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

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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

August 3, 2018

Happy Friday! Today’s digest includes the axolotl microbiome, carbon processing in thawing permafrost, and esterases discovered in hot spring microbial mats. In addition, there’s a Nature career column discussing why it’s not a ‘failure’ to leave academia. Enjoy!

Multi-site human microbiome

Optimizing body fluid recognition from microbial taxonomic profiles – Eirik Nataas Hanssen – Forensic Science International

Human oral microbiome

Dysbiosis of the buccal mucosa microbiome in primary Sjögren’s syndrome patients – Taco A van der Meulen – Rheumatology

Human respiratory microbiome

Comparison of the upper and lower airway microbiota in children with chronic lung diseases – Bushra Ahmed – PLoS One

Human vaginal microbiome

Review: Case for a role of the microbiome in gynecologic cancers: Clinician’s perspective – Ismail Mert – Journal of Obstetrics and Gynecology Research

Human gut microbiome

Enhanced preservation of the human intestinal microbiota by ridinilazole, a novel Clostridium difficile-targeting antibacterial, compared to vancomycin – Cheleste M. Thorpe – PLoS One

Animal experiments

Euphorbia kansui fry-baked with vinegar modulates gut microbiota and reduces intestinal toxicity in rats – DongjingJiang – Journal of Ethnopharmacology

Animal microbiome

Experimentally induced metamorphosis in highly regenerative axolotl (ambystoma mexicanum) under constant diet restructures microbiota – Turan Demircan – Scientific Reports

Response of host–bacterial colonization in shrimp to developmental stage, environment and disease – Jinbo Xiong – Molecular Ecology

Wild Bee Pollen Usage and Microbial Communities Co-vary Across Landscapes – Quinn S. McFrederick – Microbial Ecology

Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea) – Pavel V. Shelyakin – Scientific Reports

Effect of dietary fat to starch content on fecal microbiota composition and activity in dogs – Sofia Schauf – Journal of Animal Science

Primer: The importance of being persistent: The first true resident gut symbiont in Drosophila – Dali Ma – PLoS Biology

Plant, root, and soil microbiome

Genome-centric view of carbon processing in thawing permafrost – Ben J. Woodcroft – Nature

Review: Uptake of bacteria into living plant cells, the unifying and distinct feature of the nitrogen-fixing root nodule symbiosis – Martin Parniske – Current Opinion in Plant Biology

Pre-print: Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon – Pablo de Jesus Suarez-Moo – bioRxiv

Water and extremophile microbiome

Discovery of a diverse set of esterases from hot spring microbial mat and sea sediment metagenomes – RaviRanjan – International Journal of Biological Macromolecules

Built environment

Microbial communities and functional genes of nitrogen cycling in an electrolysis augmented constructed wetland treating wastewater treatment plant effluent – Pengfei Zhang – Chemosphere

Science, publishing, and career

Why it is not a ‘failure’ to leave academia – Philipp Kruger – Nature

July 25, 2018

Today’s digest consists of opinion paper from European MyNewGut project, review article on gut microbiota dysbiosis, and meta-analysis to find association between antibiotic associated microbiota perturbation and childhood obesity. Also includes application of contraceptive rings and probiotic capsules to increase vaginal lactobacilli, and how preprint publishing could create confusion in public journalism!

General microbiome

Towards microbiome-informed dietary recommendations for promoting metabolic and mental health: Opinion papers of the MyNewGut project – Yolanda Sanz – Clinical Nutrition

Review: The gut microbiota: A new target in the management of alcohol dependence? – Sophie Leclercq – Alcohol

Review: Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery – Michael Kriss – Current Opinion in Microbiology

Review: Environmental factors, gut microbiota, and colorectal cancer prevention – Mingyang Song – Clinical Gastroenterology and Hepatology

Review: The association between antibiotic use in infancy and childhood overweight or obesity: a systematic review and meta-analysis – SA Miller – Obesity Reviews

Multi-site human microbiome

Unique subgingival microbiota associated with periodontitis in cirrhosis patients – Anders Jensen – Scientific Reports

Human respiratory microbiome

A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota – Katrina Kalantar – bioRxiv

Human vaginal microbiome

Contraceptive rings promote vaginal lactobacilli in a high bacterial vaginosis prevalence population: A randomised, open-label longitudinal study in Rwandan women – Tania Crucitti – PlosOne

Comparative phase I randomized open-label pilot clinical trial of Gynophilus® (Lcr regenerans®) immediate release capsules versus slow release muco-adhesive tablets – Caroline Dausset – European Journal of Clinical Microbiology and Infectious Diseases

Human gut microbiome

Association Between Intestinal Microbiota Collected at Hospital Admission and Outcomes of Patients with Cirrhosis – Jasmohan S Bajaj – Clinical Gastroenterology and Hepatology

Animal experiments

Butyrate regulates inflammatory cytokine expression without affecting oxidative respiration in primary astrocytes from spontaneously hypertensive rats – Tao Yang – Physiological Reports

Plant, root, and soil microbiome

Quantitative stable isotope probing with H218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA – Katerina Papp – The ISME Journal

Community structure and plant growth-promoting potential of cultivable bacteria isolated from Cameroon soil – Gylaine VT Tchakounte – Microbiological Research

Water and extremophile microbiome

Effects of mercury addition on microbial community composition and nitrate removal inside permeable reactive barriers – Kenly Hiller-Bittrolff – Environmental Pollution

Food microbiology

Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems – Clemence Defois – Scientific Reports

Polyol-producing lactic acid bacteria isolated from sourdough and their application to reduce sugar in a quinoa-based milk substitute – Stephanie Jeske – International Journal of Food Microbiology

Probiotics / prebiotics

Probiotics in cystic fibrosis patients: A double blind crossover placebo controlled study: Pilot study from the ESPGHAN Working Group on Pancreas/CF – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Phages and viruses

Parvovirus Minute Virus of Mice Interacts with Sites of Cellular DNA Damage to Establish and Amplify its Lytic Infection – Kinjal Majumder – eLife

Techniques

Review: The evolving interface between synthetic biology and functional metagenomics – Eric Van der Helm – Nature Chemical Biology

Targeted analysis of microbial-generated phenolic acid metabolites derived from grape flavanols by gas chromatography-triple quadrupole mass spectrometry – Eileen Carry – Journal of Pharmaceutical and Biomedical Analysis

Science, publishing, and career 

Preprints could promote confusion and distortion – Nature News

Science-adjacent’ conferences and why they matter – Nature News

Tulika’s non-microbiology picks

Metformin inhibits gluconeogenesis via a redox-dependent mechanism in vivo – Anila K Madiraju – Nature Medicine

 

July 20, 2018

Happy Friday! Today’s digest includes the bacterial diversity of bat guano, cyanobacterial blooms in oil-contaminated sediments, and the shrimp gut microbiome. Also, an NPR interview with astrophysicist Adam Frank about how to be a savvy consumer of science news.

Pregnancy and early life

Maternal peripartum antibiotic exposure and the risk of postpartum depression – Jordan R. Murphy – Research in Nursing and Health

Review: Breast milk, formula, the microbiome and overweight – Elisabetta Mueller – Nature Reviews Endocrinology

Human vaginal microbiome

Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome – Somaieh Afiuni-Zadeh – Scientific Reports

Human gut microbiome

Review: The Gut Microbiota and Healthy Aging: A Mini-Review – Sangkyu Kim – Gerontology

Animal experiments

Western diet feeding influences gut microbiota profiles in apoE knockout mice – Baoning Liu – Lipids in Health and Disease

Animal microbiome

Bacterial diversity of bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines: A first report on the metagenome of Philippine bat guano – Marian P. De Leon – PLoS One

Disease outbreak accompanies the dispersive structure of shrimp gut bacterial community with a simple core microbiota – Zhiyuan Yao – AMB Express

In ovo microbial communities: a potential mechanism for the initial acquisition of gut microbiota among oviparous birds and lizards – Brian K. Trevelline – Biology Letters

Plant, root, and soil microbiome

Plant diversity and density predict belowground diversity and function in an early successional alpine ecosystem – Dorota L. Porazinska – Ecology

Water and extremophile microbiome

Cyanobacterial blooms in oil-contaminated subtidal sediments revealed by integrated approaches – Cuixiao Xie – Environmental Microbiology Reports

ddPCR applied on archived Continuous Plankton Recorder samples reveals long-term occurrence of class 1 integrons and a sulphonamide resistance gene in marine plankton communities – Andrea Di Cesare – Environmental Microbiology Reports

Structure of Microbial Communities of the Sediments of Alkaline Transbaikalia Lakes with Different Salinity – S. V. Zaitseva – Microbiology

Diversity of Heterotrophic Halophilic Bacteria Isolated from Coastal Solar Salterns, Bulgaria and Their Ability to Synthesize Bioactive Molecules with Biotechnological Impact – I. Boyadzhieva – Microbiology

Diversity of Prokaryotes in Planktonic Communities of Saline Sol-Iletsk lakes (Orenburg Oblast, Russia) – E. A. Selivanova – Microbiology

Pre-Print: Genetic evidence for two carbon fixation pathways in symbiotic and free-living bacteria: The Calvin-Benson-Bassham cycle and the reverse tricarboxylic acid cycle – Maxim Rubin Blum – BioRxiv

Science, publishing, and career

Track the fate of postdocs to help the next generation of scientists – Nature

How To Be A Savvy Consumer Of Science News – NPR’s All Things Considered

Non-microbiology picks

Jupiter has 10 more moons we didn’t know about — and they’re weird – Nature

July 12, 2018

Bacteria in desert soils, mycobacteria in showerhead biofilms, metabolic diversity of microbes from commercial probiotics.

Human gut microbiome

Pre-print: Evaluating bacterial and functional diversity of human gut microbiota by complementary metagenomics and metatranscriptomics – Ravi Ranjan – bioRxiv

Animal microbiome

Pre-print: Olive fruit fly rearing procedures affect the vertical transmission of the bacterial symbiont Candidatus Erwinia dacicola – Patrizia Sacchetti – bioRxiv

Pre-print: Survey of bacteria associated with western corn rootworm life stages reveals no difference between insects reared in different soils – Dalton C Ludwick – bioRxiv

Plant, root, and soil microbiome

Influences of fertilization on soil environment and microorganism in continuous cropping based on high-throughput sequencing – Zhang YiJie – Journal of Agricultural Science and Technology

Review: Consortia of cyanobacteria/microalgae and bacteria in desert soils: an underexplored microbiota – Isiri Perera – Applied Microbiology and Biotechnology

Effects of cover crop in an apple orchard on microbial community composition, networks, and potential genes involved with degradation of crop residues in soil – Wei Zheng – Biology and Fertility of Soils

Microbial Community Level Physiological Profiles of Active Mud Volcano Soils in Andaman and Nicobar Islands – N Amaresan – National Academy Science Letters

Water and extremophile microbiome

Pre-print: Interspecies interactions mediated by conductive minerals in the sediments of the ferruginous Lake La Cruz, Spain – Amelia-Elena Rotaru – bioRxiv

Pre-print: Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes – Dean J Horton – bioRxiv

Pre-print: Hidden in plain sight – highly abundant and diverse planktonic freshwater Chloroflexi – Maliheh Mehrshad – bioRxiv

Built environment

Pre-print: Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health – Matthew Gebert – bioRxiv

Probiotics/prebiotics

Pre-print: Metabolic diversity of bacteria and yeast from commercial probiotic products illustrated by phenotypic profiling – Juliana Mastronunzio Ansari – bioRxiv

Phages and viruses

Pre-print: Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow – Antonin Bal – bioRxiv

More microbes

Species-specific activity of antibacterial drug combinations – Ana Rita Brochado – Nature

Science, career, and publishing

Hot streaks in artistic, cultural, and scientific careers – Lu Liu – Nature

Amy’s non-microbiology picks

Reprogramming human T cell function and specificity with non-viral genome targeting – Theodore L Roth – Nature