November 7, 2018

There’s lots of new work to catch up on! Some highlights include the skin virome in patients with immune deficiency, a mechanism for host-microbe mutualism in zebrafish, ecological pressures in soil that lead to smaller genomes, and a book chapter about the future of microbial forensics.

General Microbiome
Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness – Wen C. Aw – PLOS Genetics

Antifungal immune responses: emerging host–pathogen interactions and translational implications – Vinod Kumar – Genome Medicine

Pregnancy and early life
Childhood Adversity Impact on Gut Microbiota and Inflammatory Response to Stress During Pregnancy. – Liisa Hantsoo – Brain, Behavior, and Immunity

Enabling precision medicine in neonatology, an integrated repository for preterm birth research – Marina Sirota – Scientific Data

Associations of birth mode with cord blood cytokines, white blood cells, and newborn intestinal bifidobacteria – Isabel Cristina Ribas Werlang – PLOS One

HPV infection and bacterial microbiota in breast milk and infant oral mucosa – Heidi Tuominen – PLOS One

Human skin microbiome
Expanded skin virome in DOCK8-deficient patients – Osnat Tirosh – Nature Medicine

Microbiological Profile of Sarecycline: A Novel Targeted Spectrum Tetracycline for the Treatment of Acne Vulgaris – George Zhanel – Antimicrobial Agents and Chemotherapy

Human vaginal microbiome
Preprint: Glycan cross-feeding drives mutualism between Fusobacterium and the vaginal microbiota – Kavita Agarwal – bioRxiv

Human multi-site microbiome
The altered human serum metabolome induced by a marathon – Zinandré Stander – Metabolomics

The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media
Andrea Coleman
Microbiome

Human gut microbiome
An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men – Abigail J. S. Armstrong – Microbiome

Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent Clostridium difficile infection: A randomized clinical trial – Zhi-Dong Jiang – PLOS One

The long term effect of metabolic profile and microbiota status in early gastric cancer patients after subtotal gastrectomy – Xi-Hsuan Lin – PLOS One

Animal experiments
A bacterial immunomodulatory protein with lipocalin-like domains facilitates host–bacteria mutualism in larval zebrafish – Annah S Rolig – eLife

Gut microbiota and intestinal FXR mediate the clinical benefits of metformin – Lulu Sun – Nature Medicine

Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model – Kazuyuki Kasahara – Nature Microbiology

Enteric infection coupled with chronic Notch pathway inhibition alters colonic mucus composition leading to dysbiosis, barrier disruption and colitis – Ishfaq Ahmed – PLOS One

Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A. Hatter – PLOS One

Plant, root, and soil microbiome
Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient – Jackson W. Sorensen – Nature Microbiology

Decomposition responses to climate depend on microbial community composition -Sydney I. Glassman – PNAS

The nanotechnology among US: are metal and metal oxides nanoparticles a nano or mega risk for soil microbial communities? – J. Parada – Critical Reviews in Biotechnology

Water and extremophile microbiome
Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia. – Nyok-Sean Lau – Microbial Ecology

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient – Alexandra Meziti – The ISME Journal

Probiotics
Anti-diabetic effects of Lactobacillus casei fermented-yogurt through re-shaping gut microbiota structure in type 2 diabetic rats – Ling Qu – Journal of Agricultural and Food Chemistry

Probiotics-fermented Massa Medicata Fermentata ameliorates weaning stress in piglets related to improving intestinal homeostasis – Yanbo Wang – Applied Microbiology and Biotechnology

Techniques
Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling – Fei Teng – Scientific Reports

Science career/training and publishing
Preprint: The CURE for Culturing Fastidious Microbes – Arundhati Bakshi – bioRxiv

Meeting Report: Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. – Jacquelyn S. Meisel -Microbiome

In win for open access, two major funders won’t cover publishing in hybrid journals

Microbial Forensics
Book Chapter: Unique Individualistic Microflora: The Future of DNA Fingerprinting Technique – Pankaj Shrivastava – DNA Fingerprinting: Advancements and Future Endeavors

Alyson’s non-microbiology picks
Science candidates prevail in US midterm elections

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November 3, 2018

Human Microbiome

Defining Dysbiosis in Disorders of Movement and Motivation – Christopher T. Fields – The Journal of Neuroscience

The Microbiotic Highway to Health-New Perspective on Food Structure, Gut Microbiota, and Host Inflammation – Nina Wærling Hansen – Nutrients

Compounding to Prevent and Treat Dysbiosis of the Human Vaginal Microbiome – Riepl Mike – International Journal Of Pharmaceutical Compounding

Multiple sessions of antimicrobial photodynamic therapy associated with surgical periodontal treatment in patients with chronic periodontitis – Uislen B. Cadore – Journal of Periodontology

Gastrointestinal microbiota disruption and risk of colonization with carbapenem-resistant Pseudomonas aeruginosa in ICU patients – Melinda M Pettigrew – Clinical Infectious Diseases

Efficacy of Probiotics Supplementation On Chronic Kidney Disease: a Systematic Review and Meta-Analysis – L. Jia – Kidney and Blood Pressure Research

Antibiotic resistance genes distribution in microbiomes from the soil-plant-fruit continuum in commercial Lycopersicon esculentum fields under different agricultural practices – Francisco Cerqueira – Science of The Total Environment

Repeated rectal application of a hyperosmolar lubricant is associated with microbiota shifts but does not affect PrEP drug concentrations: results from a randomized trial in men who have sex with men – Richard E Haaland – Journal of The International AIDS Society

Modulation of gut microbiome in nonalcoholic fatty liver disease: pro-, pre-, syn-, and antibiotics – Min Seok Cho – Journal of Microbiology

Does Modification of the Large Intestinal Microbiome Contribute to the Anti-Inflammatory Activity of Fermentable Fiber? – Shiu-Ming Kuo – Current Developments in Nutrition

 

Animal Microbiome

Pubertal exposure to the endocrine disruptor mono-2-ethylhexyl ester at body burden level caused cholesterol imbalance in mice – Cui Wang – Environmental Pollution

Effects of hexavalent chromium on intestinal histology and microbiota in Bufo gargarizans tadpoles – Qiong Yao – Chemosphere

Dietary shifts influenced by livestock grazing shape the gut microbiota composition and co-occurrence networks in a local rodent species – Guoliang Li – Journal of Animal Ecology

The Impact of Fructo-Oligosaccharides on Gut Permeability and Inflammatory Responses in the Cecal Mucosa Quite Differs between Rats Fed Semi-Purified and Non-Purified Diets – Tomomi Genda – Journal of Nutritional Science and Vitaminology

Temperature-mediated inhibition of a bumblebee parasite by an intestinal symbiont – Evan C. Palmer-Young – Proceedings of The Royal Society B

Combined Consumption of Beef-Based Cooked Mince and Sucrose Stimulates Oxidative Stress, Cardiac Hypertrophy, and Colonic Outgrowth of Desulfovibrionaceae in Rats – Thomas Van Hecke – Molecular Nutrition and Food Research

Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota – Berra Erkosar – Ecology and Evolution

 

Food Microbiome

Monitoring of assertive Lactobacillus sakei and Lactobacillus curvatus strains using an industrial ring trial experiment – Dorothee Janßen – Journal of Applied Microbiology

 

Plant Microbiome

The bacterial volatile dimethyl-hexa-decylamine reveals an antagonistic interaction between jasmonic acid and cytokinin in controlling primary root growth of Arabidopsis seedlings – Ernesto Vázquez-Chimalhua – Protoplasma

Smells from the desert: microbial volatiles that affect plant growth and development of native and non-native plant species – David A. Camarena‐Pozos – Plant, Cell and Environment

 

Bioinformatics, Methodologies and Analysis

Identification and removal of contaminating microbial DNA from PCR reagents: impact on low biomass microbiome analyses – Lisa F Stinson – Letters in Applied Microbiology

A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links – Helle Krogh Pedersen – Nature Protocols

 

Other

Studying the microbiome and its complexities: an interview with Alan WalkerBMC Biology

When a physicist wanders into biology…: an interview with KC HuangBMC Biology

From bacterial genomics to clinical epidemiology: an interview with Bill HanageBMC Biology

 

October 10, 2018

Microbiota conservation and diversity in butterfly species, air and waterborne microbiota of a pharmaceutical plant, the a study on the oral microbiota of rugby players.

General microbiome

Preserving microbial diversity – Maria G Dominguez Bello – Science

Pregnancy and early life

Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy – Kristine M Wylie – BMC Research Notes

Human skin microbiome

The microbiome of the “sterile” pustules in palmoplantar pustulosis – Kana Masuda-Kuroki – Experimental Dermatology

Human oral microbiome

Oral health and microbiota status in professional rugby players: A case-control study – Matthieu Minty – Journal of Dentistry

Oral Bacteriome Compositions Identified by 16S rRNA Metagenomics in a Randomly Selected “Healthy” Nigerian Male and Female Subjects – Kingsley C Anukam – International Journal of Research and Reports in Dentistry

Human gut microbiome

Review: The Gut-Brain Axis and the Microbiome: Mechanisms and Clinical Implications – Vadim Osadchiy – Clinical Gastroenterology and Hepatology

Animal experiments

Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota – Kathryn Eaton – eLIFE

Animal microbiome

Pre-print: Conserved microbiota among young Heliconius butterfly species – Bas van Schooten – PeerJ

Gastrointestinal Microbial Flora in Wild and Captive Olive Baboons (Papio anubis) – Senelwa Davis Lugano – American Journal of Infectious Diseases and Microbiology

Plant, root, and soil microbiome

Rhizosphere microbiome structure alters to enable wilt resistance in tomato – Min-Jung Kwak – Nature Biotechnology

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition – Xiaofen Chai – Journal of Applied Microbiology

Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing – Huan Li – Journal of Basic Microbiology

Ectomycorrhizal fungi may not act as a barrier inhibiting host plant absorption of heavy metals – Yangze Tang – Chemosphere

Pre-print: Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances – Rodrigo G Taketani – PeerJ

Water and extremophile microbiome

Structure of Microbial Mats in the Mramornaya Bay (Crimea) Coastal Areas – NV Pimenov – Microbiology

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles – Sheila Powell – The ISME Journal

High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing – Otakar Strunecky – Extremophiles

Built environment

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

Food microbiology

Review: The Effect of Gluten-Free Diet on Health and the Gut Microbiota Cannot Be Extrapolated from One Population to Others – Jose F Garcia-Marzcorro – Nutrients

Phages and viruses

Characterization of dog serum virome from Northeastern Brazil – MN Weber – Virology

Bioinformatics

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets – Bhusan K Kuntal – The ISME Journal

Techniques

A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus – Matthew E Mokszycki – Applied and Environmental Microbiology

Science, career, and publishing

Inoculating science against potential pandemics and information hazards – Kevin M Esvelt – PLOS Pathogens

October 1, 2018

To kick off October, we have a Microbiome Digest filled with ecological approaches to microbial communities and techniques for analysis. Plus: what the Nobels are doing to encourage diversity, and what ecstasy does to octopuses. Happy reading!

General Microbiome
Neutral and selective dynamics in a synthetic microbial community. – Nate J. Cira – PNAS

Microbiomes as Metacommunities: Understanding Host-Associated Microbes through Metacommunity Ecology. – Elizabeth Theresa Miller – Trends in Ecology and Evolution

Clinician Guide to Microbiome Testing – Christopher Staley – Digestive Diseases and Sciences

Human Urinary Microbiome
NMR-based metabonomic approach reveals changes in the urinary and fecal metabolome caused by resveratrol. – Gabriela Torres Santiago – Journal of Pharmaceutical and Biomedical Analysis

Urinary microbes and postoperative urinary tract infection risk in urogynecologic surgical patients – Krystal J. Thomas-White – International Urogynecology Journal

Human Gut Microbiome
Metagenomic insights into resistant starch degradation by human gut microbiota. – Marius Vital – Applied and Environmental Microbiology

Pathogenic functions of host microbiota. – Silke Rath – Microbiome

Prebiotics and Probiotics in Digestive Health – Eamonn M.M. Quigley – Clinical Gastroenterology and Hepatology

Animal Experiments
Isolation and characterization of the Bacillus cereus BC7 strain, which is capable of zearalenone removal and intestinal flora modulation in mice. – Yue Wang – Toxicon

Sulfated Polysaccharide from Sea Cucumber and its Depolymerized Derivative Prevent Obesity in Association with Modification of Gut Microbiota in High‐Fat Diet‐Fed Mice – Zhenjun Zhu – Molecular Nutrition and Food Research

Animal Microbiome
Cultivable microbiome and its resistance to antimicrobials isolated from Zaprionus indianus – Graziele Aparecida Fernandes da Cruz – Environmental Monitoring and Assessment

Plant, root, and soil microbiome
Impact of weather conditions, leaf age and irrigation water disinfection on the major epiphytic bacterial genera of baby spinach grown in an open field – Pilar Truchado – Food Microbiology

Influence of light on plant – phyllosphere interaction – Sofia D. Carvalho – Frontiers in Plant Science

Techniques
PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. – Fabian Bonk – Journal of Microbiological Methods

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. – Johannes Alneberg – Microbiome

Progress of analytical tools and techniques for human gut microbiome research – Eun-Ji Song – Journal of Microbiology

Preprint: Dynamic interaction network inference from longitudinal microbiome data – Jose Lugo-Martinez – bioRxiv

Science, Publishing, and Career
What the Nobels are — and aren’t — doing to encourage diversity – Elizabeth Gibney -Nature

Alyson’s Non-Microbiology Pick
What Ecstasy Does to Octopuses – Ed Yong – The Atlantic

September 17, 2018

In today’s Microbiome Digest, look for rhizobacteria that affect plant size, methanogenesis in salt marsh sediments, a murine model for periodontitis, and an exciting preprint that identifies a microbiome in dinosaur bones! Plus, as bonus non-microbiology topics, we consider authorship norms across different disciplines and how forensics might work on Mars.

General Microbiome
(preprint) Life Inside A Dinosaur Bone: A Thriving Microbiome – Evan Thomas Saitta – bioRxiv

Metabolic Interactions of a Chain Elongation Microbiome – Wenhao Han – Applied and Environmental Microbiology

Human Gut Microbiome
Passing the “Acid Test”: Do Proton Pump Inhibitors Affect the Composition of the Microbiome? – Tien Dong – Digestive Diseases and Sciences

The gastric mucosal-associated microbiome in patients with gastric polyposis – Rongrong Ren – Scientific Reports

Animal Experiments
An experimental murine model to study periodontitis – Julie Marchesan – Nature Protocols

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice – Alida Kindt – Nature Communications

Animal Microbiome
Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont – Rachele Bernasconi – Microbial Ecology

(preprint) Gut microbial compositions mirror caste-specific diets in a major lineage of eusocial insects – Saria Otani -bioRxiv

Plant, Root, and Soil Microbiome
Plant growth-promoting rhizobacteria promote plant size inequality – Alan C. Gange – Scientific Reports

Diversity of active viral infections within the Sphagnum microbiome – Joshua MA Stough – Applied and Environmental Microbiology

The impact of high throughput sequencing on plant health diagnosticsThe impact of high throughput sequencing on plant health diagnostics – Ian Adams -European Journal of Plant Pathology

Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment – Eleanor Jameson – ISME Journal

Water and Extremophile Microbiome
Living at the frontiers of life: extremophiles in Chile and their potential for bioremediation – Roberto Orellana – Frontiers in Microbiology

Spatial structuring of bacterial communities in epilithic biofilms in the Acquarossa river (Italy) – Carolina Chiellini – FEMS Microbial Ecology

Bioinformatics
A small‐sample kernel association test for correlated data with application to microbiome association studies – Xiang Zhan – Genetic Epidemiology

Science, Publishing, and Career
Thousands of scientists publish a paper every five days – John P. A. Ioannidis – Nature

Alyson’s Non-Microbiology Picks
Sensing with tools extends somatosensory processing beyond the body – Luke E. Miller- Nature

How Will Police Solve Murders on Mars? – Geoff Manaugh – The Atlantic

September 7, 2018

Happy Friday everyone! Today’s digest covers microbiota dysbiosis in bowel obstruction, the soil microbial communities in apple orchards, and the bacterial and diatom composition of killer whale skin. Enjoy!

Human oral microbiome

Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis – Abusleme – JCI Insight

High-resolution ISR amplicon sequencing reveals personalized oral microbiome – Mukherjee – Microbiome

Human gut microbiome

Review: Inflammasomes in the gastrointestinal tract: infection, cancer and gut microbiota homeostasis – Man – Nature Reviews Gastroenterology and Hepatology

Review: Norovirus interactions with the commensal microbiota – Sullender – PLoS Pathogens

Microbiota dysbiosis and its pathophysiological significance in bowel obstruction – Hegde – Scientific Reports

Microbiota-derived short-chain fatty acids promote Th1 cell IL-10 production to maintain intestinal homeostasis – Sun – Nature Communications

Animal experiments

Irreversible effects of trichloroethylene on the gut microbial community and gut-associated immune responses in autoimmune-prone mice – Khare – Journal of Applied Toxicology

Animal microbiome

Preprint: Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota – Yan – BioRxiv

Preprint: Diet influences early microbiota development in dairy calves without long-term impacts on milk production – Dill-McFarland – BioRxiv

Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin – Hooper – Molecular Ecology

Plant, root, and soil microbiome

Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera – Lin – Frontiers in Microbiology

Spatial structuring of soil microbial communities in commercial apple orchards – Deakin – Applied Soil Ecology

Isolation and characterization of antagonistic bacteria with the potential for biocontrol of soil-borne wheat diseases – Wang – Journal of Applied Microbiology

Science, publishing, and career

Experimental technique isn’t my strong suit, but I can still be a scientist – Anderson – Science Careers

August 6, 2018

In today’s digest, look for probiotic trials for renal insufficiency and metabolic syndrome, experimental dysbiosis in SIV-infected primates, bacterial and fungal network analyses in soils, and recombination in the human virome. Plus, bacteria in the popular press, hints for scientists using Twitter, the first stem cell therapies for Parkinson’s Disease, and more!

Human gut microbiome
Antigenic mimicry of ubiquitin by the gut bacterium Bacteroides fragilis: a potential link with autoimmune disease – Linda Stewart – Clinical and Experimental Immunology

Animal experiments
Experimental microbial dysbiosis does not promote disease progression in SIV-infected macaques – Alexandra M. Ortiz – Nature Medicine

Addition of dairy lipids and probiotic Lactobacillus fermentum in infant formula programs gut microbiota and entero-insular axis in adult minipigs – Marion Lemaire – Scientific Reports

Animal microbiome
Increased Numbers of Culturable Inhibitory Bacterial Taxa May Mitigate the Effects of Batrachochytrium dendrobatidis in Australian Wet Tropics Frogs – Sara C. Bell – Frontiers in Microbiology

Characterization of the fecal microbiota of healthy horses – Holly L. Stewart – American Journal of Veterinary Research

Plant, root, and soil microbiome
Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes – Andrew T. Nottingham – Ecology

Soil bacterial networks are less stable under drought than fungal networks – Franciska T. de Vries – Nature Communications

Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits – Miguel A. Redondo – The ISME Journal

Variations in microbial community and di-(2-ethylhexyl) phthalate (DEHP) dissipation in different rhizospheric compartments between low- and high-DEHP accumulating cultivars of rice (Oryza sativa L.) – Xue-Xue Chen – Ecotoxicology and Environmental Safety

Water and extremophile microbiome
Evaluation of performance and microbial community successional patterns in an integrated OCO reactor under ZnO nanoparticle stress – Zhenghui Liu – RSC Advances

Screening of quorum quenching activity of the bacteria isolated from dairy industry waste activated sludge – J. Kaur – International Journal of Environmental Science and Technology

Food Microbiology
Identification of Mesophilic Spore-formers in Whey Powder using Shotgun Metagenomic Sequencing – Aoife J. McHugh – Applied and Environmental Microbiology

Probiotics/Prebiotics
An open-label, randomized, placebo-controlled study on the effectiveness of a novel probiotics administration protocol (ProbiotiCKD) in patients with mild renal insufficiency (stage 3a of CKD) – Mariadelina Simeoni – European Journal of Nutrition

Probiotic and synbiotic supplementation could improve metabolic syndrome in prediabetic adults: A randomized controlled trial – Nazila Kassaian – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

Phages and viruses
Investigation of recombination-intense viral groups and their genes in the Earth’s virome – Jan P. Meier-Kolthoff – Scientific Reports

Microbes in the news
Hong Kong Subway Study Shows How Quickly Bacteria Travel Across a City – Gizmodo

Bacteria hysteria
Please Don’t Give Up Your Pet Over The Fear Of Dog-Lick Bacteria – Huffington Post

Science, publishing, and career
Scientists on Twitter: Preaching to the choir or singing from the rooftops? – Isabelle Côté – Facets

Alyson’s non-microbiology picks
‘Reprogrammed’ stem cells to be tested in people with Parkinson’s

These tiny, stretchy speakers and microphones let your skin play music