July 29, 2019

Good Morning! Highlights of today’s digest include a revisited study that showed a significant alterations in the gut microbiome by the consumption of low/no-calorie sweeteners (LNCS), such as Splenda, and raising safety concerns, another work tells us development of Burkholderia-free host plant model to show how Burkholderia helps plant development, and finally a study finds a mechanistic link between the gut microbiome and early childhood asthma as shown with highthened expression of bacterial genes that make 12,13-diHOME which alters immune response.

Human gut microbiome

***Revisited: Assessing the in vivo data on low/no-calorie sweeteners and the gut microbiota – Susan S. Schiffman et al. – Food and Chemical Toxicology

A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study – Fabian Frost et al. – PLOS ONE

Human respiratory microbiome

Chronic obstructive pulmonary disease upper airway microbiome is associated with select clinical characteristics – Alexa A. Pragman et al. – PLOS ONE

Animal experiments

***Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance – Sophia R. Levan et al. – Nature Microbiology

Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets – Tadele G. Kiros et al. – PLOS ONE

Low-dose inoculation of Escherichia coli achieves robust vaginal colonization and results in ascending infection accompanied by severe uterine inflammation in mice – Valerie P. O’Brien – PLOS ONE

Probiotic strains improve high-fat diet-induced hypercholesterolemia through modulating gut microbiota in ways different from atorvastatin – Dun Su et al. – bioRxiv

Host Genotype-shaped Gut Microbiome Modulate Atherosclerosis Development in Mice – Kazuyuki Kasahara et al. – Arteriosclerosis, Thrombosis, and Vascular Biology

Animal microbiome

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae – Osiris Gaona et al. – PLOS ONE

Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis – Emilie Lejal et al. – bioRxiv

Characterization of the gastrointestinal bacterial microbiome of farmed juvenile and adult white Cachama (Piaractus brachypomus) – Victor Alfonso et al. – Aquaculture

Biosynthesis and Characterization, Antioxidant and Antimicrobial Activities
of Selenium Nanoparticles from Ethanol Extract of Bee Propolis
– Shubharani R. et al. – Journal of Nanomedicine & Nanotechnology

Plant, root and soil microbiome

The role of inoculum dispersal and plant species identity in the assembly of leaf endophytic fungal communities – Kevin D. Ricks et al. – PLOS ONE

***Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant – Arne Sinnesael et al. – PLOS ONE

AOA and AOB communities respond differently to changes of soil pH under long-term fertilization – Rubio Sun et al. – Soil Ecology Letters

***Negative plant-microbiome feedback limits productivity in aquaponics – Jessica A. Day et al. – bioRxiv

Do plant–microbe interactions and aluminum tolerance influence
alpine sedge species’ responses to nitrogen deposition?
– Teal S. Potter et al. – Ecosphere

Plant diversity and fertilizer management shape the belowground microbiome of native grass bioenergy feedstocks – Daniel Revillini et al. – Frontiers in Plant Science

Microbial taxonomical composition in spruce phyllosphere, but not community functional structure, varies by geographical location – Yunshi Li et al. – PeerJ

Responses of plant growth, physiological, gas exchange parameters of super and non-super rice to rhizosphere temperature at the tillering stage – Shuying Li at al. – Nature Scientific Reports

Influence of introduced arbuscular mycorrhizal fungi and phosphorus sources on plant traits, soil properties, and rhizosphere microbial communities in organic legume-flax rotation – Yunliang Li et al. – Plant and Soil

Effects of arbuscular mycorrhizal fungi on inoculated seedling growth and rhizosphere soil aggregates – Zhongfeng Zhang et al. – Soil and Tillage Research

Properties of bacterial community in the rhizosphere soils of Achyranthes bidentata tolerant to consecutive monoculture – Juanying Wang et al. – Plant Growth Regulation

The role of volatile organic compounds and rhizosphere competence in the mode of action of the non-pathogenic Fusarium oxysporum FO12 towards Verticillium wilt – Mulero-Aparicio et al. – Frontiers in Microbiology

Dynamic changes in soil chemical properties and microbial community structure in response to different nitrogen fertilizers in an acidified celery soil – Yuping Wu et al. – Soil Ecology Letters

Improved rhizoremediation for decabromodiphenyl ether (BDE-209) in E-waste contaminated soils – Jiayin Feng et al. – Soil Ecology Letters

Review: Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization – Peng Cai et al. – Soil Ecology Letters

Organic amendment effects on nematode distribution within aggregate fractions in agricultural soils – Xiaoke Zhang et al. – Soil Ecology Letters

Water and extermophile microbiome

Book chapter: New Perspectives on the Distribution and Roles of Thermophilic Fungi – Miriam I. Hutchinson et al. – Fungi in Extreme Environments: Ecological Role and Biotechnological Significance

Diversity and biogeography of eukaryotic microorganism in the deepsea sediment of the Eastern Indian Ocean – Xiaoxia Ma et al. – International Journal of Science

Phages and viruses

Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames – Stefania Pacini et al. – bioRxiv


Modelling approaches for studying the microbiome – Manish Kumar et al. – Nature Microbiology

Guest Editorial: Beyond sequencing: fast and easy microbiome profiling by flow cytometry – Charlotte Esser at al. – Archives of Toxicology

View Point: Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation – Pablo Carbonell et al. – ACS Synthetic Biology

Microbes in the News

***Elevated Concentration of Lipid in Neonatal Microbiome Predicts Later Risk for Asthma, Allergy – Allison Inserro – AJMC Newsroom

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