity, and Threats

Fasting boosts stem cells’ regenerative capacity

Eggs not linked to cardiovascular risk, despite conflicting advice

Noninvasive spinal stimulation method enables paralyzed people to regain use of hands, study finds

Cannabidiol significantly reduces seizures in patients with severe form of epilepsy

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