April 25, 2017

A bit of a late morning Digest today, as it is packed with articles! Diverse themes, such as rhizosphere microbiome, lots of biotechnology pieces, and insightful reviews on gut microbiota and herbivory, “wild” microbiomes and ecological stoichiometry.

General microbiome

Review: The microbiome in anti-cancer therapy
Stavros Bashiardes et al – Seminars in Immunology

Perspective: Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk
Marco Romano – Frontiers in Microbiology

Multi-site human microbiome

Review: Lung Homeostasis: Influence of Age, Microbes, and the Immune System
Clare M. Lloyd & Benjamin J. Marsland – Immunity

Human epitelial microbiome

The oral microbiome community variations associated with normal, potentially malignant disorders and malignant lesions of the oral cavity
Mok Shao Feng et al – Malaysian Journal of Pathology

Human gut microbiome

‘Microbes in sport’ -The potential role of the gut microbiota in athlete health and performance
Rankin A. et al – Journal of Sports Medicine

Effect of pistachio consumption on the modulation of urinary gut microbiota-related metabolites in prediabetic subjects
Hernandéz-Alonso P et al – Journal of Nutritional Biochemistry

Microbial diseases

Alteration of stomach microbiota compositions in the progression of gastritis induces nitric oxide in gastric cell
Tianyi Dong et al – Experimental and Therapeutic Medicine

General environmental microbiome

Review: Evolutionary Biology Needs Wild Microbiomes
Sarah M. Hird – Frontiers in Microbiology

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites
Diego M. Toneatti et al – Frontiers in Microbiology

Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms
Daniella Gat et al – Environmental Science and Technology

Animal experiments

Urinary and Fecal Metabonomics Study of the Protective Effect of Chaihu-Shu-Gan-San on Antibiotic Induced Gut Microbiota Dysbiosis in Rats
Meng Yu et al – Nature Scientific Reports

Proteomic analysis of a mosquito host cell response to persistent Wolbachia infection
Gerald Baldridge et al – Research in Microbiology

Effect of ensiled mulberry leaves and sun-dried mulberry fruit pomace on the fecal bacterial community composition in finishing steers
Yan Li et al – BMC Microbiology

Effects of various weaning times on growth performance, rumen fermentation and microbial population of yellow cattle calves
Mao H et al – Asian-Australasian Journal of Animal Science

Effects of various levels of dietary copper supplementation with copper sulfate and copper hydroxychloride on Pacific white shrimp Litopenaeus vannamei performance and microbial communities
Yangen Zhou et al – Aquaculture

Plant, root, and soil microbiome

Soil Acidification Aggravates the Occurrence of Bacterial Wilt in South China
Shili Li et al – Frontiers in Microbiology

Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato
Mélanie M. Paulin et al – Applied and Environmental Microbiology

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil
Yang W et al – Environmental Science and Pollution Research

Rhizosphere Engineering: Enhancing Sustainable Plant Ecosystem Productivity in a Challenging Climate
Amirhossein Ahkami et al – Rhizosphere

Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies
Feigl V et al – Science of the Total Environment

Response of microbial community of organic-matter-impoverished arable soil to long-term application of soil conditioner derived from dynamic rapid fermentation of food waste
Jiaqi Hou et al – Plos One

Effects of adding trace elements on rice straw anaerobic mono-digestion: Focus on changes in microbial communities using high-throughput sequencing
Yafan Cai et al – Bioresource Technology

Cereal-legume intercropping modifies the dynamics of the active rhizospheric bacterial community
E. Taschen et al – Rhizosphere

Water, estuarine and sediment microbiome

Microbial Community Response on Wastewater Discharge in Boreal Lake Sediments
Jatta Saarenheimo et al – Frontiers in Microbiology

Perspective: The Hadal Biosphere: Recent insights and new directions
Rulong Liu et al – Deep Sea Research Part II: Topical Studies in Oceanography

Bacterial community dynamics and functional variation during the long-term decomposition of cyanobacterial blooms in-vitro
Limei Shi et al – Science of the Total Environment

Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean
Julie Dinasquet et al – Environmental Microbiology

DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom
Christian Wurzbacher et al – Environmental Microbiology Reports

Shifts in soil microbial metabolic activities and community structures along a salinity gradient of irrigation water in a typical arid region of China
Lijuan Chen et al – Science of the Total Environment

Large-scale seaweed cultivation diverges water and sediment microbial communities in the coast of Nan’ao Island, South China Sea
Xinfei Xie et al – Science of The Total Environment

Extremophile and space microbiome

Review: Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth
Fathi Karouia – Biotechnology Advances

Built environment

Diversity changes of microbial communities into hospital surface environments
Rika Yano et al – Journal of Infection and Chemotherapy

Microbial communities in the functional areas of a biofilm reactor with anaerobic-aerobic process for oily wastewater treatment
Li J et al – Bioresource Technology

Dominance of candidate Saccharibacteria in a membrane bioreactor treating medium age landfill leachate: Effects of organic load on microbial communities, hydrolytic potential and extracellular polymeric substances
Remmas N. et al – Bioresource Technology

Microbial biotechnology

Review: Uncovering Potential Applications of Cyanobacteria and Algal Metabolites in Biology, Agriculture and Medicine: Current Status and Future Prospects
Rachana Singh et al – Frontiers in Microbiology

The Ability of Typha angustifolia L. for Degradation of BOD and COD in Wastewater of Tofu Industry Using Phytoremediation
Pertiwi Andarani et al – Advanced Science Letters

Reversible Anaerob-Evapotranspiration Process for Removal of High Strength Ammonium in Leachate from Tropical Landfill
Badrus Zaman et al – Advanced Science Letters

Strain specific variation in plant growth promoting volatile organic compound production by five different Pseudomonas spp. as confirmed by response of Vigna radiata seedlings
Jishma P et al – Journal of Applied Microbiology

Microbial reductive dehalogenation of trihalomethanes by a Dehalobacter-containing co-culture
Zhao S. et al – Applied Microbiology and Biotechnology

Inhibitory effect of coumarin on syntrophic fatty acid oxidizing and methanogenic cultures and biogas reactor microbiomes
Denny Popp et al – Applied and Environmental Microbiology

Food microbiology

Impact of solar radiation exposure on phyllosphere bacterial community of red-pigmented baby leaf lettuce
Pilar Truchado et al – Food Microbiology

Effect of abattoir and cut on variations in microbial communities of vacuum-packaged beef
Mandeep Kaur et al – Meat Science

Smokeless tobacco products harbor diverse bacterial microbiota that differ across products and brands
Smyth EM et al – Applied Microbiology and Biotechnology
General Microbiology

Protein Acetylation and Its Role in Bacterial Virulence
Jie Ren et al – Trends in Microbiology

Perspective: Ecological Stoichiometry beyond Redfield: An Ionomic Perspective on Elemental Homeostasis
Punidan D. Jeyasingh et al – Frontiers in Microbiology

Genomes

Complete Genome Sequence of Pseudomonas protegens H78, a Plant Growth–Promoting Rhizobacterium
Xianqing Huang et al – Genome Announcements

Draft Genome Sequences of Two Hydrogenogenic Carboxydotrophic Bacteria, Carboxydocella sp. Strains JDF658 and ULO1, Isolated from Two Distinct Volcanic Fronts in Japan
Yuto Fukuyama et al – Genome Announcements

The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Ana Gutiérrez-Preciado et al – PeerJ

Phages and viruses

A novel type of polyhedral viruses infecting hyperthermophilic archaea
Ying Liu et al – Journal of Virology

Phage therapy: an alternative or adjunct to antibiotics?
Shawna McCallin & Harald Brüssow – Emerging Topics in Life Sciences

Highlights from the HIV Research for Prevention Conference (R4P)
Sandhya Vasan et al – Journal of Virus Eradication

Bioinformatics and statistics

A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping
Hyunwook Koh et al – Microbiome

The BRENDA Enzyme Information System–From a Database to an Expert System
I. Schomburg et al – Journal of Biotechnology

HirBin: high-resolution identification of differentially abundant functions in metagenomes
Tobias Österlund et al – BMC Genomics

A novel genome signature based on inter-nucleotide distances profiles for visualization of metagenomic data
Xian-Hua Xie et al – Physica A: Statistical Mechanics and its Applications

Data Intensive Genome Level Analysis for Identifying Novel,Non-Toxic Drug Targets for Multi Drug Resistant Mycobacterium tuberculosis
Divneet Kaur et al – Nature Scientific Reports

Techniques and methods

Building a Translational Microbiome Toolbox
Payal Joglekar & Julia Segre – Cell

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