June 13, 2019

Good morning everyone!

Today the focus is almost entirely on environmental microbiology- plant, soil and water habitats. Check also the methods paper regarding activating silent BGCs (a true challenge for drug discovery).

General Microbiology

A multiphase theory for spreading microbial swarms and films, Siddarth Srinivasan, eLIFE

Methods

Advances in microbial culturing conditions to activate silent biosynthetic gene clusters for novel metabolite production, Hailey A. Tomm, J. Industrial Microbiology % Biotechnology

A set of modular and integrative vectors for synthetic biology in Streptomyces, Celine Aubry, AEM

Revealing microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation, Shion Hosoda, bioRxiv

Animal microbiome

The Insect Virome: Opportunities and Challenges, BC Bonning, Curr. Issues Mol Bio.

Host species and site of collection shape the microbiota of Rift Valley fever vectors in Kenya, David P. Tchouassi, PLOS Neglected Tropical Diseases

Microbiomes of stony and soft deep-sea corals share rare core bacteria, Christina A. Kellogg, Microbiome

Plant Microbiome

Identification and Characterization of the Core Rice Seed Microbiome, Alexander W. Eyre, Phytobiome

Microbiota Associated with Sclerotia of Soilborne Fungal Pathogens – A Novel Source of Biocontrol Agents Producing Bioactive Volatiles, Pascal Mulner, Phytobiome

ffects of agricultural management on rhizosphere microbial structure and function in processing tomato, Jennifer E. Schmidt, AEM

Environmental microbiome

Methylotrophs and Methylotroph Populations for Chloromethane Degradation, F Bringel, Curr Issues Mol Bio.

Diversity of Methane Cycling Microorganisms in Soils and Their Relation to Oxygen, C Knief, Curr Issues Mol Bio.

Microbiomes in Ground Water and Alternative Irrigation Water, and Spinach Microbiomes Impacted by Irrigation with Different Types of Water, Ganyu Gu, Phytobiome

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Microbiome in the market

Macrogen Announces Strategic Investment in Australian Microbiome Company, Microba

New DuPont research pact has animal microbiome focus

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June 11, 2019

Today’s digest is about microbiome and Alzheimer’s disease association, global survey of arsenic related genes in soil microbiome,  Bifidobacterium bifidus in infant gut and a preprint on selection in host microbiome evolution.

General microbiome

Understanding the Role of the Gut Microbiome and Microbial Metabolites in Obesity and Obesity-Associated Metabolic Disorders: Current Evidence and Perspectives – Natalia Vallianou – Current Obesity Reports

Alzheimer’s disease and symbiotic microbiota: an evolutionary medicine perspective – Molly Fox – Annals of the New York Academy of Sciences

Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis – Jessica L. Mark Welch – Annual Review of Microbiology

Human microbiome

Colonic mucosal and exfoliome transcriptomic profiling and fecal microbiome response to a flaxseed lignan extract intervention in humans – Johanna W. Lampe – American journal of Clinical Nutrition

Analysis of Transcriptionally Active Bacteria Throughout the Gastrointestinal Tract of Healthy Individuals – Riccardo Vasapolli – Gastroenterology

Identification of Salivary Microbiota and its Association with Host Inflammatory Mediators in Periodontitis – Anna Lundmark – Frontiers in Cellular and Infection Microbiology

Effect of the Degree of Polymerization of Fructans on Ex Vivo Fermented Human Gut Microbiome – Erola Astó – Nutrients

Inflammatory skin is associated with changes in the skin microbiota composition on the back of severe acne patients – Marie-Ange Dagnelie – Experimental Dermatology

Gut microbiota development of preterm infants hospitalised in intensive care units – H. Tauchi – Beneficial Microbes

Animal experiments

Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota – Devin B. Holman – Microbiome

Sequential changes in the host gut microbiota during infection with the intestinal parasitic nematode Strongyloides venezuelensis – Tanzila Afrin – Frontiers in Cellular and Infection Microbiology

Plant, root, soil microbiome

A global survey of arsenic-related genes in soil microbiomes – Taylor K. Dunivin – BMC Biology

Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics – Nengfei Wang – Microbes and Environments

Water microbiome and extremophiles

Comparison of the microbiomes of two drinking water distribution systems—with and without residual chloramine disinfection – Michael B. Waak – Microbiome

Probiotics

Probiotics may not prevent the deterioration of necrotizing enterocolitis from stage I to II/III – Zheng-Li Wang – BMC Pediatrics

Bifidobacterium bifidum and the infant gut microbiota: an intriguing case of microbe‐host co‐evolution – Sabrina Duranti – Environmental Microbiology

Techniques

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes – G.A.Arango-Argoty – Microbiome

Metabolic route computation in organism communities – Markus Krummenacker – Microbiome

The role of multilevel selection in host microbiome evolution – Simon van Vliet – BioRxiv

Microbes and the market

Human Microbiome Therapeutics Market Analysis 2019: With Top 20 Countries data, Product Types, Segmentation, Market Share Analysis, Influential Trends And Challenges, Forecast To 2023 – Saginaw Daily

Global Human Microbiome Based Drugs and Diagnostics Market Potential Growth 2019 | Second Genome Inc., Enterome Bioscience, Yakult – Business Tech Hub

Human Microbiome Market 2024 Significant Development | Future Trends of Key Players by Size and Share – The Warren Daily

In-Depth Research Report of Global Microbiome Sequencing Services Market (2019 Version), with Types, Application, and Manufactures – the Pueblo Daily

Microbiome Sequencing Services Market Key Players, Industry Overview, Demand & Supply Chain Analysis, Forecast To 2024 – Burbank Observer

Human Microbiome Market Growth, Trend and Forecast 2018-2026 – Business Herald

 

June 5, 2019

Today’s short Digest features many preprints, including an attempt to explain the emergence of a multi-drug resistant fungal pathogen, and another piece of evidence for the placenta microbiome?

Antimicrobial resistance

A novel anti Candida albicans drug screening system based on high-throughput microfluidic chips – Le Qiang et al. – Scientific Reports

** Preprint: On the emergence of Candida auris: climate change, azoles, swamps and birds – Arturo Casadevall et al. – bioRxiv

Preprint: The Evolution of Fluoroquinolone-Resistance in Mycobacterium tuberculosis is Modulated by the Genetic Background – Rhastin A. D. Castro et al. – bioRxiv

Pregnancy and early life

** Preprint: Placenta microbiome diversity is associated with maternal pre-pregnancy obesity and placenta biogeography – Paula Benny et al. – bioRxiv

Human gut microbiome

Preprint: Pneumococcal Colonisation is an Asymptomatic Event in Healthy Adults using an Experimental Human Colonisation Model – Ashleigh Trimble et al. – bioRxiv

Plant, root and soil microbiome

The effects of chemical and organic fertilizer usage on rhizosphere soil in tea orchards – Weiwei Lin et al. – PLoS One

Preprint: Root development is maintained by specific bacteria-bacteria interactions within a complex microbiome – Omri M. Finkel et al. – bioRxiv

Water and extremophile microbiome

Preprint: Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area – Jodie Belilla et al. – bioRxiv

Phages and viruses

Recombinant Strains of Human Parechovirus in Rural Areas in the North of Brazil – Élcio Leal et al. – Viruses

Preprint: Dynamic pneumococcal genetic adaptations support bacterial growth and inflammation during coinfection with influenza – Amanda P Smith et al. – bioRxiv

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

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

May 24, 2019

Today we have a short Digest before the Memorial Day weekend in America. Highlights include a comparative metabolomic study on Mycobacterium tuberculosis and a live attenuated strain as a potential vaccine, a report on oral cavity resistome worldwide and last but not least, fossils of early fungi that are about 1 billion years old!

General microbiology

Quorum Sensing Circuits in the Communicating Mechanisms of Bacteria and Its Implication in the Biosynthesis of Bacteriocins by Lactic Acid Bacteria: a Review – Ourdia Kareb & Mohammed Aïder – Probiotics and Antimicrobial Proteins

** Early fungi from the Proterozoic era in Arctic Canada – Corentin C. Loron et al. – Nature

Antimicrobial resistance

** Preprint: Abundance and diversity of resistomes differ between healthy human oral cavities and gut – Victoria R. Carr et al. – bioRxiv

Human skin microbiome

Skin Microbiome Differences in Atopic Dermatitis and Healthy Controls in Egyptian Children and Adults, and Association with Serum Immunoglobulin E – Mohammed Ramadan et al. – OMICS: A Journal of Integrative Biology

Review: Microbiome and skin biology – Lunjani, Nonhlanhla et al. – Current opinion in allergy and clinical immunology

Human oral microbiome

Intra‐oral single site comparisons of periodontal and peri‐implant microbiota in health and disease – Xiao‐Lin Yu et al. – Clinical Oral Implants Research

Built environment microbiome

Spatial Gradients of Fungal Abundance and Ecology throughout a Damp Building – Bridget Hegarty et al. – Environmental Science & Technology Letters

Metabolomics

** COMPARATIVE METABOLOMICS BETWEEN Mycobacterium tuberculosis AND THE MTBVAC VACCINE CANDIDATE – Caridad Díaz Navarro et al. – ACS Infectious Diseases

Animal microbiome

The Role of Tissue Type, Sampling and Nucleic Acid Purification Methodology on the Inferred Composition of Pacific Oyster (Crassostrea gigas) Microbiome – Erandi Pathirana et al. – Journal of Applied Microbiology

Plant, root and soil microbiome

Vertical distribution of microbial communities in chromium-contaminated soil and isolation of Cr(Ⅵ)-Reducing strains – Bang Liu & Guirong Su et al. – Ecotoxicology and Environmental Safety

Preprint: Root development is maintained by specific bacteria-bacteria interactions within a complex microbiome – Omri M. Finkel et al. – bioRxiv

Microbes in the news

Microbiome: Small Organisms Play Big Shots in Plants – Soumya Kumar Sahoo et al. – Biomolecule Reports

May 21, 2019

Today’s digest is short and sweet but includes interesting articles. A brilliant essay on multidisciplinarity in microbiome research 🥰

General Microbiome

ESSAY: Multidisciplinarity in Microbiome Research: A Challenge and Opportunity to Rethink Causation, Variability, and Scale. KR Amato – BioEssays

REVIEW:Contribution of the Mucosal Microbiota to Bovine Respiratory HealthM Zeineldin. Trends in Microbiology

Characterization of a novel salt-, xylose-and alkali-tolerant GH43 bifunctional β-xylosidase/α-l-arabinofuranosidase from the gut bacterial genome. B Xu. Journal of Bioscience and Bioengineering

Gut Microbiome

Circulating Microbiota-Based Metagenomic Signature for Detection of Hepatocellular CarcinomaEJ Cho. Scientific Reports

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

Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approachesGA Lugli. BMC Genome Biology

Plant, Soil, and Water Microbiome

Microbial production and consumption of dissolved organic matter in glacial ecosystems on the Tibetan PlateauL Zhou. Water Research

Engineering banana endosphere microbiome to improve Fusarium wilt resistance in banana. Y Liu.Microbiome
Toxic responses of metabolites, organelles and gut microorganisms of Eisenia fetida in a soil with chromium contaminationR Tang. Environmental Pollution

Roles of microbes in supporting sustainable rice production using the system of rice intensificationF Doni. Applied Microbiology and Biotechnology

Cover crop species have contrasting influence upon soil structural genesis and microbial community phenotype.A Bacq-Labreuil. Scientific Reports

Preprint

Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn’s Disease Cohort . Daniel Sprockett. bioRxiv posted 19 May 2019

May 17, 2019

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 murisChansu 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