March 25, 2022

Human gut microbiome

In Vitro and In Silico Based Approaches to Identify Potential Novel Bacteriocins from the Athlete Gut Microbiome of an Elite Athlete Cohort – Wosinska et al. Microorganisms

Cancer pharmacomicrobiomics: targeting microbiota to optimise cancer therapy outcomes – Ting et al. Gut

Human respiratory microbiome

Inhibition of lung microbiota-derived proapoptotic peptides ameliorates acute exacerbation of pulmonary fibrosis – D’Alessandro-Gabazza et al. Nature Communications

Probiotics

Gut microbiota and fermentation-derived branched chain hydroxy acids mediate health benefits of yogurt consumption in obese mice – Daniel et al. Nature Communications

Animal experiments

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue – Agranyoni et al. npj biofilms and microbiomes

The microbiota restrains neurodegenerative microglia in a model of amyotrophic lateral sclerosis – Cox et al. Microbiome

Water & Extremophile microbiome

Spatial organization of the kelp microbiome at micron scales – Ramirez-Puebla et al. Microbiome

Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite – Murakami et al. Microbiome.

Virome

Phages and their satellites encode hotspots of antiviral systems – Rousset et al. Cell Host & Microbe

Fungi

Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity – Li et al. Cell Host & Microbe

The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors – Sharma et al. npj Biofilms and microbiomes

Bioinformatics

Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases – Armstrong et al. mSystems

December 24, 2021

Happy Holidays from the MicrobiomeDigest Team!

Human and General Microbiome

Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response – Christine N Spencer – Science 

Association of the gut microbiota and fecal short-chain fatty acids with skeletal muscle mass and strength in children – Fengyan Chen – FASEB Journal

Characteristics of Fecal Microbiota and Machine Learning Strategy for Fecal Invasive Biomarkers in Pediatric Inflammatory Bowel Disease – Xinqiong Wang – Frontiers in Cellular and Infection Microbiology

The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota L-carnitine catabolism – Jennifer A Buffa – Nature Microbiology

Gut Microbiota Exceeds Cervical Microbiota for Early Diagnosis of Endometriosis – Liujing Huang – Frontiers in Cellular and Infection Microbiology

Natural selection for imprecise vertical transmission in host-microbiota systems – Marjolein Bruijning – Nature Ecology & Evolution

Comparison of the airway microbiota in children with chronic suppurative lung disease – Bushra Ahmed – BMJ Open Respiratory Research

VicRK and CovR polymorphisms in Streptococcus mutans strains associated with cardiovascular infections – Letícia T Oliveira – Journal of Medical Microbiology

Oral Colonization by Entamoeba gingivalis and Trichomonas tenax: A PCR-Based Study in Health, Gingivitis, and Periodontitis – Alaa Yaseen – Frontiers in Cellular and Infection Microbiology

Human and General Microbiome – Reviews

Systematic Review: Probiotics Evaluation in Oncological Surgery: A Systematic Review of 36 Randomized Controlled Trials Assessing 21 Diverse Formulations – Elise Cogo – Current Oncology

Review: Untangling human milk oligosaccharides and infant gut microbiome – Andrea C Masi – iScience

Review: Periodontal Disease: The Good, The Bad, and The Unknown – Lea M Sedghi – Frontiers in Cellular and Infection Microbiology

Review: Clinical implications of preterm infant gut microbiome development – David B Healy – Nature Microbiology

COVID19 and Microbiome

Genomic characterization of the dominating Beta variant carrying vaccinated (Oxford-AstraZeneca) and non-vaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole genome approach – Md Mizanur Rahaman – Journal of Medical Virology

Animal Microbiome

Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development – Daphne Perlman – Annual Review of Animal Biosciences

Playing by their own rules: the vertebrate archaeome – Sarah M Hird – Trends in Microbiology

Integration of whole genome sequencing and transcriptomics reveals a complex picture of the reestablishment of insecticide resistance in the major malaria vector Anopheles coluzzii – Victoria A Ingham – PLoS Genetics

Comparative Study of Intestinal Microbiota Composition of Six Edible Fish Species – Tamir Ofek – Frontiers in Microbiology

Captivity Influences the Gut Microbiome of Rhinopithecus roxellana – Xiaochen Wang – Frontiers in Microbiology

Assessment of Changes in the Oral Microbiome That Occur in Dogs with Periodontal Disease – Rodrigo Santibáñez – Veterinary Sciences

Beneficial Microbes and Compounds

Evaluation of Microbiome Alterations Following Consumption of BIOHM, a Novel Probiotic – Mahmoud A Ghannoum – Current Issues in Molecular Biology

Lactobacillus rhamnosus attenuates Thai chili extracts induced gut inflammation and dysbiosis despite capsaicin bactericidal effect against the probiotics, a possible toxicity of high dose capsaicin – Wimonrat Panpetch – PloS ONE

Plant and Soil Microbiome

May the dark be with roots: A perspective on how root illumination may bias in vitro research on plant-environment interactions – Javier Cabrera – The New Phytologist

Site and land-use associations of soil bacteria and fungi define core and indicative taxa – Gschwend Florian – FEMS Microbiology Ecology

Bioinformatics

tascCODA: Bayesian Tree-Aggregated Analysis of Compositional Amplicon and Single-Cell Data – Johannes Ostner – Frontiers in Genetics

June 28, 2020

Greetings from Wiltshire, England!

Today’s digest brings a little bit of everything. We’ve been cataloguing the latest COVID-19 publications during this pandemic, and today I’m please to bring you a paper combining both COVID-19 and microbiome research!

Elsewhere, there are plenty of environmental microbiome publications, including a great paper on the challenges of studying microbiology in space, an analysis of how aerosols spread COVID-19 and other infectious agents in dental practices, and plenty of articles on various aspects of soil microbiomes.

I hope everyone’s coping well during these times. On a personal level, I’m delighted to be returning to the lab this week to resume my PhD research into gut microbiomes and cancer. I’m glad to be back, but worried about how my pipetting skills have suffered during my time off!

Stay safe, and happy reading!

COVID-19

Intestinal Flora as a Potential Strategy to Fight SARS-CoV-2 Infection – He et al.Frontiers in Microbiology

Preprint: Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry – Ozono et al.

Human vaginal microbiome

Novel Potential Probiotic Lactobacilli for Prevention and Treatment of Vulvovaginal Infections – Kumherová et al. – Probiotics and Antimicrobial Proteins

Preprint: The structure and diversity of strain level variation in vaginal bacteria –Tortelli et al.

Human gut microbiome

Early exposure to food contaminants reshapes maturation of the human brain-gut-microbiota axis – Sarron et al.World Journal of Gastroenterology

Luminal microbiota related to Crohn’s disease recurrence after surgery – Hamilton et al.Gut Microbes

Animal experiments

Preprint: The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet – Mims et al.

Animal microbiome

Germ-free housing conditions do not affect aortic root and aortic arch lesion size of late atherosclerotic low-density lipoprotein receptor-deficient mice – Kiouptsi et al.Gut Microbes

The effects of environment and ontogeny on the skin microbiome of two Stegastes damselfishes (Pomacentridae) from the eastern Caribbean Sea – Xavier et al.Marine Biology

Variations and Potential Factors of Gut Prokaryotic Microbiome During Spawning Migration in Coilia nasus – Ying et al.Current Microbiology

Plant, root, and soil microbiome

Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov. – Delamuta et al.International Journal of Systematic and Evolutionary Microbiology

Efects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil – Salam et al.Bioresources and Bioprocessing

Differences in soil microbial communities and enzyme activity due to the application of bioslurry under cultivation – Mofokeng et al.South African Journal of Plant and Soil

Microbial Communities in the Fynbos Region of South Africa: What Happens during Woody Alien Plant Invasions – Jacobs et al.Diversity

Water and extremophile microbiome

Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location – Schulhof et al.Molecular Ecology

Preprint: Fungal communities in sediments along a depth gradient in the Eastern Tropical Pacific – Rojas-Jimenez et al

Built environment

Preprint: Evaluating aerosol and splatter following dental procedures – Allison et al.

Microbes in space

Current Progression: Application of High-Throughput Sequencing Technique in Space Microbiology – Chen et al.BioMed Research International

Food microbiology

Swine Methicillin-resistant Staphylococcus aureus carrying toxic-shock syndrome toxin gene in Hong Kong, China – Sapugahawatte et al. – Emerging Microbes and Infections

Probiotics / prebiotics

Moving from probiotics to precision probiotics – Veiga, et al. – Nature Microbiology

Phages and viruses

Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia – Gaccioli et al. – Nature Microbiology

Techniques

Developing standards for the microbiome field – Amos et al.Microbiome

Microbes in the news

Team Examines Microbiome of Marine Invertebrate That Produces Anticancer CompoundTechnology Networks

Bacteria live on our eyeballs — and understanding their role could help treat common eye diseasesYahoo! News

May 13, 2020

Happy Wednesday, y’all! Before we get to today’s papers, I wanted to let everyone know about a webinar happening on June 3rd at 12:00 PM E.T. called “Unraveling the link between the gut microbiome, human health, and disease.” Tomoya Yamashita, M.D., Ph.D. from Kobe University Graduate School of Medicine and Meredith Hullar, Ph.D. from the Fred Hutchinson Cancer Research Center will both be speaking. If you’re interested you can register here.

Now onto the highlights! We have some super interesting research to share with you today including an examination of the efficacy of transplanting the human gut microbiota into mice and its impact on studying immunological responses; evidence that early-life intestinal colonizers may influence brain development; and a new tool, pepFUNK, which uses a peptide-centric approach to identify KEGG pathways in metaproteomic datasets. Enjoy!

General microbiome
Human Microbiota-Transplanted C57BL/6 Mice and Offspring Display Reduced Establishment of Key Bacteria and Reduced Immune Stimulation Compared to Mouse Microbiota-Transplantation. Lundberg, R. et al. Scientific Reports.

Review: The role of the microbiome in the neurobiology of social behaviour. Sarkar, A. et al. Biological Reviews.

Pregnancy and early life
Neonatal diet alters fecal microbiota and metabolome profiles at different ages in infants fed breast milk or formula. Brink, L.R. et al. The American Journal of Clinical Nutrition.

Investigating Bifidobacteria and Human Milk Oligosaccharide Composition of Lactating Mothers. Lugli, A.G. et al. FEMS Microbiology Ecology.

Human respiratory microbiome
Bioorthogonal Non-Canonical Amino Acid Tagging Reveals Translationally Active Subpopulations of the Cystic Fibrosis Lung Microbiota. Valentini, T.D. et al. Nature Communications.

Human gut microbiome
Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 With Clostridia and Insulin Sensitivity in Humans. Zhou, X. et al. Diabetes.

Berberine and Its Structural Analogs Have Differing Effects on Functional Profiles of Individual Gut Microbiomes. Li, L. et al. Gut Microbes.

Animal experiments
Developmental Signatures of Microbiota-Derived Metabolites in the Mouse Brain. Swann, J.R. et al. Metabolites.

Bifidobacteria Shape Host Neural Circuits During Postnatal Development by Promoting Synapse Formation and Microglial Function. Luck, B. et al. Scientific Reports.

Glycerol Monolaurate, an Analogue to a Factor Secreted by Lactobacillus, Is Virucidal Against Enveloped Viruses, Including HIV-1. Welch, J.L. et al. mBio.

Gut Microbiome Communication With Bone Marrow Regulates Susceptibility to Amebiasis. Burgess, S.L. et al. The Journal of Clinical Investigation.

The Protective Effects of 2′-Fucosyllactose Against E. Coli O157 Infection Are Mediated by the Regulation of Gut Microbiota and the Inhibition of Pathogen Adhesion. Wang Y. et al. Nutrients.

Capsaicin Improves Glucose Homeostasis by Enhancing Glucagon-Like peptide-1 Secretion Through the Regulation of Bile Acid Metabolism via the Remodeling of the Gut Microbiota in Male Mice. Hui, S. et al. FASEB Journal.

Microbiota-Induced Type I Interferons Instruct a Poised Basal State of Dendritic Cells. Schaupp L. et al. Cell.

Intratumoral Accumulation of Gut Microbiota Facilitates CD47-based Immunotherapy via STING Signaling. Shi, Y. et al. Journal of Experimental Medicine.

Animal microbiome
Housefly (Musca domestica L.) associated microbiota across different life stages. de Jonge, N. et al. Scientific Reports.

Honey-bee–associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential. Deboutte, W. et al. PNAS.

Bayesian Modeling Reveals Host Genetics Associated With Rumen Microbiota Jointly Influence Methane Emission in Dairy Cows. Zhang, Q. et al. ISME Journal.

Review: The role of the gut microbiome in sustainable teleost aquaculture. Perry, W.B. et al. Proceedings of the Royal Society B.

Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. Wikberg E.C. Animal Behaviour.

Plant, root, and soil microbiome
Global Warming Shifts the Composition of the Abundant Bacterial Phyllosphere Microbiota as Indicated by a Cultivation Dependent and Independent Study of the Grassland Phyllosphere of a Long-Term Warming Field-Experiment. Aydogan, E.L. et al. FEMS Microbiology Ecology.

Probiotics / prebiotics
A Human-Origin Probiotic Cocktail Ameliorates Aging-Related Leaky Gut and Inflammation via Modulating the Microbiota/Taurine/Tight Junction Axis. Ahmadi, S. et al. JCI Insight.

Bioinformatics
SHOGUN: A Modular, Accurate, and Scalable Framework for Microbiome Quantification. Hillmann, B. et al. Bioinformatics.

pepFunk: A Tool for Peptide-Centric Functional Analysis of Metaproteomic Human Gut Microbiome Studies. Simopoulos, C.M.A. et al. Bioinformatics.

Microbes in the news
Mapping the Microbiome in Saliva of COVID-19 Patients.

Inside the Belly of the Horse – Doctoral candidate Alexa Johnson goes inside the gut to investigate equine health.

13 July, 2019

Good morning everyone!

Today’s digest is kind of diverse (as always), with great papers about women microbiome, sardines gut microbiome, a great review about soil aggregates and, corals microbiomes and much more. Be sure to read the first paper right down here- The Conceptual Ecology of the Human Microbiome. Have a great weekend!

Human microbiome

**From June 2019, but a must-read nonetheless: The Conceptual Ecology of the Human Microbiome, Morar and Bohannan, Q. R. Biology

Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine, Wouter A. A. de Steenhuijsen Piters, Nature Communications

Selected Immunological Mediators and Cervical Microbial Signatures in Women with Chlamydia trachomatis Infection, Simone Filardo, mSystems

Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli, Chunhua Zhao, MPMI

Secondary bile acid ursodeoxycholic acid (UDCA) alters weight, the gut microbiota, and the bile acid pool in conventional mice, Jenessa A. Winston, bioRxiv

Microbiota supplementation with Bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome, Cristina Alcon-Giner, bioRxiv

Animal microbiome

A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians, Lu Wu, mSystems

Contribution of gut microbiota to metabolism of dietary glycine betaine in mice and in vitro colonic fermentation, Ville M. Koistinen, Microbiome

Coral bacterial community structure responds to environmental change in a host-specific manner, Maren Ziegler, Nature Communications

Soil microbiome

**Mini-review: Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales, Regina L. Wilpiszeski , AEM

Continuous monoculture shapes root and rhizosphere fungal communities of corn and soybean in soybean cyst nematode-infested soil, Noah Strom, Phytobiomes

Engineered root bacteria release plant-available phosphate from phytate, Christine N. Shulse, AEM

Diversity and Characterization of Oomycetes Associated with Corn Seedlings in Michigan, J. A. Rojas, Phytobiomes

Environmental microbiome

Diverse, abundant and novel viruses infecting “unculturable” but abundant marine bacteria, Zefeng Zhang, bioRxiv

Biocide resistance and transmission of Clostridium difficile spores spiked onto clinical surfaces from an American healthcare facility, Calie Dyer, AEM

Microbiome in the news

Lab Startup uBiome Laying Off About Half of Global Workforce

Microbiome Repairing Food for Malnourished Children Beats Current Therapy

February 14, 2019

If you are feeling butterflies in your stomach today, it might not be a gut microbiome imbalance – you might’ve caught the love bug! Happy Valentines Day!  Today’s digest features some human gut/FMT studies, a few animal gut biome studies and a couple probiotic publications.  Enjoy!

General microbiome

The next step towards anticancer microbiota therapeutics – Ursula Hofer – Nature Reviews [letter]

Expanding diversity of the human microbiome – Andrea Du Toit – Nature Reviews [in brief]

FMT in the clinic – Ashley York – Nature Reviews [research highlight]

Human respiratory microbiome

Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects – Anny Camelo-Castillo – Frontiers in Microbiology

Human gut microbiome

Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome – Daniel E. Almonacid – PLoS One

[pre -print] The Human Nickel Microbiome and its relationship to Allergy and Overweight in Women – Elena Angela Lusi – bioRxiv

The Relationship between Platelet Count and Host Gut Microbiota: A Population-Based Retrospective Cross-Sectional Study – Hee-Yong Yoon – Journal of Clinical Medicine

Data-driven multiple-level analysis of gut-microbiome-immune-joint interactions in rheumatoid arthritis – QuanQiu Wang – BMC Genomics

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes – J. Alfredo Blakeley-Ruiz – BMC Microbiome

Role of the Gut Microbiome in Autism Spectrum Disorders – Joby Pulikkan – Reviews on Biomarker Studies in Psychiatric and Neurodegenerative Disorders

Faecal microbiota transplantation in Australia: bogged down in regulatory uncertainty – Samuel P. Costello – Internal Medicine Journal

Animal experiments

Characterization of oral microbiota in marmosets: Feasibility of using the marmoset as a human oral disease model – Sachiko Takehara – PLoS One

The Effect of Multispecies Probiotic Supplementation on Iron Status in Rats – Katazyna Skrypnik – Biological Trace Element Research

Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples – Susakul Palakawong Na Ayudthaya – Current Microbiology

Animal microbiome

A Diverse Microbial Community Supports Larval Development and Survivorship of the Asian Tiger Mosquito (Diptera: Culicidae) – Nicholas V Travanty – Journal of Medical Entomology

Plant, root, and soil microbiome

Belowground biota responses to maize biochar addition to the soil of a Mediterranean vineyard – Pilar Andrés – Science of The Total Environment

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining – Markus Gastauer – Scientific Data

Probiotics / prebiotics

Infant Complementary Feeding of Prebiotics for the Microbiome and Immunity – Starin McKeen – Nutrients

Techniques

Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis – James B. Thissen – PLoS One

Microbes in the news

Tube pollution: Could bacteria create clean air on the London Underground?

Ed’s non-microbiology picks

Adjunctive vitamin D in tuberculosis treatment: meta-analysis of individual participant data – David A. Jolliffe – European Respiratory Journal

Physical activity protects against depression

Want Healthier Eating Habits? Start with a workout

GMO Cassava Can Provide Iron, Zinc To Malnourished African Children

August 15, 2018

A nice crop of plant/root/soil microbiome studies, some interesting analyses of early life/pregnancy and vaginal microbiota, a belly-load of gut microbiome science, a herd of animal studies, and a few really bad puns… Enjoy!

Events and jobs

A summary of the third annual HIV microbiome workshop – Dr. Brett Williams – AIDS Research and Human Retroviruses

Pregnancy and early life

Early childhood antibiotics use and autism spectrum disorders: a population-based cohort study – Amani F Hamad – International Journal of Epidemiology

The effects of gut microbiota on metabolic outcomes in pregnant women and their offspring – You Lv – Food & Function

Human vaginal microbiome

Cervicovaginal microbiota, women’s health, and reproductive outcomes – Samuel J. Kroon – Fertility and Sterility

Relevance of assessing the uterine microbiota in infertility – Inmaculada Moreno – Fertility and Sterility

Cervicovaginal microbiota, women’s health, and reproductive outcomes – Samuel J. Kroon – Fertility and Sterility

Human nearly-sterile sites

Ursodeoxycholic acid improves liver function via phenylalanine/tyrosine pathway and microbiome remodelling in patients with liver dysfunction – Da Jung Kim – Scientific Reports

Human gut microbiome

Assessing antibiotic resistance gene load in vegan, vegetarian and omnivore human gut microbiota – Losasso Carmen – International Journal of Antimicrobial Agents

Immunomodulatory tetracyclines ameliorate DNBS-colitis: Impact on microRNA expression and microbiota composition – J. Garrido-Mesa – Biochemical Pharmacology

Effects of anthocyanins from the fruit of Lycium ruthenicum Murray on intestinal microbiota – Yamei Yan – Journal of Functional Foods

Disparate Effects of Antibiotics on Hypertension – Sarah Galla – Physiological Genomics

Variability of core microbiota in newly diagnosed treatment-naïve paediatric inflammatory bowel disease patients – T. G. J. de Meij – PLOS One

Dietary soybean protein ameliorates high-fat diet-induced obesity by modifying the gut microbiota-dependent biotransformation of bile acids – Keita Watanabe – PLOS One

Gut microbiota alterations in moderate to severe acne vulgaris patients – Hui‐Min Yan – The Journal of Dermatology

Implication of gut microbiota metabolites in cardiovascular and metabolic diseases – Francois Brial – Cellular and Molecular Life Sciences

Making Sense of… the Microbiome in Psychiatry – Thomaz F S Bastiaanssen – International Journal of Neuropsychopharmacology

The Microbiome in Cirrhosis and its Complications – Chathur Acharya – Clinical Gastroenterology and Hepatology

Lactobacillus rhamnosus GG induced protective effect on allergic airway inflammation is associated with gut microbiota – Juan Zhang – Cellular Immunology

The gut microbiome as a driver of individual variation in cognition and functional behaviour – Gabrielle L. Davidson – Philosophical Transactions of the Royal Society B

Animal experiments

The impact of Clostridium butyricum MIYAIRI 588 on the murine gut microbiome and colonic tissue – Mao Hagihara – Anaerobe

Monitoring and evaluation of the interaction between deoxynivalenol and gut microbiota in Wistar rats by mass spectrometry-based metabolomics and next-generation sequencing – Eugènia Miró-Abella – Food and Chemical Toxicology

Lentil (Lens culinaris Medikus) Diet Affects the Gut Microbiome and Obesity Markers in Rat – Niroshan Siva – Journal of Agricultural and Food Chemistry

Gut bacterial composition in a mouse model of Parkinson’s disease – P. Perez-Pardo – Beneficial Microbes

Gut Microbiome in BALB/c and C57BL/6J Mice Undergoing Experimental Thyroid Autoimmunity Associate with Differences in Immunological Responses and Thyroid Function – Sajad Moshkelgosha – Hormone and Metabolic Research

Ultraviolet Irradiation of Skin Alters the Faecal Microbiome Independently of Vitamin D in Mice – Simon Ghaly – Nutrients

Impact of lincosamides antibiotics on the composition of the rat gut microbiota and the metabolite profile of plasma and feces – C. Behr – Toxicology Letters

Animal microbiome

Understanding bacterial communities for informed biosecurity and improved larval survival in Pacific oysters – Olivier Laroche – Aquaculture

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota – Fernanda Cornejo-Granados​ – PeerJ

Do the microorganisms from laboratory culture spent growth medium affect house dust mite fitness and microbiome composition? – Vit Molva – Insect Science

Plant, root, and soil microbiome

Microbial diversity associated to the intestinal tract of soil invertebrates – Dayana da Silva Correia – Applied Soil Ecology

Yellow Canopy Syndrome in sugarcane is associated with shifts in the rhizosphere soil metagenome but not with overall soil microbial function – Kelly Hamonts – Soil Biology and Biochemistry

Anthropogenic influence shapes the distribution of antibiotic resistant bacteria (ARB) in the sediment of Sundarban estuary in India – Anish Bhattacharyya – Science of the Total Environment

Disentangling effects of temperature on microbial community and copper extraction in column bioleaching of low grade copper sulfide – Yuguang Wang – Bioresource Technology

Long-term Plastic Greenhouse Cultivation Changes Soil Microbial Community Structures: A Case Study – Yang Song – Journal of Agricultural and Food Chemistry

Flooding and prolonged drought have differential legacy impacts on soil nitrogen cycling, microbial communities and plant productivity – Linh T. T. Nguyen – Plant and Soil

[PhD Dissertation] Microbial Communities and Their Impact on Bioenergy Crops in Dynamic Environments – Brandon Monier, South Dakota State University – Open Prairie

[PDF] Characterization of osmotolerant rhizobacteria for plant growth promoting
activities in vitro and during plant-microbe association under osmotic stress – Bandeppa – Indian Journal of Experimental Biology

Isolation and Analysis of Microbial Communities in Soil, Rhizosphere, and Roots in Perennial Grass Experiments – Morgan R. McPherson – J. Vis. Exp

Water and extremophile microbiome 

[PDF download] Monitoring biofilm communities in operational drinking water distribution systems and the impact on water quality – I. Douterelo – 1st International WDSA

Molecular detection of microbial communities associated with Microcystis vs Synechococcus dominated waters in Tianjin, China – Da Huo – Journal of Oceanology and Limnology

Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia – Katherine Bedoya – Science of the Total Environment

Profiling microbial communities in a watershed undergoing intensive anthropogenic activities – Hehuan Liao – Science of the Total Environment

The gut microbiome and aquatic toxicology: An emerging concept for environmental health – Ondrej Adamovsky – PeerJ

Microbial community composition of a hydrocarbon reservoir 40 years after a CO2 enhanced oil recovery flood – Jenna L K Shelton – FEMS Microbiology Ecology

Temporal dynamics of activated sludge bacterial communities in two diversity variant full-scale sewage treatment plants – Xiao-Tao Jiang – Applied Microbiology and Biotechnology

The Nile River Microbiome Reveals a Remarkably Stable Community Between Wet and Dry Seasons, and Sampling Sites, in a Large Urban Metropolis (Cairo, Egypt) – Eraqi WA – OMICS

Probiotics / prebiotics

Influence of monostrain and multistrain probiotics on immunity, intestinal ultrastructure and microbiota in experimental dysbiosis – E. Ermolenko – Beneficial Microbes

Effects of Probiotics on Inflammation and Uremic Toxins Among Patients on Dialysis: A Systematic Review and Meta-Analysis – Charat Thongprayoon – Digestive Diseases and Sciences

Bioinformatics

Biomarker panels for characterizing microbial community biofilm formation as composite molecular process – Magnus Bosse – PLOS One

* Maximal viral information recovery from sequence data using VirMAP – Nadim J Ajami – Nature Communications

Techniques

Using Bioreactors to Study the Effects of Drugs on the Human Microbiota – Mabel Guzman-Rodriguez – Methods

Ed’s non-microbiology picks

Human activities might influence oncogenic processes in wild animal populations – Mathieu Giraudeau – Nature Ecology & Evolution

In apoptosis, cell death spreads through perpetuating waves – James Ferrell – Stanford Medicine

Study finds Tdap vaccination for pregnant women does not increase risk of autism

Boys should be given HPV vaccine, says joint committee

New Study: Omega-3s Can Help Keep Kids Out of Trouble

Mars (probably) has a lake of liquid water

May 23, 2018

Today’s digest is packed full of awesome gut microbiome studies, a bunch of plant/soil studies, new features to QIIME and other bioinformatics, as well as a good serving of interesting pre-prints, editorials, and doctoral theses. Enjoy!

General microbiome

Microbial micropatches within microbial hotspots – Lisa M. Dann – PLOS ONE

Pregnancy and early life

The matter of the reproductive microbiome – Sam Schoenmakers – Obstetric Medicine

Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum – Mie Korslund Wiinblad Crusell – Microbiome

The importance of appropriate initial bacterial colonization of the intestine in newborn, child, and adult health – W Allan Walker – Pediatric Research

Human oral microbiome

Oral health status in historic population: Macroscopic and metagenomic evidence – Claire Willmann – PLOS ONE

The Subgingival Microbiome of Periodontal Pockets With Different Probing Depths in Chronic and Aggressive Periodontitis: A Pilot Study – Meng Shi – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

[Pre-print] Gut microbiota markers in obese adolescent and adult patients: age-dependent differential patterns – Federica Del Chierico – Frontiers in Microbiology

Clinical applications of gut microbiota in cancer biology – Sunny H. Wong – Seminars in Cancer Biology

* Microbiome-Mediated Effects of the Mediterranean Diet on Inflammation – Melisa A Bailey – Advances in Nutrition

** Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury – Benjamin M Howard – Trauma Surgery & Acute Care Open

Hypoxia induces senescence of bone marrow mesenchymal stem cells via altered gut microbiota – Junyue Xing – Nature Communications

Animal experiments

The bacterial and archaeal community structures and methanogenic potential of the cecal microbiota of goats fed with hay and high-grain diets – Wei Jin – Antonie van Leeuwenhoek

Effects of whole-grain rice and wheat on composition of gut microbiota and short-chain fatty acids in rats – Fei Han – Journal of Agriculture and Food Chemistry

Animal microbiome

Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles – Chelsea L. Blankenchip – PeerJ

Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – World Journal of Microbiology and Biotechnology

The gut microbiome is associated with behavioural task in honey bees – J. C. Jones – Insectes Sociaux

The role of the gut microbiome in health and disease of adult honey bee workers – Kasie Raymann – Current Opinion in Insect Science

Plant, root, and soil microbiome

Microbial communities in soil profile are more responsive to legacy effects of wheat-cover crop rotations than tillage systems – Anil Somenahally – Soil Biology and Biochemistry

New insights into the effects of support matrix on the removal of organic micro-pollutants and the microbial community in constructed wetlands – Liang Zhang – Environmental Pollution

[Doctoral thesis] Imprint of management on microbial communities in arable soil – Putz, Martina

Study of microbial diversity in plant–microbe interaction system with oil sludge contamination – Dhote, Monika – International Journal of Phytoremediation

Effect of different potassium levels on nitrogen metabolism, nitrogen bacteria and nitrogen archaea bacteria communities in rhizosphere of tobacco plant – WENG Zebin – Acta Tabacaria Sinica

Canola Root–Associated Microbiomes in the Canadian Prairies – Chih-Ying Lay – Frontiers in Microbiology

Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves – Leandro Pio de Sousa – Genetics and Molecular Biology

[Review] Organic Amendments, Beneficial Microbes, and Soil Microbiota: Toward a Unified Framework for Disease Suppression – Giuliano Bonanomi – Annual Review of Phytopathology

[Pre-print] Metagenomic sequencing provides insights into the location of microbial detoxification in the gut of a small mammalian herbivore – Kevin D. Kohl – bioRxiv

[Pre-print] Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California – Sabah Ul-Hasan – bioRxiv

Water and extremophile microbiome 

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community – M.Peces – Water Research

Built environment

[Editorial] Microbiome Yarns: microbiome of the built environment, paranormal microbiology, and the power of single cell genomics – Kenneth Timmis – microbial biotechnology

New Techniques for the Generation and Analysis of Tailored Microbial Systems on Surfaces – Ariel L. Furst – Biochemistry

* [Pre-print] Strain­level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes – Matthew R. Olm – bioRxiv

Probiotics / prebiotics

The effects of probiotics supplementation on metabolic health in pregnant women: An evidence based meta-analysis – Jia Zheng – PLOS ONE

Bioinformatics

[Pre-print / doctoral thesis] Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binning – Alneberg, Johannes – DiVA

** Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin – Nicholas A. Bokulich – Microbiome

Techniques

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia – Martina Lardi – High-Throughput

VSITA, an Improved Approach of Target Amplification in the Identification of Viral Pathogens – Yi Zhang – Europe PMC

Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol – Ankur Naqib – Gene Expression Analysis

Ed’s non-microbiology picks 

The Environmental Protection Agency in the Early Trump Administration: Prelude to Regulatory Capture

Perspectives on the Great Amazon Reef: Extension, Biodiversity, and Threats

Fasting boosts stem cells’ regenerative capacity

Eggs not linked to cardiovascular risk, despite conflicting advice

Noninvasive spinal stimulation method enables paralyzed people to regain use of hands, study finds

Cannabidiol significantly reduces seizures in patients with severe form of epilepsy

March 21, 2018

A long digest today – lots of science on the gut, environment, and some interesting editorials on techniques, bioinformatics, and methodologies applied to microbiome studies.

General microbiome

[pre print] Oscillating bacterial expression states generate herd immunity to viral infection – Christopher J. R. Turkington – bioRxiv

Retraction: Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – The PLOS ONE Editors – PLOS ONE

DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy – Elisa Banchi – PLOS ONE

Mobile Technologies for the Discovery, Analysis, and Engineering of the Global Microbiome – Zachary S. Ballard – ACS Nano

Unraveling Interactions between the Microbiome and the Host Immune System To Decipher Mechanisms of Disease – Catherine A. Lozupone – mSystems

Making Millennial Medicine More Meta – Peter J. Turnbaugh – mSystems

Pregnancy and early life

Neonatal intestinal dysbiosis in necrotizing enterocolitis – Naomi-Liza Denning – Molecular Medicine

Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units – Zhi-Hui Zou – Annals of Clinical Microbiology and Antimicrobials

* The Effect of Early Limited Formula on Breastfeeding, Readmission, and Intestinal Microbiota: A Randomized Clinical Trial – Valerie J. Flaherman – The Journal of Pediatrics

Multi-site human microbiome

The Complex Interplay between Chronic Inflammation, the Microbiome, and Cancer: Understanding Disease Progression and What We Can Do to Prevent It – Heather Armstrong – Cancers

Human oral microbiome

Salivary microbial profiles in relation to age, periodontal, and systemic diseases – Ronaldo Lira-Junior – PLOS ONE

Human respiratory microbiome

Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective – Georgios D. Kitsios – mSystems

Host-Microbe Interactions in Airway Disease: toward Disease Mechanisms and Novel Therapeutic Strategies – Emily K. Cope – mSystems

Human gut microbiome

The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome – Christopher John Kiely – Gut Microbes

Species Level Description of the Human Ileal Bacterial Microbiota – Heidi Cecilie Villmones – Nature

* Systematic Bias Introduced by Genomic DNA Template Dilution in 16S rRNA Gene-Targeted Microbiota Profiling in Human Stool Homogenates – Francesco Multinu – mSphere

* Extensive impact of non-antibiotic drugs on human gut bacteria – Lisa Maier – Nature

In this issue: Effect of gut microbiome on mucosal immunity and enteric diseases – Kumar, Himanshu – International Reviews of Immunology

Characterization of intestinal microbiota in alcoholic patients with and without alcoholic hepatitis or chronic alcoholic pancreatitis – Dragos Ciocan – Nature

Clostridium difficile Exposures, Colonization, and the Microbiome: Implications for Prevention – Sara L. Revolinski – Infection Control and Hospital Epidemiology

Of Microbes and Minds: A Narrative Review on the Second Brain Aging – Riccardo Calvani – Frontiers in Medicine

Microbiome: Viral hormones activate human insulin signalling – Ashley York – Nature

Modulation of Gut Microbiota: A Novel Paradigm of Enhancing the Efficacy of Programmed Death-1 and Programmed Death Ligand-1 Blockade Therapy – Yiming Wang – Frontiers in Immunology

Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study – Carmen Losasso – Frontiers in Microbiology

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies – Melanie Tramontano – Nature

Animal experiments

Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E. Dahlhausen – PeerJ

Low dose brain estrogen prevents menopausal syndrome while maintaining the diversity of the gut microbiomes in estrogen-deficient rats – Sunmin Park – American Journal of Physiology-Endocrinology and Metabolism

Oral supplementation of Bifidobacterium longum strain BR-108 alters cecal microbiota by stimulating gut immune system in mice irrespectively of viability – Yuko Makioka – Bioscience, Biotechnology, and Biochemistry

Animal microbiome

Mapping the virome in wild-caught Aedes aegypti from Cairns and Bangkok – Martha Zakrzewski – Nature

Changes in Larval Mosquito Microbiota Reveal Non-target Effects of Insecticide Treatments in Hurricane-Created Habitats – Joseph P. Receveur – Microbial Ecology

Dissecting cause and effect in host-microbiome interactions using the combined worm-bug model system – Marina Ezcurra – Biogerontology

Plant, root, and soil microbiome

[pre print] Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ pre prints

Changes in the Metagenome of Prokaryotic Community as an Indicator of Fertility of Arable Soddy-Podzolic Soils upon Fertilizer Application – A. N. Naliukhin – Eurasian Soil Science

Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification – Jun Lou – PeerJ

Plant growth-promoting rhizobacteria associated with avocado display antagonistic activity against Phytophthora cinnamomi through volatile emissions – Alfonso Méndez-Bravo – PLOS ONE

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields – Xuhong Song – PLOS ONE

Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6 – Betina Cecilia Agaras – PLOS ONE

Water and extremophile microbiome

Microbial communities underpinning mesophilic anaerobic digesters treating food wastewater or sewage sludge: a full-scale study – Joonyeob Lee – Bioresource Technology

Bacteria from Antarctic environments: diversity and detection of antimicrobial, antiproliferative, and antiparasitic activities – Tiago R. Silva – Polar Biology

Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Drought – Debra A. Davis – Microorganisms

Diversity and assembly patterns of activated sludge microbial communities: A review – Yu Xia – Biotechnology Advances

Temperature-induced changes in a microbial community under autotrophic denitrification with sulfide – Michal Sposob – Process Biochemistry

Metagenomic Exploration of Microbial Signatures on Periyar River Sediments from the Periyar Tiger Reserve in the Western Ghats – Aparna Chakkamadathil Rajeev – Genome Announcements

Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes – Ian Hewson – PLOS One

Shifts in dissolved organic matter and microbial community composition are associated with enhanced removal of fecal pollutants in urban stormwater wetlands – Xiao Huang – Water Research

Effect of semi-permeable cover system on the bacterial diversity during sewage sludge composting – Tatiana Robledo-Mahón – Journal of Environmental Management

* Life at extreme elevations on Atacama volcanoes: the closest thing to Mars on Earth? – S. K. Schmidt – Antonie van Leeuwenhoek

Rapid alterations to marine microbiota communities following an oil spill – Brad J. Gemmell – Ecotoxicology

Microbial communities and their potential for degradation of dissolved organic carbon in cryoconite hole environments of Himalaya and Antarctica – Aritri Sanyal – Microbiological Research

Built environment

Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms – John A. Handley – Frontiers in Microbiology

Food microbiology

Characterization of Bacteria in Nigerian Yogurt as Promising Alternative to Antibiotics in Gastrointestinal Infections – Anthony Opeyemi Ayeni – Journal of Dietary Supplements

Probiotics / prebiotics

Polyphenols’ Gut Microbiota Metabolites: Bioactives or Biomarkers? -Francisco A. Tomas-Barberan – Journal of Agriculture and Food Chemistry

A Multi-strain Probiotic Reduces the Fatty Liver Index, Cytokines and Aminotransferase levels in NAFLD Patients: Evidence from a Randomized Clinical Trial – Nazarii Kobyliak – Journal of Gastrointestinal and Liver Diseases

Bioinformatics

Species classifier choice is a key consideration when analysing low-complexity food microbiome data – Aaron M. Walsh – Microbiome

Data and Statistical Methods To Analyze the Human Microbiome – Levi Waldron – mSystems

* Discovery of enzymes for toluene synthesis from anoxic microbial communities – Beller HR – Nature

Techniques

Community Assembly Processes of the Microbial Rare Biosphere – Xiu Jia – Trends in Microbiology

Metabolomics: A High-Throughput Platform for Metabolite Profile Exploration – Jing Cheng – Computational Systems Biology

[Patent] Spectrometric Analysis of Microbes – Zoltan Takats

* Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics – Stefan A. Boers – European Journal of Clinical Microbiology & Infectious Diseases

Comparative analysis of four commercial on-farm culture methods to identify bacteria associated with clinical mastitis in dairy cattle – Jair C. Ferreira – PLOS One

Beyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized Therapeutics – Casey M. Theriot – mSystems

Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research – Nicole A. Hynson – mSystems

Microbiomes In Natura: Importance of Invertebrates in Understanding the Natural Variety of Animal-Microbe Interactions – Jillian M. Petersen – mSystems

Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies – Isabelle Laforest-Lapointe – mSystems

Microbes on the market 

DuPont Expands Microbiome Research Program, Adds Second Partnership with Fermentation Specialist

Science, publishing, and career

Biocodex Microbiota Foundation Awards Grants to Two Innovative Researchers in the Microbiome Field

Early-Career Systems Microbiology Scientists – Jack A. Gilbert – mSystems

Ed’s non-microbiology picks (can use your own name of course!) (cool non-microbiology science)

Self-employed people happier and more engaged at work, study finds

Health Care Spending in the United States and Other High-Income Countries

Ancient DNA Is Rewriting Human (and Neanderthal) History

Sturdy Insulator Made of Wood

How exercise in old age prevents the immune system from declining

October 26, 2017

In today’s digest we have some interesting discussion about lab/bioinformatics techniques, a few editorials on the microbiome job market, and even a little bit of philosophy learned from our tiny microbial friends.

Events and jobs

BioData World West 2018 – 13-14 March 2018 – San Francisco, CA

General microbiome

Cooperation and cheating as innovation: insights from cellular societies – Athena Aktipis – Philosophical Transactions of The Royal Society B

[Pre-Print] Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal – bioRxiv

Pregnancy and early life

Preterm Birth Affects the Risk of Developing Immune-Mediated Diseases – Sybelle Goedicke-Fritz – Frontiers in Immunology

Human oral microbiome

Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus – E. A. Babaev – Bulletin of Experimental Biology and Medicine

Human urinary tract microbiome

Re: Evaluation of the Urinary Microbiota of Women with Uncomplicated Stress Urinary Incontinence – Alan J. Wein – The Journal of Urology

Human gut microbiome

* The fecal microbiome of ALS patients – David Brenner – Neurobiology of Aging

Plant, root, and soil microbiome

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Ying Zhao – PLOS ONE

Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a Black soil of Northeastern China – Li Wang – Soil Biology and Biochemistry

Water and extremophile microbiome 

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents – Julien Crovadore – Heliyon

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents – Rika E. Anderson – Nature

Food microbiology

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage – Barbora Zalewska – Current Microbiology

Probiotics / prebiotics

Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen – Molecules

[Review] Recurrent urinary tract infections in women: How promising is the use of probiotics? – Varsha Gupta – Indian Journal of Medical Microbiology

Bioinformatics

Using convolutional neural networks to explore the microbiome – Derek Reiman – Engineering in Medicine and Biology Society (EMBC)

Techniques

‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov., three halophilic species isolated from salty human stools by culturomics – B. Senghor – New Microbes and New Infections

Proteomic and metaproteomic approaches to understand host-microbe interactions – Amanda E. Starr – Analytical Chemistry

Impact of Method Variables on Microbiota Sample Disruption – Jaclyn Zecca and David Burden – OPS Diagnostics LLC

Microbes on the market 

Patenting the microbiome: trends, challenges and insights – Anthony D Sabatelli – Future Science

[Editorial] The aquaculture microbiome at the centre of business creation – Karen K. Dittmann – Microbial Biotechnology

Ed’s non-microbiology picks

I put quite a few on here today – enjoy 🙂

More than 75 percent decline over 27 years in total flying insect biomass in protected areas – Caspar A. Hallman – PLOS ONE

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth – Natan-Haim Kalson – ACS Central Science

Games people play: How video games improve probabilistic learning – Sabrina Schenk – Behavioural Brain Research

A process-oriented model linking adolescents’ sleep hygiene and psychological functioning: the moderating role of school start times -Jack S. Peltz – Sleep Health

Decreases in self-reported sleep duration among U.S. adolescents 2009-2015 and links to new media screen time – Jean M. Twenge – Sleep Medicine

Dogs’ recognition of human selfish and generous attitudes requires little but critical experience with people – Fabricio Carballo – PLOS ONE