Today’s rich Digest features a report on how an invasive fungus restructures bat skin microbiome and a review on how plant-based culture media might come about. How is authorship determined? Enjoy reading!
Human gut microbiome
Review: Gut Microbiota in Alzheimer’s Disease, Depression, and Type 2 Diabetes Mellitus: The Role of Oxidative Stress – Maria Luca et al. – Oxidative Medicine and Cellular Longevity
Cancer microbiome
Review: Exploring the emerging role of the microbiome in cancer immunotherapy – Jessica Fessler & Vyara Matson et al. – Journal for ImmunoTherapy of Cancer
Salivary Microbial Dysbiosis is Associated with Systemic Inflammatory Markers and Predicted Oral Metabolites in Non-Small Cell Lung Cancer Patients – Weiquan Zhang et al. – Journal of Cancer
Metabolomics
Review: Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community – Farhana R. Pinu et al. – Metabolites
BLANKA: an Algorithm for Blank Subtraction in Mass Spectrometry of Complex Biological Samples – Jessica L. Cleary et al. – Journal of The American Society for Mass Spectrometry
Review: Comparative genomics and metagenomics of the metallomes – Yan Zhang et al. – Metallomics
Animal experiments
Analysis of the In Vivo Transcriptome of Bordetella pertussis during Infection of Mice – Ting Y. Wong et al. – mSphere
Structural modulation of gut microbiota reveals Coix seed contributes to weight loss in mice – Sheng Liu et al. – Applied Microbiology and Biotechnology
Supplementation with compound polysaccharides contributes to the development and metabolic activity of young rat intestinal microbiota – Mengxia Wang et al. – Food & Function
Animal microbiome
Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) – Typhaine Le Doujet et al. – Microbiome
Comparative analysis of intestinal bacteria among venom secretion and non-secrection snakes – Zuodong Qin et al. – Scientific Reports
Parallel sequencing of porA reveals a complex pattern of Campylobacter genotypes that differs between broiler and broiler breeder chickens – Frances. M. Colles et al. – Scientific Reports
** Preprint: White-nose syndrome restructures bat skin microbiomes – Meghan A. Ange-Stark et al. – bioRxiv
Food microbiome
Establishment limitation constrains the abundance of lactic acid bacteria in the Napa cabbage phyllosphere – Esther R. Miller et al. – Applied and Environmental Microbiology
Plant, root and soil microbiome
Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status – Hazem Sharaf et al. – Microbiome
Fungi Originating From Tree Leaves Contribute to Fungal Diversity of Litter in Streams – Pirjo Koivusaari et al. – Frontiers in Microbiology
Successional trajectories of soil bacterial communities in mine tailings: The role of plant functional traits – Yannick Colin et al. – Journal of Environmental Management
Elevated CO2, chlorpyrifos and biochar influence nitrification and microbial abundance in the rhizosphere of wheat cultivated in a tropical vertisol – Bharati Kollah et al. – Rhizosphere
Increasing livestock wastewater application in alternate-furrow irrigation reduces nitrification gene abundance but not nitrification rate in rhizosphere – Yuan Liu et al. – Biology and Fertility of Soils
** Review: Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – A review – Mohamed S. Sarhan et al. – Journal of Advanced Research
Water and extremophile microbiome
Coupling growth kinetics modeling with machine learning reveals microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process – Ran Mei et al. – Microbiome
Fungal Community Composition and Potential Depth-Related Driving Factors Impacting Distribution Pattern and Trophic Modes from Epi- to Abyssopelagic Zones of the Western Pacific Ocean – Wei Li et al. – Microbial Ecology
Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters – Susanne G. Langer et al. – Microbial Biotechnology
Increasing livestock wastewater application in alternate-furrow irrigation reduces nitrification gene abundance but not nitrification rate in rhizosphere – Yuan Liu et al. – Biology and Fertility of Soils
Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities – John I. Miller et al. – Frontiers in Microbiology
Bacterial Community 16S rRNA Gene Sequencing Characterizes Riverine Microbial Impact on Lake Michigan – Cindy H. Nakatsu et al. – Frontiers in Microbiology
Patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge in Lhasa River – Ke Tao et al. – Ecotoxicology and Environmental Safety
Potentially toxic metal contamination and microbial community analysis in an abandoned Pb and Zn mining waste deposit – M.C. Kasemodel et al. – Science of The Total Environment
Structure and function of microbial community associated with phenol co-substrate in degradation of benzo[a]pyrene in coking wastewater – Haizhen Wu et al. – Chemosphere
Phages and viruses
Distribution and Phylogeny of Erythrocytic Necrosis Virus (ENV) in Salmon Suggests Marine Origin – Veronica A. Pagowski et al. – Viruses
Interaction of RNA viruses of the natural virome with the African malaria vector, Anopheles coluzzii – Ferdinand Nanfack-Minkeu et al. – Scientific Reports
Technology
Active harvesting enhances energy recovery and function of electroactive microbiomes in microbial fuel cells – Lu Lu et al. – Applied Energy
Bioinformatics
Letter to Editor: Towards precision quantification of contamination in metagenomic sequencing experiments – M. S. Zinter et al. – Microbiome
Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data – Krithika Arumugam et al. – Microbiome
Review: Evolution of biosequence search algorithms: a brief survey – Gregory Kucherov – Bioinformatics
Microbes in the news
Two new studies reveal universal gut microbiome signatures in colorectal cancer – Andreu Prados – Gut Microbiota for Health
Prime the Pump – Robert B Corbett – Bovine Vet Online
Germ-Killing Brands Now Want to Sell You Germs – Caroline Winter – Bloomberg
Podcast: What is Functional Medicine’s Role In Gut Healing? – The Microbiome Report
Microbes on the market
Viome Raised $25M for its Microbiome-based Dietary Guide Platform – Chris Albrecht – The Spoon
Non-microbiology pick
** Preprint: A qualitative study exploring researchers’ perspectives on authorship decision-making – Lauren A Maggio et al. – bioRxiv
Microbiome Digest - Bik's Picks 