August 24, 2019

This weekend, read about the microbial index of skin health for children with eczema, gut microbiome of koalas, and interactions between the gut bacterial microbiome and virome of rhesus monkey. Happy reading!

General microbiome

Why we need a small data paradigm – Eric B. Hekler – BMC Medicine

Correspondence: The importance of genome sequence quality to microbial comparative genomics – Theo H. M. Smits – BMC Genomics

The applications of Big Data in molecular diagnostics – Yin Kwan Evelyn Wong – Expert Review of Molecular Diagnostics

Tiny Hidden Genes within Our Microbiome – Karin Mittelman & David Burstein – Cell

Skin microbiome

*A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children – Zheng Sun – mSystems

Gut microbiome

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight – Peng Jiang – Microbiome

Review: Gut Microbiota, Dietary Phytochemicals, and Benefits to Human Health – Ran Yin – Current Pharmacology Reports

Mild cognitive impairment has similar alterations as Alzheimer’s disease in gut microbiota – Binyin Li – Alzheimer’s & Dementia

Design of synthetic microbial consortia for gut microbiota modulation – Jorge F. Vázquez-Castellanos – Current Opinion in Pharmacology

Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease – Sandra Aparecida dos Reis – Journal of Medical Microbiology

Review: Celiac disease: a comprehensive current review – Giacomo Caio – BMC Medicine

Pregnancy and early life

Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants – Kathyayini P. Gopalakrishna – Nature Medicine

Oral microbiome

Oral Microbiome and Cancer Therapy-Induced Oral Mucositis – Jean-Luc C Mougeot – JNCI Monographs

Respiratory microbiome

Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration – Annamaria Bevivino – Trends in Molecular Medicine

Water and extremophile microbiome

Effects of water recirculation rate on the microbial community and water quality in relation to the growth and survival of white shrimp (Litopenaeus vannamei) – Zhao Chen – BMC Microbiology

Pseudomethylobacillus aquaticus gen. nov., sp. nov., a new member of the family Methylophilaceae isolated from an artificial reservoir – Ceshing Sheu – International Journal of Systematic and Evolutionary Microbiology

Bacterial Communities from Extreme Environments: Vulcano Island – Camilla Fagorzi – Diversity

Diversity and biogeography of SAR11 bacteria from the Arctic Ocean – Susanne Kraemer – bioRxiv

Review: Metal and organic pollutants bioremediation by extremophile microorganisms – Patricia Giovanella – Journal of Hazardous Material

Animal microbiome

*Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala – Michaela D. J. Blyton – Animal microbiome

Impact of pine leaf biochar amendment on bacterial dynamics and correlation of environmental factors during pig manure composting – Jiao Li – Bioresource Technology

Animal experiment

Potential roles of gut microbiome and metabolites in modulating ALS in mice – Eran Blacher – Nature

Plant microbiome

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples – Tonia DeBellis – PeerJ

Non-target Effects of Trichoderma on Plants and Soil Microbial Communities – Monika Jangi – Plant Microbe Interface

Inhibitory and nutrient use phenotypes among co‐existing Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil – Adil Essarioui – Environmental Microbiology

Phages and viruses

*The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites – Heng Li – Virology Journal

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August 15, 2019

Have a nice Thursday! Today we have a set of papers showing randomized trials related to antibiotic use and alimentary interventions, metabolic networks associated with C. difficile infection, and analysis of E. coli isolates from human stool. Today, we also include a couple of protocol papers about the use of stable isotope probing in plant microbiome research.

 

Human and General Microbiome

Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution – T. Doan – Nature Medicine 

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial – Xuan He – Scientific Reports

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects – Stefano Raimondi – Microorganisms

Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections – John I. Robinson – The Journal of Clinical Investigation

Antibiotic exposure and ‘response failure’ for subsequent respiratory tract infections: an observational cohort study of UK preschool children in primary care – Oliver van Hecke – British Journal of General Practice 

Abnormal vaginal microbiome associated with vaginal mesh complications – Nikolaus Veit‐Rubin – Neurology and Urodynamics

Acceptability, Tolerability and Safety of Faecal Microbiota Transplantation in patients with active Ulcerative Colitis (AT&S Study) – Ajit Sood – Journal of Gastroenterology and Hepatology

The bacteriome of otitis media with effusion: Does it originate from the adenoid? – Oguz Ari – International Journal of Pediatric Otorhinolaryngology 

An Exploratory Analysis of Fecal Immunochemical Test Performance for Colorectal Cancer Screening in Nigeria – Gregory C. Knapp – World Journal of Surgery

Isolates from colonic spirochaetosis in humans show high genomic divergence and potential pathogenic features but are not detected using standard primers for the human microbiota – Kaisa Thorell – Journal of Bacteriology

Microbiota-derived Trimethylamine N-oxide Predicts Cardiovascular Risk After STEMI – Yasushi Matsuzawa – Scientific Reports

Review: Targeting Microbiota: What Do We Know about It at Present? – Aleksejs Derovs – Medicina

Tech News: Reproducibility: the search for microbiome standards – Joseph Martin – BioTechniques

 

Animal Microbiome

Intestinal microbial products from alcohol-fed mice contribute to intestinal permeability and peripheral immune activation – Derrick R. Samuelson – Alcoholism

Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers – Zhao Qi – 3 Biotech

Oligosaccharides Modulate Rotavirus-Associated Dysbiosis and TLR Gene Expression in Neonatal Rats – Ignasi Azagra-Boronat – Cells

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan – Atsushi Kobayashi – Journal of Veterinary Medical Science

 

Beneficial compounds and microbes

Review: The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders – Timo A. Thumann – Journal of Ethnopharmacology

Commentary: Microbiome, probiotics and dermatology – J.A. Cardenas‐de la Garza – British Journal of Dermatology

Cooked Red Lentils Dose-Dependently Modulate the Colonic Microenvironment in Healthy C57Bl/6 Male Mice – Daniela Graf – Nutrients

Health Benefits of Lactobacillus gasseri CP2305 Tablets in Young Adults Exposed to Chronic Stress: A Randomized, Double-Blind, Placebo-Controlled Study – Kensei Nishida – Nutrients 

Effect of coffee on the compositional shift of oral indigenous microbiota cultured in vitro – 

 

Food Microbiome

Microbial Transformations of Organically Fermented Foods – Ruma Raghuvanshi – Metabolites

 

Plant Microbiome

Protocol: Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere – Wafa Achouak – Stable Isotope Probing (Methods in Molecular Biology)

Protocol: Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing – Ang Hu – Stable Isotope Probing (Methods in Molecular Biology)

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles – Francesco Vitali – Applied Microbiology and Biotechnology

August 3, 2019

Have a happy weekend! Today, in this Digest: an interesting study of the human placenta microbiome, papers showing associations between microbiome and pancreatic or lung cancer, and an update of the pathogenesis of bacterial vaginosis. In addition, a paper showing that the microbiome in primates has a different evolutionary pattern in comparison with the host.  Enjoy!

 

Human and General Microbiome

Human placenta has no microbiome but can contain potential pathogens – Marcus C. de Goffau – Nature

Microbial dysbiosis and polyamine metabolism as predictive markers for early detection of pancreatic cancer – Roberto Mendez – Carcinogenesis

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints – Andres Gomez – mSphere

Whole genome sequencing revealed microbiome in lung adenocarcinomas presented as ground-glass nodules – Yijiu Ren – Translational Lung Cancer Research

An Updated Conceptual Model on the Pathogenesis of Bacterial Vaginosis – Christina A Muzny – The Journal of Infectious Diseases

Review: Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health – Aimeé Parker – Gut Microbes

Editorial: The only thing that stops a bad microbiome, is a good microbiome – Jessica R. Galloway-Peña – Haematologica

Review: Consumer Safety Considerations of Skin and Oral Microbiome Perturbation – Andrew J. McBain – Clinical Microbiology Reviews

News: Microbiome therapeutics go small molecule – Megan Cully – Nature Reviews Drug Discovery

Pharmacomicrobiomics informs clinical pharmacogenomics – Theodora Katsila – Future Medicine

Each Additional Day of Antibiotics is Associated with Lower Gut Anaerobes in Neonatal Intensive Care Unit Patients – Ashley M Rooney, BSc – Clinical Infectious Diseases

Prevention and treatment of recurrent Clostridioides difficile infection – Jae Shin – Current Opinion in Infectious Diseases

An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia – Wenkui Dai – Gigascience

Review: Connection between gut microbiome and the development of obesity – Cuiting Zhi – European Journal of Clinical Microbiology & Infectious Diseases

Animal Microbiome

Hyperuricemia is associated with impaired intestinal permeability in mice – Daxing Xu – Gastrointestinal and Liver Physiology

 

Beneficial compounds and Foods

Prevention of Vascular Inflammation by Pterostilbene via Trimethylamine-N-Oxide Reduction and Mechanism of Microbiota Regulation – Yen‐Chun Koh – Molecular Nutrition and Food Research

Interactions of tea polyphenols with intestinal microbiota and their implication for cellular signal conditioning mechanism – Yongyong Li – Journal of Food Biochemistry

Hass Avocado Inclusion in a Weight-Loss Diet Supported Weight Loss and Altered Gut Microbiota: A 12-Week Randomized, Parallel-Controlled Trial – Susanne M Henning – Current Developments in Nutrition

 

Plant Microbiome

Host plant-dependent effects of microbes and phytochemistry on the insect immune response – Su’ad A. Yoon – Oecologia

Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria – Barney A. Geddes – Nature Communications 

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

Techniques

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 9, 2019

Today’s digest features an overview of the “microbiota–nutrient metabolism–epigenetics” axis, a study on the human bile microbiota, an interesting selection of probiotics studies, and more. Check out the new Everything Hertz podcast episode “Improving the scientific poster”. Happy reading/listening!

Gut microbiome

*Epigenetic Regulation at the Interplay Between Gut Microbiota and Host Metabolism – Joan Miro-Blanch and Oscar Yanes – Frontiers in Genetics

Microbiome and type 1 diabetes – Heli Siljander – EBioMedicine

Framework for rational donor selection in fecal microbiota transplant clinical trials – Claire Duvallet – medRxiv

A calcium-rich multi-mineral intervention to modulate colonic microbial communities and metabolic profiles in humans: Results from a 90-day trial – Muhammad N. Aslam – medRxiv

*The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile – Natalia Molinero – Microbiome

Oral microbiome

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage – Irina M. Velsko – Microbiome

Respiratory microbiome

Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status – Tao Ding – mBio

Skin microbiome

Trait-based analysis of the human skin microbiome – Sharon Bewick – Microbiome

Probiotics

Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: Safety and Preliminary Efficacy by Microscopy and Sequencing – Janneke H.H.M. van de Wijgert – medRxiv

Impact of spray‐drying on the pili of Lactobacillus rhamnosus GG – Shari Kiekens – Microbial Biotechnology

The Probiotic Mixture VSL#3 Reverses Olanzapine-Induced Metabolic Dysfunction in Mice – Navneet Dhaliwal – Psychiatric Disorders

Prophylactic Effects of Bifidobacterium adolescentis on Anxiety and Depression-Like Phenotypes After Chronic Stress: A Role of the Gut Microbiota-Inflammation Axis – Ying Guo – Frontiers in Behavioral Neuroscience

Water microbiome

Active eukaryotes in drinking water distribution systems of ground and surface waterworks – Jenni Inkinen – Microbiome

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water – Luke E. Holman – bioRxiv

Plant/root/soil microbiome

Microscale interactions between immigrant bacteria and plant leaf microbiota as revealed by live imaging – Shifra Steinberg – bioRxiv

Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow – Alexander Crits-Christoph – bioRxiv

Bioinformatics

DeepMicrobes: taxonomic classification for metagenomics with deep learning – Qiaoxing Liang – bioRxiv

Misclassification of a whole genome sequence reference defined by the Human Microbiome – DJ Darwin R. Bandoy – medRxiv

CarboLogR: a Shiny/R application for statistical analysis of bacterial utilisation of carbon sources – Kevin Vervier – bioRxiv

Using collaboration networks to identify authorship bias in meta-analyses – Thiago C. Moulin and Olavo B. Amaral – medRxiv

Podcast

*Episode 87: Improving the scientific poster (with Mike Morrison) – Dan Quintana and James Heathers – Everything Hertz

A terrific interview with @mikemorrison about the Better Poster format and UX design principles in science.

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 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