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

E

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 10, 2019

This Monday, read about the precision of microbiome wording, cryopreservation of the human gut microbiota, water infrastructure microbiomes, and more. Happy reading!

General microbiome

Determining Microbial Roles in Ecosystem Function: Redefining Microbial Food Webs and Transcending Kingdom Barriers – Kim M. Handley – mSystems

Digitalizing the Microbiome for Human Health – Kirti Nath and Christoph A. Thaiss – mSystems

New Approaches to Microbiome-Based Therapies – Andrea C. Wong and Maayan Levy – mSystems

Benefits and Costs of Animal Virulence for Microbes – Arturo Casadevall and Liise-anne Pirofski – mSystems

*Language, numeracy and logic in microbiome science – Fergus Shanahan and Colin Hill – Nature Reviews Gastroenterology & Hepatology

Gut microbiome

*Cryopreservation of the human gut microbiota: current state and perspectives – Daria V.Smirnovaa – International Journal of Medical Microbiology

Metaproteomics of the human gut microbiota: challenges and contributions to other OMICS – Ngom Issa Isaac – Clinical Mass Spectrometry

Mapping human microbiome drug metabolism by gut bacteria and their genes – Michael Zimmermann – Nature

MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing – William S Taylor – bioRxiv

Assessment of Causal Direction Between Gut Microbiota-Dependent Metabolites and Cardiometabolic Health: Abi-Directional Mendelian Randomisation Analysis – Jinzhu Jia – Diabetes

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer – Shinichi Yachida – Nature Medicine

Dysbiosis of gut microbiota in a selected population of Parkinson’s patients – Daniele Pietrucci – Parkinsonism & Related Disorders

Animal experiment

Heterochronic faecal transplantation boosts gut germinal centres in aged mice – Marisa Stebegg – Nature communications

High fat diet alters gut microbiota but not spatial working memory in early middle-aged Sprague Dawley rats – Nikita Girish Deshpande – PlosOne

Animal microbiome

Fibre digestion by rumen microbiota – a review of recent metagenomic and metatranscriptomic studies – Stephanie A Terry – Canadian Journal of Animal Science

Correlation between Disease Severity and the Intestinal Microbiome in Mycobacterium tuberculosis-Infected Rhesus Macaques – Sivaranjani Namasivayam – mBio

Water microbiome

*Integrating biotechnology and microbial ecology in urban water infrastructure through a microbiome continuum viewpoint – Lutgarde Raskin and Per Halkjær Nielsen – Current Opinion in Biotechnology

Techniques

MOBN: an interactive database of multi-omics biological networks – Cheng Zhang – bioRxiv

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 4, 2019

General microbiome
Rigorous Statistical Methods for Rigorous Microbiome Science – Amy D. Willis – mSystems

Understanding microbial community dynamics to improve optimal microbiome selection – Robyn J. Wright – Microbiome

Toward a Better Understanding of Species Interactions through Network Biology – Ryan S. McClure – mSystems

Human respiratory microbiome
Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus – Hyun Jik Kim – Microbiome

Human gut microbiome
A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans – Alfonso Benítez-Páez – mSystems

Gut microbiome identifies risk for colorectal polyps – Ezzat Dadkhah – BMJ Open Gastroenterology

Yogurt improves insulin resistance and liver fat in obese women with nonalcoholic fatty liver disease and metabolic syndrome: a randomized controlled trial – Yang Chen – American Journal of Clinical Nutrition

Preprint: Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids – Robert A Quinn – bioRxiv

Animal models
Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model – Limei Lin – Microbiome

Missing Links: the Role of Primates in Understanding the Human Microbiome – Katherine R. Amato – mSystems

Plant, root, and soil microbiome
Collaborative involvement of woody plant roots and rhizosphere microorganisms in the formation of pedogenetic clays – Frank Reith – Annals of Botany

Water and extremophile microbiome
Effects of sulfamethoxazole and sulfamethoxazole-degrading bacteria on water quality and microbial communities in milkfish ponds – Bea-Ven Chang – Environmental Pollution

Preprint: Temporal dynamics of Bacteria, Archaea and protists in equatorial coastal waters – Caroline Chénard – bioRxiv

Built environment
Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area – Miles Richardson – Microbiome

Phages and viruses
Preprint: The human gut virome is highly diverse, stable and individual-specific – Andrey Shkoporov – bioRxiv

Bioinformatics
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language – Luis Pedro Coelho – Microbiome

Science, publishing, and career
Preprint: The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training – Rochelle E. Tractenberg – bioRxiv

Alyson’s non-microbiology picks
Why Your Metro Commute Is So Insanely Windy – Julie Bogen – The Atlantic

The 2019 Wellcome photography prize: close focus on the human condition – Sean O’Hagan – The Guardian

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

June 2, 2019

Highlights: Harnessing principles of ecology and engineering in building microbiome, community ecology perspective of human microbiome, rhizospheric microbes, soil viruses and many more.

General microbiome

Regulating microbiome manipulation – Kjersti Aagaard – Nature Medicine

Towards a Better Understanding of Microbial Community Dynamics through High-Throughput Cultivation and Data Integration – Karoline Faust – mSystems

Reconciling Ecological and Engineering Design Principles for Building Microbiomes – Hans C. Bernstein – mSystems

Community ecology as a framework for human microbiome research – Jack A Gilbert – Nature Medicine

Multi-site human microbiome

Age-dependent dissimilarity of the nasopharyngeal and middle ear microbiota in children with acute otitis media – Silvio D. Brugger – Frontiers in Genetics

Human gut microbiome

Micronutrient requirements and sharing capabilities of the human gut microbiome – Dmitry A Rodionov – Frontiers in Microbiology

Animal experiments 

Mouse microbiomes: overlooked culprits of experimental variability – Maria-Luisa Alegre – Genome Biology

Animal microbiome 

Microbial communities associated with the parasitic copepod Lepeophtheirus salmonis – S. Dalvin – Marine Genomics

Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health – Keylie M. Gibson – Scientific Reports

Not all animals need a microbiome – Tobin J Hammer – FEMS Microbiology Letters

The Microbiome of the Maculinea-Myrmica Host-Parasite Interaction – Marco Di Salvo – Scientific Reports

Plant, root, and soil microbiome

Soil photosynthetic microbial communities mediate aggregate stability: influence of cropping systems and herbicide use in an agricultural soil – Olivier Crouzet – Frontiers in Microbiology

Fluazinam positively affected the microbial communities in clubroot cabbage rhizosphere – Chunming Liu – Scientia Horticulturae

Soil microbiome mediates positive plant diversity‐productivity relationships in late successional grassland species – Guangzhou Wang – Ecology Letters

A water stress-adapted inoculum affects rhizosphere fungi, but not bacteria nor wheat – Charlotte Giard-Laliberté – Microbiology Ecology

Variations in phyllosphere microbial community along with the development of angular leaf-spot of cucumber – Luyun Luo – AMB Express

Built environment 

Effects of biochar on the phenol treatment performance and microbial communities shift in sequencing batch reactors – Shengnan Shi – Water Research

Effects of ozone treatment on performance and microbial community composition in biofiltration systems treating ethyl acetate vapours – Itzel Covarrubias-García – Chemosphere

Phages and viruses

Characterization of the virome of Paracoccus spp. (Alphaproteobacteria) by combined in silico and in vivo approaches – Przemyslaw Decewicz – Scientific Reports

Soil Viruses: A New Hope – Joanne B. Emerson – mSystems