November 7, 2018

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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October 22, 2018

Today’s digest features a novel fecal species [Prevotella rara sp. nov.], the virome in feces from healthy children from three Amerindian villages with minimal outside contact, a review of statistical challenges in the design and analysis of longitudinal microbiome studies, and more. Happy reading!

Gut microbiome

*Prevotella rara sp. nov., isolated from human faeces – Boris A. Efimov – International Journal of Systematic and Evolutionary Microbiology

Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women – Eveliina Munukka – Frontiers in Microbiology

Association of serum bilirubin in newborns affected by jaundice with gut microbiota dysbiosis – Shaoming Zhou – The Journal of Nutritional Biochemistry

Review: Gut-microbiota-on-a-chip: an enabling field for physiological research – Grissel Trujillo-de Santiago – MicroPhysiological Systems

Review: Microbiome and diabetes: Where are we now? – Natalia G. Vallianou – Diabetes Research and Clinical Practice

Oral microbiome

Review: Biology of Oral Streptococci – Jacqueline Abranches – Microbiology Spectrum

Animal and plant microbiome

Review: How Can We Define “Optimal Microbiota?”: A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture – Wakako Ikeda-Ohtsubo – Frontiers in Nutrition

Water microbiome

Temperature-controlled thermophilic bacterial communities in hot springs of western Sichuan, China – Jie Tang – BMC Microbiology

In situ production of core and intact bacterial and archaeal tetraether lipids in groundwater – Su Ding – Organic Geochemistry

Phages and viruses

*Complex virome in feces from Amerindian children in isolated Amazonian villages – Juliana D. Siqueira – Nature Communications

Bioinformatics

*Preprint Review: Statistical Considerations in the Design and Analysis of Longitudinal Microbiome Studies – Justin D Silverman – bioRxiv

17 October,​ 2018

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 14, 2018

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 11, 2018

The effects of chronic ethanol ingestion on the fruit fly microbiota, engineering the mosquito microbiota to produce an antiplasmodial effector, how temperature change affects an ecosystems biodiversity and function.

General microbiome

Changes in temperature alter the relationship between biodiversity and ecosystem functioning – Francisca C García – PNAS

Human respiratory microbiome

Respiratory Microbiota Predicts Clinical Disease Course of Acute Otorrhea in Children With Tympanostomy Tubes – Wing Ho Man – The Pediatric Infectious Disease Journal

Human oral microbiome

Carious status and supragingival plaque microbiota in hemodialysis patients – Qi Yue – PLOS ONE

Human gut microbiome

Review: Fecal Microbiota Transplantation for the Management of Clostridium difficile Infection – Raghavendra Paknikar – Surgical Infections

Review: Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients – Chih-Yu Yang – Nephrology

Animal experiments

Risks Related to High-Dosage Recombinant Antimicrobial Peptide Microcin J25 in Mice Model: Intestinal Microbiota, Intestinal Barrier Function and Immune Regulation – Haitao Yu – Journal of Agricultural and Food Chemistry

Microbial Changes and Host Response in F344 Rat Colon Depending on Sex and Age Following a High-Fat Diet – Sun Min Lee – Frontiers in Microbiology

Animal microbiome

Pre-print: Chronic ethanol ingestion impairs Drosophila melanogaster health in a microbiome-dependent manner – James Angus Chandler – bioRxiv

Blood meal-induced inhibition of vector-borne disease by transgenic microbiota – Jackie L Shane – Nature Communications

Plant, root, and soil microbiome

Friends or foes in the rhizosphere: traits of fluorescent Pseudomonas that hinder Azospirillum brasilense growth and root colonization – Guillermo A Maroniche – FEMS Microbiology Ecology

Water and extremophile microbiome

Seasonal variation of extracellular enzymatic activity in marine snow-associated microbial communities and their impact on the surrounding water – Ingrid Ivančić – FEMS Microbiology Ecology

Food microbiology

Comparative evaluation of spoilage-related bacterial diversity and metabolite profiles in chilled beef stored under air and vacuum packaging – Ahmad Rois Mansur – Food Microbiology

Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl – Ilenys M Pérez-Díaz – Food Microbiology

Bioinformatics

Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo – Katherine A Dunn – Microbiome Analysis (Book)

Metabolomics

Targeted Metabolic Profiling Indicates Apple Rootstock Genotype-Specific Differences in Primary and Secondary Metabolite Production and Validate Quantitative Contribution From Vegetative Growth – Rachel Leisso – Frontiers in Plant Science

Techniques

Analyzing Metabolic Pathways in Microbiomes – Mobolaji Adeolu – Microbiome Analysis (Book)

More microbes

Prevalence of Yersinia Species in the Ileum of Crohn’s Disease Patients and Controls – Guillaume Le Baut – Frontiers in Cellular and Infection Microbiology

October 9, 2018

 

Pregnancy and early life

Gut Microbiota and Body Weight in School‐Aged Children: The KOALA Birth Cohort Study – Catherine A. Mbakwa – Obesity

Multi-site human microbiome

Grow With the Challenge – Microbial Effects on Epithelial Proliferation, Carcinogenesis, and Cancer Therapy – Jakob von Frieling – Frontiers in Microbiology

Human respiratory microbiome

Microbiome dataset from the upper respiratory tract of patients living with HIV, HIV/TB and TB from Myanmar – Kyaw SoeHtuna – Data in Brief

Human skin microbiome

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

Human vaginal microbiome

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

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Animal experiments

Protective effects of a triple-fermented barley extract (FBe) against HCl/EtOH-induced gastric mucosa damage in mice – Jong‐Min Lim – Food Science & Nutrition

Guarana (Paullinia cupana Mart.) alters gut microbiota and modulates redox status, partially via caffeine in Wistar rats – Alexandre Kleber Silveira – Phytotherapy Research

Gut microbiota–dependent modulation of innate immunity and lymph node remodeling affects cardiac allograft outcomes – Jonathan S. Bromberg – JCI Insight

Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny – T Swierts – FEMS Microbiology Ecology

In vitro experiments

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

Animal microbiome

Tissue-specific immune responses to Vibrio sp. infection in mussels (Perna canaliculus): A metabolomics approach – Thao V. Nguyen – Aquaculture

Conserved microbiota among young Heliconius butterfly species – Bas van Schooten – Peer J

Microbial community composition of nest-carton and adjoining soil of the ant Lasius fuliginosus and the role of host secretions in structuring microbial communities – Pina Brinker – Fungal Ecology

Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea) – Wen Wang – Microbiology Open

Microbiome and Blood Analyte Differences Point to Community and Metabolic Signatures in Lean and Obese Horses – Amy S. Biddle – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Determinants of Deadwood-Inhabiting Fungal Communities in Temperate Forests: Molecular Evidence From a Large Scale Deadwood Decomposition Experiment – Witoon Purahong –

Induction of defense mechanisms involved in disease resistance of onion blight disease caused by Botrytis allii – Mohamed M A Hussein – Egyptian Journal of Biological Pest Control

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

The impacts of deglaciation and human activity on the taxonomic structure of prokaryotic communities in Antarctic soils on King George Island – E.V. Pershina – Antarctic Science

Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific – Gian Maria Niccolò Benucci – Microbial Ecology

Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China – Xiaolan Lin – Microbial Ecology

Draft Genome Sequence of Burkholderia reimsis BE51, a Plant-Associated Bacterium Isolated from Agricultural Rhizosphere – Qassim Esmaeel – Microbiology Resource Announcements

Rhizosphere microbial response to multiple metal(loid)s in different contaminated arable soils indicates crop-specific metal-microbe interactions – Weimin Sun – Applied and Environmental Microbiology

Draft Genome Sequence of Burkholderia reimsis BE51, a Plant-Associated Bacterium Isolated from Agricultural Rhizosphere – Qassim Esmaeel – Microbiology Resource Announcements

Rhizosphere microbial response to multiple metal(loid)s in different contaminated arable soils indicates crop-specific metal-microbe interactions – Weimin Sun – Applied and Environmental Microbiology

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

Draft Genome Sequence of Pseudomonas sp. Strain MWU13-2860, Isolated from a Wild Cranberry Bog in Truro, Massachusetts – Ghazal Ebadzadsahrai – Microbiology Resource Announcements

Biotechnological potential of plant growth-promoting bacteria from the roots and rhizospheres of endemic plants in ironstone vegetation in southeastern Brazil – Érica Barbosa Felestrino – World Journal of Microbiology and Biotechnology

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

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

Spatial variability of microbial communities in a fractured sedimentary rock matrix impacted by a mixed organics plume – Gláucia da P. Lima – Journal of Contaminant Hydrology

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions – Xihui Xu – The ISME Journal

Root growth, function and rhizosphere microbiome analyses show local rather than systemic effects in apple plant response to replant disease soil – Maik Lucas – PLOS One

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

Soil microbial community structure in the rhizosphere of Robinia pseudoacacia L. seedlings exposed to elevated air temperature and cadmium-contaminated soils for 4 years – X.Jia – Science of the Total Environment

Water and extremophile microbiome

Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments – Steffi Genderjahn – Frontiers in Microbiology

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

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

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

Characterization of a novel bacteriophage specific to Exiguobacterium indicum isolated from a plateau eutrophic lake – Shiying Zhang – Journal of Basic Biology

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

The impact of iron nanoparticles on technetium-contaminated groundwater and sediment microbial communities – Laura Newsome – Journal of Hazardous Materials

Microbial diversity and antibiotic resistance in a final effluent-receiving lake – Kinga Bondarczuk – Science of the Total Environment

Reduced chlorine in drinking water distribution systems impacts bacterial biodiversity in biofilms – Claire Bertelli – Frontiers in Microbiology

Microbial Ecology

A Microbial Saga: How to Study an Unexpected Hot Spot of Microbial Biodiversity from Scratch? – Valeria Souza – Cuatro Ciénegas Ecology, Natural History and Microbiology

How Divergent Is the Cuatro Ciénegas Oasis? Genomic Studies of Microbial Populations and Niche Differentiation – Zulema Gomez-Lunar – Cuatro Ciénegas Ecology, Natural History and Microbiology

Trace metals supplementation enhanced microbiota and biohythane production by two-stage thermophilic fermentation – Chonticha Mamimin – International Journal of Hydrogen Energy

Microcosms and Mesocosms: A Way to Test the Resilience of Microbial Communities in Cuatro Ciénegas – Nguyen E. López-Lozano – Cuatro Ciénegas Ecology, Natural History and Microbiology

Resistome

Candida albicans biofilm–induced vesicles confer drug resistance through matrix biogenesis – Robert Zarnowski – PLOS One

Microbes in space

Comparing Spore Resistance of Bacillus Strains Isolated from Hydrothermal Vents and Spacecraft Assembly Facilities to Environmental Stressors and Decontamination Treatments – Vincenzo Zammuto – Mary Ann Liebert Publishers

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Probiotics / prebiotics

Understanding mode of action can drive the translational pipeline towards more reliable health benefits for probiotics – Michiel Kleerebezem – Current Opinion in Biotechnology

Systematic review with meta‐analysis: the efficacy of prebiotics, probiotics, synbiotics and antibiotics in irritable bowel syndrome – Alexander C. Ford – Alimentary Pharmacology and Therapeutics

Phages and viruses

Characterization of dog serum virome from Northeastern Brazil – M.N.Weber – Virology

Hyperdiverse Viral Communities in an Oligotrophic Oasis (Cuatro Ciénegas): Marine Affinities and Microgeographic Differentiation – P. Isa – Cuatro Ciénegas Ecology, Natural History and Microbiology

Bioinformatics

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes – I-Min A Chen – Nucleic Acids Research

Strain-GeMS: Optimized subspecies identification from microbiome data based on accurate variant modeling – Chongyang Tan – Bioinformatics

Strain-GeMS: Optimized subspecies identification from microbiome data based on accurate variant modeling – Chongyang Tan – Bioinformatics

 

 

4 October, 2018

Today’s digest is full of exciting wine and animal microbiome studies!😁🐌🍷

General Microbiome

Editorial: Microbe and host lipids.Nigou J. Biochimie

Obesity alters composition and diversity of the oral microbiota in patients with type 2 diabetes mellitus independently of glycemic control.Tam J. PLoS One

Impact of the preoperative use of synbiotics in colorectal cancer patients: A prospective, randomized, double-blind, placebo-controlled study. Polakowski CB

The time response of anaerobic digestion microbiome during an organic loading rate shock. Braz GHR. Applied Microbiology and Biotechnology

REVIEW: Childhood weight gain and oral microbiota.Greenhill C. Nature Reviews Endocrinology

Glycan recognition at the saliva – Oral microbiome interface.Cross BW, Ruhl S. Cellular Immunology.

Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis. Lueschow SR. PLoS One

Direct Utilization of Organic Nitrogen by Phytoplankton and Its Role in Nitrogen Cycling Within the Southern California Bight. Morando M. Frontiers in Microbiology.

Persistence and reversal of plasmid-mediated antibiotic resistance.Lopatkin AJ. Nature Communications

Gut Microbiome

REVIEW: Effects of Metabolites Derived From Gut Microbiota and Hosts on Pathogens.Li Z.Frontiers in Cellular and Infection Microbiology

Food and Wine Microbiome

The effect of sulfur dioxide addition at crush on the fungal and bacterial communities and the sensory attributes of Pinot gris wines. Morgan SC. International Journal of Food Microbiology

Techniques

Comparison of sampling methods for profiling cervicovaginal microbiome in rhesus macaques. Schmidt BA. Journal of  Medical Primatology.

Qiita: rapid, web-enabled microbiome meta-analysis.Gonzalez A. Nature Methods

Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.Rotimi AM. BMC Bioinformatics

Animal Microbiome and Experiments

White spot syndrome virus (WSSV) infection impacts intestinal microbiota composition and function in Litopenaeus vannamei.Wang Jl; Fish and Shellfish Immunology

Dietary or supplemental fermentable fiber intake reduces the presence of Clostridium XI in mouse intestinal microbiota: The importance of higher fecal bacterial load and density.Zheng W. PLoS One

<i>Diplogastrellus</i> nematodes are sexually transmitted mutualists that alter the bacterial and fungal communities of their beetle host.Ledón-Rettig CC. PNAS

The response of ruminal fermentation, epithelium-associated microbiota, and epithelial barrier function to severe feed restriction in pregnant ewes.Hu F. Journal of Animal Science

Rabbit Microbiota Changes Throughout the Intestinal Tract. Velasco-Galilea M. Frontiers in Microbiology

Antibiotic treatment of rat dams affects bacterial colonization and causes decreased weight gain in pups. Tulstrup MV. Communications Biology

Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages.Black EM. Microbiology Open

Effect of Different Disinfectants on Bacterial Aerosol Diversity in Poultry Houses.Jiang L. Frontiers in Microbiology

Effects of organic acid and medium chain fatty acid blends on the performance of sows and their piglets.  Lan R. Animal Science Journal

Microbial community composition and electricity generation in cattle manure slurry treatment using microbial fuel cells: effects of inoculum addition. Xie B. Environmental Science and Pollution Research

Plant, Soil, and Air Microbiome

Response of soil enzymes, functional bacterial groups, and microbial communities exposed to sudan I-IV. Teng Y. Ecotoxicology and Environmental Safety

Erratum: “Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification”.Salvetti E. Applied and Environmental Microbiology

Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado. de Araujo ASF. Communications Biology

Application of phosphate solubilizing bacteria in immobilization of Pb and Cd in soil.Yuan Z. Environmental Science and Pollution Research

Inland Waters and Marine Microbiome

Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities.Dittmann KK. Environmental Microbiology Reports

Novel T4 bacteriophages associated with black band disease in corals.Buerger P. Environmental Microbiology

Environmental conditions affect activity and associated microorganisms of marine sponges.Batista D. Marine Environmental Research

The link between the microbial ecology, gene expression, and biokinetics of denitrifying polyphosphate-accumulating systems under different electron acceptor combinations.Vieira A. Applied Microbiology and Biotechnology

Antibiotics/Probiotics

Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes. Cairns J. Communications Biology

Metabolome/ Proteomics

Metaproteomics Study of the Gut Microbiome.Lai LA. Methods Molecular Biology: Functional Proteomics

COMMENTARY: Making the Case for Functional Proteomics. Perkins RC. Methods Molecular Biology: Functional Proteomics

REVIEW:Metabolome analysis for investigating host-gut microbiota interactions.Chen MX. Journal of Formosan Medical Association