Category Archives: Fungi

December 15, 2018

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Colonizing FMT patients with donor bacteriophages, the microbial communities of tigers, fruit bats, hemlocks, and rainbow trout, a review on the advances in urinary microbiome research.

Multi-site human microbiome

Review: The role of the microbiota in infectious diseases – Josie Libertucci – Nature Microbiology

Human skin microbiome

Ultraviolet radiation, both UVA and UVB, influences the composition of the skin microbiome – Erin M Burns – Experimental Dermatology

Human urinary microbiome

Review: Urobiome updates: advances in urinary microbiome research – Alan J Wolfe – nature Reviews Urology

Human gut microbiome

Pre-print: Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context – Monica Barone – bioRxiv

Difference in Pathomechanism Between Crohn’s Disease and Ulcerative Colitis Revealed by Colon Transcriptome – Lili Yang – Inflammatory Bowel Diseases

GABA-modulating bacteria of the human gut microbiota – Philip Strandwitz – Nature Microbiology

Impact of Individual Traits, Saturated Fat, and Protein Source on the Gut Microbiome – Jennifer M Lang – mBio

Animal experiments

Microbiome interactions shape host fitness – Alison L Gould – PNAS

Gut microbiota dysbiosis worsens the severity of acute pancreatitis in patients and mice – Yin Zhu – Journal of Gastroenterology

Microbiota-Derived Lactate Accelerates Intestinal Stem-Cell-Mediated Epithelial Development – Yong-Soo Lee – Cell Host & Microbe

A Microbiota-Derived Bacteriocin Targets the Host to Confer Diarrhea Resistance in Early-Weaned Piglets – Jun Hu – Cell Host & Microbe

Animal microbiome

Exploring variation in phyllosphere microbial communities across four hemlock species – Timothy J Rogers – Ecosphere

Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss) – Ryan M Brown – Fish & Shellfish Immunology

Metagenomic analysis of captive Amur tiger faecal microbiome – Fengping He – BMC Veterinary Research

Coordinated change at the colony level in fruit bat fur microbiomes through time – Oren Kolodny – Nature Ecology & Evolution

Plant, root, and soil microbiome

Remediation of deterioration in microbial structure in continuous Pinellia ternata cropping soil by crop rotation – Zhigui He – Candadian Journal of Microbiology

Plant compartment and genetic variation drive microbiome composition in switchgrass roots – Esther Singer – Environmental Microbiology Reports

Desert plant bacteria reveal host influence and beneficial plant growth properties – Abdul Aziz Eida – PLOS ONE

Water and extremophile microbiome

Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation – Phillipe M Rosado – The ISME Journal

Microbes in space

International Space Station conditions alter genomics, proteomics, and metabolomics in Aspergillus nidulans – Jillian Romsdahl – Applied Microbiology and Biotechnology

Phages and viruses

Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation – L A Draper – Microbiome

Metatranscriptomic Analysis and In Silico Approach Identified Mycoviruses in the Arbuscular Mycorrhizal Fungus Rhizophagus spp. – Achal Neupane – Viruses

The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics – Diane A Lima – Virus Research

Techniques

Detection of Bacteriophages: Sequence-Based Systems – Siân V Owen – Bacteriophages

More microbes

Pseudomonas aeruginosa quorum-sensing metabolite induces host immune cell death through cell surface lipid domain dissolution – Dingka Song – Nature Microbiology

December 14, 2018

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The microbiota of chigger mites and praying mantids, the prevalence of thermophiles in domestic water heaters, the bacteria that colonize and degrade centuries-old art.

General microbiome

Migration alters oscillatory dynamics and promotes survival in connected bacterial populations – Shreyas Gokhale – Nature Communications

Pre-print: A probabilistic model to identify the core microbial community – Thiago Gumiere – bioRxiv

Human oral microbiome

Pre-print: Correlation between the oral microbiome and brain resting state connectivity in smokers – Dongdong Lin – bioRxiv

Animal experiments

Host-targeted niclosamide inhibits C. difficile virulence and prevents disease in mice without disrupting the gut microbiota – John Tam – Nature Communications

Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets – Ann-Sofie Riis Poulsen – PLOS ONE

Animal microbiome

Bacterial microbiome of the chigger mite Leptotrombidium imphalum varies by life stage and infection with the scrub typhus pathogen Orientia tsutsugamushi – Loganathan Ponnusamy – PLOS ONE

The hindgut microbiota of praying mantids is highly variable and includes both prey-associated and host-specific microbes – Kara A Tinker – PLOS ONE

Plant, root, and soil microbiome

Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient – Max E. Schön – PLOS ONE

Treating wheat seeds with neonicotinoid insecticides does not harm the rhizosphere microbial community – Yaofa Li – PLOS ONE

Water and extremophile microbiome

Pre-print: An archaeal symbiont-host association from the deep terrestrial subsurface – Katrin Schwank – bioRxiv

Marine-Derived Fungi: Promising Candidates for Enhanced Bioremediation – Anjana K Vala – Approaches in Bioremediation

Built environment

Biogeography of thermophiles and predominance of Thermus scotoductus in domestic water heaters – Regina L Wilpiszeski – Extremophiles

Probiotics/prebiotics

Dopamine production in Enterococcus faecium: A microbial endocrinology-based mechanism for the selection of probiotics based on neurochemical-producing potential – Daniel Villageliú – PLOS ONE

Phages and viruses

A chemical defence against phage infection – Sarah Kronheim – Nature

Bioinformatics

Pre-print: Metagenome-wide measurement of protein synthesis in the human fecal microbiota using MetaRibo-Seq – Brayon J Fremin – bioRxiv

Pre-print: Large-scale analyses of human microbiomes reveal thousands of small, novel genes and their predicted functions – Hila Sberro – bioRxiv

Metabolomics

Rumen and plasma metabolomics profiling by UHPLC-QTOF/MS revealed metabolic alterations associated with a high-corn diet in beef steers – You Yang – PLOS ONE

More microbes

Pre-print: Real-time capture of horizontal gene transfers from gut microbiota by engineered CRISPR-Cas acquisition – Christian Munck – bioRxiv

Bacteria art

A detailed look at the microorganisms that colonize, and degrade, a 400-year-old painting – ScienceDaily

Inside SAIC’s Bio Art Lab, where art is life—literally – Paul Dailing – Chicago Reader

Across China: Medical students paint “Mona Lisa” with bacteria – Xinhua Net

Science, career, and publishing

Pre-print: Non-academic employability of life science PhDs: the importance of training beyond the bench – Sohyoung Her – bioRxiv

November 29, 2018

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Today’s digest covers updates on human milk oligosaccharides, microbial life in cemetry, intestinal resistome, and benefits of intermittent fasting in human cohort and the gut microbiota in mice.

General microbiome
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017 – Rashmi Sinha – Microbiome

Human gut microbiome

Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection – Sasirekha Ramani – Nature Communications

Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions – Caspar Bundgaard-Nielsen – Scientific Reports

In-and-Out Molecular Changes Linked to the Type 2 Diabetes Remission after Bariatric Surgery: An Influence of Gut Microbes on Mitochondria Metabolism – Paulina Samczuk – International Journal of Molecular Sciences

Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease – Takayuki Imai – Journal of Gastroenterology

Gut microbiota features of the geographically diverse Indian population – Sudarshan A. Shetty – BioRxiv

Animal experiments

Intermittent administration of a fasting-mimicking diet intervenes in diabetes progression, restores β cells and reconstructs gut microbiota in mice – Siying Wei – Nutrition and Metabolism

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – Microbiome

Mouse intestinal microbiota reduction favors local intestinal immunity triggered by antigens displayed in Bacillus subtilis biofilm – Cédric M. Vogt – Microbial Cell Factories

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus – Alison Vrbanac – BMC Microbiology

Use of next generation sequencing to investigate the microbiota of experimentally induced wounds and the effect of bandaging in horses – Louis J. Kamus – PlosOne

Soil microbiome

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments – Nina Dombrowski – Nature Communications

Built Environment

Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments – Akebe Luther King Abia – Science of the Total Environment

Techniques

Prediction of the intestinal resistome by a three-dimensional structure-based method – Etienne Ruppé – Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling – Ching Jian – BioRxiv

Microbes in the news

Poo found on every McDonald’s touchscreen tested – Metro

Non-microbiology picks

Effects of intermittent and continuous calorie restriction on body weight and metabolism over 50 wk: a randomized controlled trial – Ruth Schübel – The American Journal of Clinical Nutrition

 

November 28, 2018

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Influence of bacterial biofilms from vats on cheese characteristics, the fecal virome of wild ducks, variation in fungal diversity associated with olive trees.

Pregnancy and early life

Review: Strategies for the Preservation, Restoration and Modulation of the Human Milk Microbiota. Implications for Human Milk Banks and Neonatal Intensive Care Units – Leónides Fernández – Frontiers in Microbiology

Human vaginal microbiome

Vaginal microbiome in pregnant women according to trimester and its association with preterm birth: critical appraisal of a cross-sectional study – Dimitrios Papoutsis – Obstetrics & Gynecology Science

Human gut microbiome

Microbial-Host Interactions in Inflammatory Bowel Disease, Functional Bowel Disease, Obesity and Obesity-Related Metabolic Disease – Shailja C Shah – Gastroenterology

Animal experiments

Bioactive Food Abates Metabolic and Synaptic Alterations by Modulation of Gut Microbiota in a Mouse Model of Alzheimer’s Disease – Tauqeerunnisa Syeda – Journal of Alzheimer’s Disease

Extract of the Microalga Nitzschia laevis Prevents High-Fat-Diet Induced Obesity in Mice by Modulating the Composition of Gut Microbiota – Bingbing Guo

Effects of Taste Signaling Protein Abolishment on Gut Inflammation in an Inflammatory Bowel Disease Mouse Model – Ya-Wen Du – Journal of Visualized Experiments

Animal microbiome

Use of next generation sequencing to investigate the microbiota of experimentally induced wounds and the effect of bandaging in horses – Louis J Kamus – PLOS ONE

Plant, root, and soil microbiome

The chirality of imazethapyr herbicide selectively affects the bacterial community in soybean field soil – Hao Wu – Environmental Science and Pollution Research

Genome‐Wide Association studies on the phyllosphere microbiome: embracing complexity in host‐microbe interactions – Kathleen Beilsmith – The Plant Journal

Invasive plants differentially affect soil biota through litter and rhizosphere pathways: a meta‐analysis – Pei Zhang – Ecology Letters

Analysis of the community composition and bacterial diversity of the rhizosphere microbiome across different plant taxa – Shaonan Lei – MicrobiologyOpen

Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars – Patrick Materatski – Fungal Biology

Water and extremophile microbiome

Pre-print: Metagenomic Insights Unveil the Dominance of Undescribed Actinobacteria in Pond Ecosystem of an Indian Shrine – Radhakrishnan Manikkam – bioRxiv

Built environment

A procedure for identifying chemical and biological risks for books in historic libraries based on microclimate analysis – Eva Schito – Journal of Cultural Heritage

Food microbiology

Influence of the early bacterial biofilms developed on vats made with seven wood types on PDO Vastedda della valle del Belìce cheese characteristics – Raimondo Gaglio – International Journal of Food Microbiology

Probiotics/prebiotics

Microbial consortia: promising probiotics as plant biostimulants for sustainable agriculture – Sheridan L Woo – Frontiers in Plant Science

Phages and viruses

Fecal virome composition of migratory wild duck species – Luis Alfonso Ramírez-Martínez – PLOS ONE

November 7, 2018

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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

October 30, 2018

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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

17 October,​ 2018

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General Microbiome

ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling.Zhang C. Frontiers in Physiology

Skin Microbiome

The emerging role of skin microbiome in atopic dermatitis and its clinical implication.Stalder JF. Journal of Dermatological Treatment

Oral Microbiome

Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes.Hardy K. Environmental Anthropology

Gut Microbiome

Gut Microbial Product Predicts Cardiovascular Risk in Chronic Kidney Disease Patients.Jadoon A. American Journal of Nephrology

Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes.Luis AS. Current Opinions in Chemical Biology

Vitamin D and the gut microbiome: a systematic review of in vivo studies.Waterhouse M. European Journal of Nutrition

A Review: The Fate of Bacteriocins in the Human Gastro-Intestinal Tract: Do They Cross the Gut-Blood Barrier?Dicks LMT. Frontier in Microbiology

Precision identification of diverse bloodstream pathogens in the gut microbiome.Tamburini FB. Nature Medicine

Animal Microbiome

Rickettsia diversity in southern Africa: A small mammal perspective.Essbauer S. Tick and Tick-Borne Disease

Response of Gut Microbiota to Dietary Fiber and Metabolic Interaction With SCFAs in Piglets.Liu B. Frontier in Microbiology

Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau.Bai X. Frontier in Microbiology

Microbiome-assisted carrion preservation aids larval development in a burying beetle.Shukla SP. PNAS

The gut microbiome: Relationships with disease and opportunities for therapy.Durack J. Journal of Experimental Medicine

Water Microbiome

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater.Fan XY. Bioresource Technology

Fine-scale spatial homogenization of microbial habitats: a multivariate index of headwater wetland complex condition.Moon JB. Ecological Applications

Functional and taxonomic classification of a greenhouse water drain metagenome.López-Leal G. Standards in Genomic Sciences

Plant and Soil Microbiome

Changes in the soil microbial communities of alpine steppe at Qinghai-Tibetan Plateau under different degradation levels.Zhou H. Science of the Total Environment

Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation.Beckmann S. ISME Journal

October 15, 2018

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In today’s Digest, you’ll find a method for museum collections to identify helminth communities in small mammals, new results in the urinary and vaginal microbiome, the effects of HIV PrEP and broccoli on the gut microbiome, and fungal communities associated with plant roots. Happy reading!

General microbiome
Review: Probiotics importance and their immunomodulatory properties. – Bahman Yousefi – Journal of Cellular Physiology

Review: An insight into gut microbiota and its functionalities. – Atanu Adak – Cellular and Molecular Life Sciences

Gut-brain axis
Review: A primer on investigating the role of the microbiome in brain and cognitive development. – Caroline Kelsey – Developmental Psychobiology

Human vaginal microbiome
Preprint: Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota – Charlotte van der Veer – bioRxiv

Human urinary microbiome
Community profiling of the urinary microbiota: considerations for low-biomass samples. – Lisa Karstens – Nature Reviews Urology

Human gut microbiome
Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus and increased Erysipelotrichaceae in rectal microbiota. – Michael P. Dubé – Scientific Reports

Broccoli consumption affects the human gastrointestinal microbiota – Jennifer L. Kaczmarek – The Journal of Nutritional Biochemistry

Intestinal dysbiosis in Inflammatory Bowel Disease associated with primary immunodeficiency. – Harry Sokol – Journal of Allergy and Clinical Immunology

Chronic kidney disease after 5/6 nephrectomy disturbs the intestinal microbiota and alters intestinal motility. – Kazuhiro Nishiyama – Journal of Cellular Physiology

Animal microbiome
Museum metabarcoding: a novel method revealing gut helminth communities of small mammals across space and time. – Stephen E. Greiman – International Journal for Parasitology

Showcasing the role of seawater in bacteria recruitment and microbiome stability in sponges. – Marta Turon – Scientific Reports

Animal experiments
Microcapsule of sweet orange essential oil changes gut microbiota in diet-induced obese rats. – Dahu Li – Biochemical and Biophysical Research Communications

Changes in ruminal and reticular pH and bacterial communities in Holstein cattle fed a high-grain diet. – Yo-Han Kim – BMC Veterinary Research

Plant, root, and soil microbiome
Dibutyl phthalate contamination remolded the fungal community in agro-environmental system – Xiao Kong – Chemosphere

Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in Arabidopsis thaliana – Izabela Fabiańska – New Phytologist

Water and extremophile microbiome
Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System. – I. Mania – Microbial Ecology

Preprint: Response of extremophile microbiome to a rare rainfall reveals a two-step adaptation mechanism – Gherman Uritskiy – bioRxiv

Bioinformatics
Preprint: Nomenclature Errors in Public 16S rRNA Gene Reference Databases – Kyle James Lesack – bioRxiv

October 14, 2018

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General microbiome

16S rRNA Gene Analysis with QIIME2 – Michael Hall, Microbiome Analysis

Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt – Gavin M. Douglas, Microbiome Analysis

Single-Cell Genomics of Microbial Dark Matter – Christian Rinke, Microbiome Analysis

An ecosystem framework for understanding and treating disease – Michael E. Hochberg, Foundation for Evolution, Medicine, and Public Health

Diet, Gut Microbes and Host Mate Choice – Philip T. Leftwich, BioEssays

Pregnancy and early life

Methods and Strategies to Examine the Human Breastmilk Microbiome – Lauren LeMay-Nedjelski, Microbiome Analysis

Multi-site human microbiome

Potential mechanisms linking gut microbiota and portal hypertension – Gyorgy Baffy, Liver International

Enlisting commensal microbes to resist antibiotic-resistant pathogens –  James W. Keith, Journal of Experimental Medicine

Human oral microbiome

Oral mucosa-on-a-chip to assess layer-specific responses to bacteria and dental materials – Christopher Rahimi, Biomicrofluidics

The effect of breastmilk and saliva combinations on the in vitro growth of oral pathogenic and commensal microorganisms – E. L. Sweeney, Scientific Reports

Human skin microbiome

A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes – David L. A. Wood, mBio

Human gut microbiome

The microbiome of Crohn’s disease aphthous ulcers – Claire L. O’Brien, Gut Pathogens

Gut microbiome can be restored without adverse events after Helicobacter pylori eradication therapy in teenagers – Takuji Gotoda, Helicobacter

Animal microbiome

Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere – Alejandra Hernandez-Agreda, mBio

Host differentiation and compartmentalization of microbial communities in the azooxanthelate cupcorals Tubastrea coccinea and Rhizopsammia goesi in the Caribbean – Aschwin H. Engelen, Frontiers in Microbiology

Comparison of intestinal microbes in female and male Chinese concave‐eared frogs (Odorrana tormota) and effect of nematode infection on gut bacterial communities – Yilin Shu, Microbiology Open

Change in the intestinal bacterial community structure associated with environmental microorganisms during the growth of Eriocheir sinensis – Chenhe Wang, Microbiology Open

Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging – Marie Lisandra Zepeda Mendoza, Acta Veterinaria Scandinavica

Animal experiments 

Fecal Microbiota Transplantation Beneficially Regulates Intestinal Mucosal Autophagy and Alleviates Gut Barrier Injury – Saisai Cheng, mSystems

Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows – Gareth Frank Difford, Plos Genetics

Inhibitory effects of dietary soy isoflavone and gut microbiota on contact hypersensitivity in mice – Takao Nagano, Food Chemistry

Lichen microbiome

Plasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiota – Tomislav Cernava, ISME

Plant, root, and soil microbiome

Short-term effect of Eucalyptusplantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange – Caroline A. Cuer, Scientific Reports

Microbial community structure and functional potential of lava-formed Gotjawal soils in Jeju, Korea – Jong-Shik Kim, Plos One

Diversity of fungi and bacteria in species-rich grasslands increases with plant diversity in shoots but not in roots and soil – Diana Navrátilová, FEMS Microbiology Ecology

Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas – Maarten Van Geel, FEMS Microbiology Ecology

Influence of triazole pesticides on tillage soil microbial populations and metabolic changes – Praveen Satapute, Science of The Total Environment

Soil Nutrient Status and Microbial Communities as Influenced by Bio-Fuel Trees Plantation – Agnes Imoya P. O., Environment and Ecology

Various Phyllosphere and Soil Bacterial Communities of Natural Grasses and the Impact Factors in a Copper Tailings Dam – Tong Jia, Current Microbiology

Effects of wine-cap Strophariacultivation on soil nutrients and bacterial communities in forestlands of northern China – Sai Gong, PeerJ

Effect of pH and temperature on microbial community structure and carboxylic acid yield during the acidogenic digestion of duckweed – Ozgul Calicioglu, Biotechnology for Biofuels

Trichoderma harzianum T-22 and BOL-12QD inhibit lateral root development of Chenopodium quinoa in axenic co-culture – Oscar M. Rollano-Peñaloza, Cogent Biology

Water, wastewater, and extremophile microbiome

Microbial communities in the nepheloid layers and hypoxic zones of the Canary Current upwelling system – Stefan Thiele, Microbiology Open

The effects of litter quality and living plants on the home-field advantage of aquatic macrophyte decomposition in a eutrophic urban lake, China – Van Biak Luai, Science of The Total Environment

The microbiome and antibiotic resistance in integrated fishfarm water: Implications of environmental public health – Gary Klase, Science of The Total Environment

Changes in the drinking water microbiome: effects of water treatments along the flow of two drinking water treatment plants in a urbanized area, Milan (Italy) – Antonia Bruno, Frontiers in Microbiology

Organic particles: heterogeneous hubs for microbial interactions in aquatic ecosystems – Mina Bizic-Ionescu, Frontiers in Microbiology

Importance of denitrification driven by the relative abundances of microbial communities in coastal wetlands – Yan Zhang, Environmental Pollution

A nearly uniform distributional pattern of heterotrophic bacteria in the Mariana Trench interior – Jiwei Tian, Deep Sea Research Part I: Oceanographic Research Papers

Patterns of permissiveness towards broad host range plasmids in microbial communities across the urban water cycle in Europe – Arnaud Dechesne, Abstract from 17th International Symposium on Microbial Ecology

Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP – Ana C. Reis, Applied Microbiology and Biotechnology

Molecular and microbiological insights on the enrichment procedures for the isolation of petroleum degrading bacteria and fungi – Giulia Spini, Frontiers in Microbiology

Microbial Ecology of South Florida Surface Waters: Examining the Potential for Anthropogenic Influences – Chase P. Donnelly, HCNSO Student Theses and Dissertations

Antarctic heterotrophic bacterium Hymenobacter nivis P3Tdisplays light‐enhanced growth and expresses putative photoactive proteins – Mia Terashima, Environmental Microbiology Reports

Microbial genomics

Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing – Robert Dyrdak, bioRxiv

Leveraging single-cell genomics to expand the fungal tree of life – Steven R. Ahrendt, Nature Microbiology

Microbes in space

Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere – Patricia Fajardo-Cavazos, Scientific Reports

Food microbiology

Metagenomic analysis and the functional profiles of traditional fermented pork fat ‘sa-um’ of Northeast India – Surajit De Mandal, AMB Express

Probiotics / prebiotics

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

In Vitro Fermentation of Selected Prebiotics and Their Effects on the Composition and Activity of the Adult Gut Microbiota – Sophie Fehlbaum, International Journal of Molecular Sciences

Techniques

Assessing the ratio of Bacillus spores and vegetative cells by shotgun proteomics – Charlotte Mappa, Environmental Science and Pollution Research

 

October 10, 2018

Posted on by

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