January 7, 2019

Happy Monday! Today’s digest includes the influence of ant colonies on soil microbes, the assembly of prokaryotic communities in subtropical grasslands, and lactic acid bacteria isolated from sourdough. Have a great week!

Human gut microbiome

Review: The gut microbiome in anorexia nervosa: relevance for nutritional rehabilitation – Ruusunen – Psychopharmacology

Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children – Zhong – Microbiome

Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases – Armstrong – Microbiome

Animal experiments

Preprint: The gut microbiota is associated with clearance of Clostridium difficile infection independent of adaptive immunity – Leslie – BioRxiv

Animal microbiome

Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves – Murphy – Microbial Ecology

Modulation of broiler gut microbiota and gene expression of Toll-like receptors and tight junction proteins by diet type and inclusion of phytogenics – Paraskeuas – Poultry Science

Plant, root, and soil microbiome

Responses of soil aggregates and bacterial communities to soil-Pb immobilization induced by biofertilizer – Wang -Chemosphere

Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland – Lupatini – Microbial Ecology

Ant colonies promote the diversity of soil microbial communities – Delgado-Baquerizo – ISME

Water and extemophile microbiome

Morphological response to salinity, temperature, and pH changes by marine fungus Epicoccum nigrum – Ahumada-Rudolph – Environmental Monitoring and Assessment

Thermoplasmatales and sulfur-oxidizing bacteria dominate the microbial community at the surface water of a CO2-rich hydrothermal spring located in Tenorio Volcano National Park, Costa Rica – Arce-Rodríguez – Extremophiles

Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera – Yang – Microbiome

Water pollution and observation of acquired antibiotic resistance in Bayou Lafourche, a major drinking water source in Southeast Louisiana, USA – Bird – Environmental Science and Pollution Research

Metagenomic Analysis of Zinc Surface–Associated Marine Biofilms – Ding – Microbial Ecology

Evolutionary constraints on species diversity in marine bacterioplankton communities – Lu – ISME

Built environment

Wastewater treatment and microbial community dynamics in a sequencing batch reactor operating under photosynthetic aeration – Parakh – Chemosphere

Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics – Zhu – Water Research

Food microbiology

Effect of in vitro digestion-fermentation on green and roasted coffee bioactivity: The role of the gut microbiota – Pérez-Burillo – Food Chemistry

In vitro and in vivo investigations of probiotic properties of lactic acid bacteria isolated from Chinese traditional sourdough – Li – Applied Microbiology and Biotechnology

Bacterial community dynamics and physical–chemical characteristics in natural fermentation of jiang‐shui, a traditional food made in Northwest China – Liu – Science of Food and Agriculture

Science, publishing, and career

Here’s what scientists searched for in 2018: AI is up, stress is down – Kelly Oakes – Nature News

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November 30, 2018

Happy Friday! Today’s digest features the skin microbiome of lizards and frogs, bacterial changes during palm wine fermentation, and the impact of deforestation on soils in the Amazon.

General microbiome

Review: The microbiome in threatened species conservation – West – Biological Conservation

Human oral microbiome

Oxidative stress in the oral cavity is driven by individual-specific bacterial communities – Džunková – NPJ Biofilms and Microbiomes

Human gut microbiome

Alterations of the gut microbiome and plasma proteome in Chinese patients with adolescent idiopathic scoliosis – Shen – Bone

Animal experiments

Effect of gastric fluid aspiration on the lung microbiota of laboratory rats – Finn – Experimental Lung Research

Animal microbiome

Skin bacterial diversity is higher on lizards than sympatric frogs in tropical Australia – Weitzman – PeerJ

Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets – Poulsen – PLoS One

Plant, root, and soil microbiome

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis – Zhu – Environmental Science and Technology

Deforestation Impacts Network Co-occurrence Patterns of Microbial Communities in Amazon Soils – Khan – FEMS Microbiology Ecology

Review: VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes – Tyagi – Critical Reviews in Biotechnology

Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard – Liang – Microbiological Research

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential – Martins – Microbiome

Extemophile microbiome

Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities – Kalwasińska – Science of the Total Environment

Food microbiology

Preprint: Bacterial diversity and population dynamics during the fermentation of palm wine from Guerrero Mexico – Astudillo-Melgar – BioRxiv

Assessment of biogas production and microbial ecology in a high solid anaerobic digestion of major California food processing residues – Achmon – Bioresource Technology Reports

Science, publishing, and career

Preprint: Participation and Motivations of Grant Peer Reviewers: A Comprehensive Survey of the Biomedical Research Community – Gallo – BioRxiv

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

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