July 8, 2019

Good Morning! Highlights of today’s digest include several AACR Cancer Research meeting abstracts on microbiome profiling which are promising for development of early detection cancer or treatment-associated-toxicity biomarkers and novel probiotics that can prevent HPV infections-associated cancers and oropharyngeal cancers, development of non-invasive health monitoring tools for endangered humpback whales from East Australia, and re-assemblage of rhizosphere microbiome of medicinal Chinese ginseng or Sanqi. Finally, check out the news about development of a food supplement, expected to be commercialized by 2021 and suggested only to be used as a complementary approach -not a replacement of appropriate dietary habits, that involves a probiotic gut bacterium Akkermansia muciniphila to improve metabolism and metabolic factors in obesity, type II diabetes and inflammatory bowel diseases.

Human oral microbiome

Meeting Abstract: Mucositis, candidiasis, and associations with the oral microbiome in treatment naive patients with oropharyngeal cancer – Pierce et al. – AACR Cancer Research

Multi-site human microbiome

Meeting Abstract: The microbiota associated to cervical and anal HPV infections in a Hispanic population – Vazquez-Sanchez et al. – AACR Cancer Research

Animal microbiome

Review: Coral microbiome dynamics, functions and design in a changing world – van Oppen et al. – Nature Reviews Microbiology

Interannual comparison of core taxa and community composition of the blow microbiota from East Australian humpback whales – Vendl et al. – FEMS Microbiology Ecology

Plant, root and soil microbiome

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion – Goss-Souza et al. – Microbial Ecology

Mycorrhizal frequency, physiological parameters, and yield of strawberry plants inoculated with endomycorrhizal fungi and rhizosphere bacteria – Mikiciuk et al. – Mycorrhiza

Negative plant-soil feedback driven by re-assemblage of the rhizosphere microbiome with the growth of Panax notoginseng – Zhu et al. – Frontiers in Microbiology

Water and extermophile microbiome

Microbial communities in a flow-through fish farm for lumpfish (Cyclopterus lumpus L.) during healthy rearing conditions – Roalkvam et al. – Frontiers in Microbiology

Probiotics / prebiotics

Dietary Resistant Potato Starch Alters Intestinal Microbial Communities and Their Metabolites, and Markers of Immune Regulation and Barrier Function in Swine – Trachsel et al. – Frontiers in Immunology

Phages and viruses

Virome capture sequencing does not identify active viral infection in unicentric and idiopathic multicentric Castleman disease – Nabel et al. – PLOS ONE

Wide distribution of phage that infect freshwater SAR11 bacteria – Chen et al. – BioRxiv


Meeting Abstract: Microbial sequencing using a single-pool target enrichment of multiple variable regions of the 16S rRNA gene, the nuclear ribosomal internal transcribed spacer (ITS) region, and antimicrobial resistance genes – Peck et al. – AACR Cancer Research

Microbes in the news

Microbiome Food Supplement Improves Metabolic Syndrome in Overweight People – Smith – Labiotech.eu Newsletter


June 3, 2019

Good Morning! Highlights from Monday’s digest include understanding the evolution of the E. coli chemosensory machinery from an ancient form with a stress response pathway function, curriculum design and evaluation tool for developing bioinformatics competencies and strain-dependent induction of gastric dysbiosis and gastric cancers investigated in the animal model, Mongolian gerbil.

General microbiology

Repurposing a macromolecular machine: Architecture and evolution of the F7 chemosensory system – Ortega et al. – BioRxiv

Microbiome science

** Perspectives – Moving Microbiome Science from the Bench to the Bedside: a Physician-Scientist Perspective – Surana – mSystems

Training in bioinformatics

The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training – Tractenberg et al. – BioRxiv

Human gut microbiome

Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis – Yamada et al. – BioRxiv

Animal experiments

Modification of the Gastric Mucosal Microbiota by a Strain-Specific Helicobacter pylori Oncoprotein and Carcinogenic Histologic Phenotype – Noto et al. – mBio

Metformin and DPP-4 Inhibitor Differentially Modulate the Intestinal Microbiota and Plasma Metabolome of Metabolically Dysfunctional Mice – Ryan et al. – Canadian Journal of Diabetes

Plant, root and soil microbiome

Changes in soil taxonomic and functional diversity resulting from gamma irradiation – Ogwu et al. – Scientific Reports

Chestnuts bred for blight resistance depart nursery with distinct fungal rhizobiomes – Reazin et al. – Mycorrhiza

Potential links between wood‐inhabiting and soil fungal communities: Evidence from high‐throughput sequencing – Purahong et al. – MicrobiologyOpen

Phages and Viruses

** Review – Viroids-First—A Model for Life on Earth, Mars and Exoplanets – Moelling et al. – Geosciences

Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake – Okazaki et al. – BioRxiv


Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary – Marotz et al. – BioTechniques

Microbes in the news

Gut Bacteria Linked To Autism Symptoms, Mice Study Shows – Carlos – Tech Times

Autism Mouse Models for the Microbiome? – Lowe – Science Translational Medicine

Microbes on the market

Global Microbiome Therapeutics Market Report Forecast by Development, Trends, and Forecast (2019 – 2024) – The Scripps Voice

May 13, 2019

Good Morning! Highlights from Monday’s digest include host switching ability in the Polyomaviruses carried in African bats, identification of microbial genes invloved in metal detoxification from metagenomes of oil-impacted mangrove sediments and a technical note about machine learning repository of curated classification and regression tasks derived from human microbiome datasets.

General Microbiology

Pseudomonas syringae Increases Water Availability in Leaf Microenvironments via Production of Hygroscopic Syringafactin – Hernandez et al. – BioRxiv

Pregnancy and early life

** Review – Intrauterine Microbiota: Missing, or the Missing Link? – Chen et al. – Trens in Neurosciences

Human skin microbiome

Microbiome in the hair follicle of androgenetic alopecia patients – Siu-Yin Ho et al. – PLOS ONE

Human gut microbiome

The presence of bacteria varies between colorectal adenocarcinomas, precursor lesions and non-malignant tissue – Bundgaard-Nielsen et al. – BMC Cancer

Animal experiments

Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems – Tripathi et al. – MSystems

Animal microbiome

Microbial community shifts associated with the ongoing stony coral tissue loss disease outbreak on the Florida Reef Tract – Meyer et al. – BioRxiv

Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders – Diaz-Sanchez et al. – PLOS ONE

Establishment and characterization of a competitive exclusion bacterial culture derived from Nile tilapia (Oreochromis niloticus) gut microbiomes showing antibacterial activity against pathogenic Streptococcus agalactiae – Melo-Bolivar et al. – PLOS ONE

Plant, root and soil microbiome

** Review – Assessment of the structural and functional diversities of plant microbiota: Achievements and challenges – Hartmann et al. – Journal of Advanced Research

Root renovation: how an improved understanding of basic root biology could inform the development of elite crops that foster sustainable soil health – Wong et al. – Functional Plant Biology

Phenanthrene contamination and ploidy level influence the rhizosphere microbiome of Spartina – Cave-Radet et al. – BioRxiv

Water and extremophile microbiome

Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats – Dong et al. – Astrobiology

* The metagenomic landscape of xenobiotics biodegradation in mangrove sediments – Cabral et al. – Ecotoxicology and Environmental Safety

Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones – Saunders et al. – PNAS

Influence of environmental drivers and potential interactions on the distribution of microbial communities from three permanently stratified Antarctic lakes – Morgan-Kiss et al. – Frontiers in Microbiology

Phaeobacter inhibens controls bacterial community assembly on a marine diatom – Majzoub et al. – FEMS Microbiology Ecology

Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR – Qin et al. – BMC Microbiome

Built environment

** Review – Clothing-Mediated Exposures to Chemicals and Particles – Licina et al. – Environmental Science & Technology

Phages and Viruses

*Extensive genetic diversity of bat-borne polyomaviruses reveals inter-family host-switching events – Tan et al. – BioRxiv


*Microbiome Learning Repo (ML Repo): A public repository of microbiome regression and classification tasks – Vangay et al. – GigaScience

Institutional protocols for the oral administration (gavage) of chemicals and microscopic microbial communities to mice: Analytical consensus – Rodriquez-Palacios et al. – Experimental Biology and Medicine

A New Strategy for the Selection of Epiphytic and Endophytic Bacteria for Enhanced Plant Performance – Balsanelli et al. – Plant Innate Immunity (Methods in Molecular Biology)

Sampling and Handling of Soil to Identify Microorganisms with Impacts on Plant Growth – Kremer RJ – Plant Innate Immunity (Methods in Molecular Biology)


Is useful research data usually shared? An investigation of genome-wide association study summary statistics – Thelwall et al. – BioRxiv

Microbes in the news

** Newsletter – Is there a link between gut bacteria and autism? A first-of-its-kind study investigates – USC News

** Newsletter – Localized efforts to save coral reefs won’t be enough, study suggests – Phys.org

Microbes on the market

** Report – 2019 Global Microbiome in Skincare Market – Research and Markets

** Newsletter – ‘Designer prebiotics’ are the future of food and microbiome modulation, says expert – NutraIngredients