November 16, 2018

Happy Friday! Today’s digest includes the effects of chewing gum on the oral microbiome, the gill microbiome of mangrove shipworms, and the rumen microbiome of dairy cows. Enjoy!

Human oral microbiome

Effects of xylitol-containing chewing gum on the oral microbiota – Takeuchi – Journal of Oral Science

Human gut microbiome

Gut microbiome transition across a lifestyle gradient in Himalaya – Jha – PLoS Biology

Fecal chromogranins and secretogranins are linked to the fecal and mucosal intestinal bacterial composition of IBS patients and healthy subjects – Sundin – Scientific Reports

Animal experiments

Specific Members of the Gut Microbiota are Reliable Biomarkers of Irradiation Intensity and Lethality in Large Animal Models of Human Health – Carbonero – Radiation Research

Gut microbiota development in mice is affected by hydrogen peroxide produced from amino acid metabolism during lactation – Shigeno – FASEB Journal

Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells – Bodogai – Science Translational Medicine

Estrogen-mediated gut microbiome alterations influence sexual dimorphism in metabolic syndrome in mice – Kaliannan – Microbiome

Effects of Intraoperative Vagal Nerve Stimulation on the Gastrointestinal Microbiome in a Mouse Model of Amyotrophic Lateral Sclerosis – Haney – Comparative Medicine

Animal microbiome

Assessing the Microbiota of Black Soldier Fly Larvae (Hermetia illucens) Reared on Organic Waste Streams on Four Different Locations at Laboratory and Large Scale – Wynants – Microbial Ecology

The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei – Brito – PLoS One

Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows – Tong – PLoS One

Plant, root, and soil microbiome

Rootstocks shape the rhizobiome: Rhizosphere and endosphere bacterial communities in the grafted tomato system – Poudel – Applied and Environmental Microbiology

Water and extremophile microbiome

Aquatic ecotoxicity of an antidepressant, sertraline hydrochloride, on microbial communities – Yang – Science of The Total Environment

Probing the ecological and evolutionary history of a thermophilic cyanobacterial population via statistical properties of its microdiversity – Rosen – PLoS One

Built environment

Activated sludge bacterial communities of typical wastewater treatment plants: distinct genera identification and metabolic potential differential analysis – Zhang – AMB Express

Analysis of bacteria stress responses to contaminants derived from shale energy extraction – Santos – Environmental Science: Processes & Impacts

Probiotics/prebiotics

Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial – Plummer – BMC Microbiology

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October 30, 2018

Hello everyone! Today’s digest includes gut microbiome inheritance in Drosophila, the influence of diet on dairy calf microbiomes, and axenic mosquitoes. Have a great day!

Pregnancy and early life

The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD – Soderborg – Nature Communications

Neonatal gut and respiratory microbiota: coordinated development through time and space – Grier – Microbiome

Human urinary microbiome

Urinary Microbiome Associated with Chronic Allograft Dysfunction in Kidney Transplant Recipients – Wu – Clinical Transplantation

Human gut microbiome

Review: Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach – Nogueira – Drug Development Research

Animal experiments

Microbial structure and function in infant and juvenile rhesus macaques are primarily affected by age, not vaccination status – Hasegawa – Scientific Reports

The gut microbiome participates in transgenerational inheritance of low temperature responses in Drosophila melanogaster – Zare – FEBS Letters

The impact of exercise training and resveratrol supplementation on gut microbiota composition in high-fat diet fed mice – Brandt – Physiological Reports

Effect of fecal microbiota transplantation route of administration on gut colonization and host response in preterm pigs – Brunse – ISME

Animal microbiome

Bacterial community structure and succession in nests of two megachilid bee genera – Voulgari-Kokota – FEMS Microbiology Ecology

Gut microbial divergence between two populations of the hadal amphipod Hirondellea gigas – Zhang – Applied and Environmental Microbiology

Diet influences early microbiota development in dairy calves without long-term impacts on milk production – Dill-McFarland – Applied and Environmental Microbiology

Generation of axenic Aedes aegypti demonstrate live bacteria are not required for mosquito development – Correa – Nature Communications

Plant, root, and soil microbiome

Review: Influence of Light on Plant-Phyllosphere Interaction – Carvalho – Frontiers in Plant Science

Deciphering the bacterial composition in the rhizosphere of Baphicacanthus cusia (NeeS) Bremek – Zeng – Scientific Reports

Changes in Metal Availability and Improvements in Microbial Properties After Phytoextraction of a Cd, Zn and Pb Contaminated Soil – Yang – Bulletin of Environmental Contamination and Toxicology

Legacy of land use history determines reprogramming of plant physiology by soil microbiome – Li – ISME

Adaptation of soil microbial growth to temperature: using a tropical elevation gradient to predict future changes – Nottingham – Global Change Biology

Soil pH rather than elevation determines bacterial phylogenetic community assembly on Mt. Norikura, Japan – Cho – FEMS Microbiology Ecology

Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass) – Whitaker – Ecology

Built environment

Mapping anaerobic sludge bed community adaptations to manure supernatant in biogas reactors – Synnøve Røstad Nordgård – Scientific Reports

Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics – Fontana – Microbiome

October 12, 1018

Happy Friday! Today’s post features the rhizosphere of pinot noir grape plants, the impact of colostrum on the hindgut of dairy calves, and the microbial composition of the clownfish gut.

General microbiome

Review: Microbial forensics: new breakthroughs and future prospects – Oliveira – Applied Microbiology and Biotechnology

Pregnancy and early life

Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations – Ho – Nature Communications

Human oral microbiome

Review: Microbiological changes of the ageing oral cavity – Belibasakis – Archives of Oral Biology

Review: The oral microbiota: dynamic communities and host interactions – Lamont – Nature Reviews Microbiology

Human gut microbiome

Review: Non-alcoholic fatty liver disease and obesity: the role of the gut bacteria – Schwenger – European Journal of Nutrition

Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota – Chung – FEMS Microbiology Ecology

Oral iron exacerbates colitis and influences the intestinal microbiome – Mahalhal – PLoS One

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course – Schirmer – Cell Host & Microbe

Animal experiments

Colostrum feeding shapes the hindgut microbiota of dairy calves during the first 12 h of life – Song – FEMS Microbiology Ecology

Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP – Carvalho – Scientific Reports

Animal microbiome

Preprint: A simple microbiome in esophagus and gills of the European common cuttlefish, Sepia officinalis – Lutz – bioRxiv

Preprint: Feeding rapidly alters microbiome composition and gene transcription in the clownfish gut – Parris – bioRxiv

Profiling the airway in the macaque model of tuberculosis reveals variable microbial dysbiosis and alteration of community structure – Cadena – Microbiome

The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala – Wang – BMC Microbiology

Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches – Guyomar – Microbiome

Microbial community and functions associated with digestion of algal polysaccharides in the visceral tract of Haliotis discus hannai: Insights from metagenome and metatranscriptome analysis – Nam – PLoS One

Critical Role for a Subset of Intestinal Macrophages in Shaping Gut Microbiota in Adult Zebrafish – Earley – Cell Reports

Plant, root, and soil microbiome

Soil acidification amendments change the rhizosphere bacterial community of tobacco in a bacterial wilt affected field – Shen – Applied Microbiology and Biotechnology

Geospatial variation in co‐occurrence networks of nitrifying microbial guilds – Jones – Molecular Ecology

Review: Elucidating Bacterial Gene Functions in the Plant Microbiome – Levy – Cell Host & Microbe

Amazonian deforestation and soil biodiversity – Franco – Conservation Biology

Metaproteomic characterization of Vitis vinifera rhizosphere – Bona – FEMS Microbiology Ecology

Water and extremophile microbiome

Exploring biogeographic patterns of bacterioplankton communities across global estuaries – Ghosh – MicrobiologyOpen

In situ responses of the sponge microbiome to ocean acidification – Kandler – FEMS Microbiology Ecology

Built environment

Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics – Hessler – Research in Microbiology

Techniques

Preprint: Microbial contamination screening and interpretation for biological laboratory environments – Ning – bioRxiv

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 17, 2018

Happy Friday! Today’s digest includes the tongue microbiome of elderly adults, electroactive biofilms, and the transmission of bacteria from hand washing sink traps. Also featured is a Nature commentary on Unpaywall and open-access research articles.

Pregnancy and early life

Changes in the gut microbiota composition during pregnancy in patients with gestational diabetes mellitus (GDM) – Ilario Ferrocino – Scientific Reports

Human oral microbiome

Tongue Microbiota and Oral Health Status in Community-Dwelling Elderly Adults – Mikari Asakawa – mSphere

Human respiratory microbiome

Early Airway Microbial Metagenomic and Metabolomic Signatures are Associated with Development of Severe Bronchopulmonary Dysplasia – Charitharth Vivek Lal – American Journal of Physiology-Lung Cellular and Molecular Physiology

Human vaginal microbiome

Characterization of pelvic and cervical microbiotas from patients with pelvic inflammatory disease – Yue Wang – Journal of Medical Microbiology

Human gut microbiome

Review: Unhealthy gut, unhealthy brain: The role of the intestinal microbiota in neurodegenerative diseases – Lindsay Joy Spielman – Neurochemistry International

Potential of fructooligosaccharides and xylooligosaccharides as substrates to counteract the undesirable effects of several antibiotics on elder faecal microbiota: a first in vitro approach – Beatriz Miguez – Journal of Agricultural and Food Chemistry

Lack of short-chain fatty acids and overgrowth of opportunistic pathogens define dysbiosis of neuromyelitis optica spectrum disorders: A Chinese pilot study – Junli Gong – Multiple Sclerosis

Animal experiments

Effects of Oat Bran on Nutrient Digestibility, Intestinal Microbiota, and Inflammatory Responses in the Hindgut of Growing Pigs – Beibei He – International Journal of Molecular Sciences

Animal microbiome

Preprint: Bacterial cohesion predicts spatial distribution in the larval zebrafish intestine – Brandon H. Schlomann – bioRxiv

Plant, root, and soil microbiome

Effects of lily/maize intercropping on rhizosphere microbial community and yield of Lilium davidii var. unicolor – Lijing Zhou – Journal of Basic Microbiology

Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture – Linkun Wu – International Journal of Molecular Sciences

Water and extremophile microbiome

Preprint: Shear stress mediates metabolism and growth in electroactive biofilms – Akhenaton-Andrew D Jones – bioRxiv

Characteristics of Rhizosphere Bacterial Community across Different Cultivation Years in Saline-alkaline Paddy Soils of Songnen Plain of China – Jun-Tao CUI – Canadian Journal of Microbiology

Built environment

Preprint: Droplet rather than Aerosol Mediated Dispersion is the Primary Mechanism of Bacterial transmission from Contaminated Hand Washing Sink Traps – Shireen M Kotay – bioRxiv

Probiotics / prebiotics

Review: Prebiotic and probiotic treatment of nonalcoholic fatty liver disease: a systematic review and meta-analysis – Brett R Loman – Nutrition Reviews

Science, publishing, and career

Stepping up to the podium: Wrestling with impostor syndrome as a teacher – Jeffrey Maloy – Science Careers

How Unpaywall is transforming open science – Holly Else – Nature News & Comment

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 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