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

Tecniques

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

Today’s digest featuring a detailed contribution of the human microbiome to carcinogenesis, some interesting research, and reviews focusing on the microbial role in combat neurodegeneration, neuroimmune alterations, metabolism of lipids and N-ε-Carboxymethyllysine and an antibiotic resistome from healthy pig metagenome. Enjoy reading.

General microbiome

International Cancer Microbiome Consortium consensus statement on the role of the human microbiome in carcinogenesis – Alasdair J Scott – Gut

Exploring the impacts of raw materials and environments on the microbiota in Chinese Daqu starter – HaiDu – International Journal of Food Microbiology

Review: The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut – Janneke Elzinga – Microbiology and Molecular Biology Reviews

Gut microbiome

The bacterial communities of the small intestine and stool in children with short bowel syndrome – Steven L. Zeichner – PLOS ONE

Review: Modification of the gut microbiome to combat neurodegeneration – Andrew Octavian Sasmita – Reviews in the Neurosciences

Markers of dysbiosis in patients with ulcerative colitis and Crohn’s disease – Danilova NA – Terapevticheskiĭ Arkhiv

Mid-life microbiota crises: middle age is associated with pervasive neuroimmune alterations that are reversed by targeting the gut microbiome – Marcus Boehme – Molecular Psychiatry

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease – Almut Heinken – Microbiome

Anaerobic Degradation of N-ε-Carboxymethyllysine, A Major Glycation End Product, By Human Intestinal Bacteria – Thi Phuong Nam Bui – Journal of Agricultural and Food Chemistry

Letter: Lipopolysaccharide from Gut Microbiota Modulates α-Synuclein Aggregation and Alters Its Biological Function – Dipita Bhattacharyya – ACS Chemical Neuroscience

Respiratory microbiome

Competition among Nasal Bacteria Suggests a Role for Siderophore-Mediated Interactions in Shaping the Human Nasal Microbiota – Reed M. Stubbendieck – Applied and Environmental Microbiology

Could the Sputum Microbiota Be a Biomarker That Predicts Mortality after Acute Exacerbations of Chronic Obstructive Pulmonary Disease? – Jun-Chieh J. Tsay – American Journal of Respiratory and Critical Care Medicine

Skin microbiome

Amphibian Host and Skin Microbiota Response to a Common Agricultural Antimicrobial and Internal Parasite – Obed Hernández-Gómez – Microbial Ecology

Plant microbiome

Engineering banana endosphere microbiome to improve Fusarium wilt resistance in banana – Yupei Liu – Microbiome

Review: Ecology and Evolution of Plant Microbiomes – Viviane Cordovez – Annual Review of Microbiology

Animal microbiome / Animal experiments

Does MHC heterozygosity influence microbiota form and function? – M. A. Wadud Khan – PLOS ONE

Faecal microbiota shift during weaning transition in piglets and evaluation of AO blood types as shaping factor for the bacterial community profile – Vincenzo Motta – PLOS ONE

CD1d Modulates Colonic Inflammation in NOD2^−/− Mice by Altering the Intestinal Microbial Composition Comprising Acetatifactor muris – Chansu Lee – Journal of Chron’s and Colitis

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod – Even Sannes Riiser – Environmental Microbiology

Predicting residual feed intake status using rumen microbial profiles in ewe lambs – Melinda J Ellison – Journal of Animal Science

Antibiotic resistomes of healthy pig faecal metagenomes – Aoife Joyce – Microbial Genomics

Extract of ice plant (Mesembryanthemum crystallinum) ameliorates hyperglycemia and modulates the gut microbiota composition in type 2 diabetic Goto-Kakizaki rats – Chengcheng Zhang – Food and Function

Absence of gut microbiota during early life affects anxiolytic Behaviors and monoamine neurotransmitters system in the hippocampal of mice – Jun-Xi Pan – Journal of the Neurological Science

Gut microbiota characterization and lipid metabolism disorder found in PCB77-treated female mice – YulangChi – Toxicology

Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics – Rowena Chong – Journal of Virology

Depression Promotes the Onset of Irritable Bowel Syndrome through Unique Dysbiosis in Rats – Takeshi Takajo – Gut and Liver

Hepatic progenitor cell activation is induced by the depletion of the gut microbiome in mice – Fei Wang – MicrobiologyOpen

Prebiotics/Probiotics

Saccharomyces boulardii CNCM I-745 changes lipidemic profile and gut microbiota in a hamster hypercholesterolemic model – F. Briand – Beneficial Microbes

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

Tecniques

*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)

SciComm

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