Category Archives: Water microbiome

July 19, 2017

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Today’s digest is a long one! There is high diversity of studies, with a high abundance of gut microbiome studies, a few publications on fecal transplant, and some very interesting early life/pregnancy/mother-infant science.  A normal serving of animal studies, of course a nice colony of environmental microbial studies, and a study reporting the presence of bacteria in Alzheimer’s post-mortem brains.

Events and jobs

Postdoctoral research fellow in translational microbiome research – Department of Microbiology, Tumor and Cell Biology (MTC) at Karolinska Institutet

General microbiome

Commensal bacteria modulate the tumor microenvironment – Theofilos Poutahidis – Cancer Letters

[Review]  The human microbiome – Hubert E. Blum – Advances in Medical Sciences

Microbiome and Metabolome Data Integration Provides Insight Into Health and Disease – Michael Shaffer – Translational Research

Metabolic potential and taxonomic assessment of bacterial community of an environment to chronic industrial discharge – Neelam Devpura – International Biodeterioration & Biodegradation

Impact of the Microbiota on Bacterial Infections during Cancer Treatment – Jessica Galloway-Peña – Trends in Microbiology

Pregnancy and early life

** The Bacterial Ecosystem of Mother’s Milk and Infant’s Mouth and Gut – Elana Biagi – Frontiers in Microbiology | Evolutionary and Genomic Microbiology

* What’s Normal? Immune Profiling of Human Milk from Healthy Women Living in Different Geographical and Socioeconomic Settings – Lorena Ruiz – Frontiers in Immunology | Nutritional Immunology

Microbiome Associated with Severe Caries in Canadian First Nations Children – M. Agnello – Journal of Dental Research

* Bacterial communities found in placental tissues are associated with severe chorioamnionitis and adverse birth outcomes – Ronan M. Doyle – PLoS One

Human oral microbiome

Characterization of Oral Microbiota in Removable Dental Prosthesis Users: Influence of Arterial Hypertension – Leila Maria Marchi-Alves – BioMed Research International

Human vaginal microbiome

The association between ethnicity and vaginal microbiota composition in Amsterdam, the Netherlands – Hanneke Borgdorff – PLoS One

Human nearly-sterile sites

** 16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain – David C. Emery – Frontiers in Aging Neuroscience

Human gut microbiome

The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia – Sayaka Fujio-Vejar – Frontiers in Microbiology | Microbial Symbioses

*[Review] Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients – Hoda M. Eid – Frontiers in Pharmacology | Ethnopharmacology

MOLECULAR CHARACTERIZATION OF FECAL MICROBIOTA OF HEALTHY CHINESE TOBACCO SMOKER SUBJECTS IN SHAANXI PROVINCE, XI’AN CHINA – Ishaq HM – Journal of Ayub Medical College

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study – Hemmings, Sian M.J – Psychosomatic Medicine

The Impact of Gut Microbiota on Gender-Specific Differences in Immunity – Floris Fransen – Frontiers in Immunology | Nutritional Immunology

Involvement of gut microbiota in the association between gastrointestinal motility and 5‑HT expression/M2 macrophage abundance in the gastrointestinal tract – Mo Yang – Molecular Medicine Reports

Correspondence: Fecal Microbiota Transplant from a Rational Stool Donor Improves Hepatic Encephalopathy: A Randomized Clinical Trial – Benjamin H Mullish – Hepatology

Going to the Bank: Fecal Microbiota Transplantation in Pediatrics – Elaine Barfield – Clinical Pediatrics

INTERRELATIONSHIPS BETWEEN GUT MICROBIOTA AND HOST: Paradigms, Role in Neurodegenerative Diseases and Future Prospects – Villarraso JC – CNS & Neurological Disorders Drug Targets

Faecal microbiota transplant: a novel biological approach to extensively drug-resistant organism-related non-relapse mortality – Innes AJ – Bone Marrow Transplantation

* Gut microbiota is critical for the induction of chemotherapy-induced pain – Shiqian Shen – Nature Neuroscience

Relationships between Gastrointestinal Microbiota and Blood Group Antigens – Anuhya Gampa – Physiological Genomics

[Masters Thesis] Evaluating the Effectiveness of Select Bacteria Against Clostridium difficile – Choquette, Kelsey Rose – Iowa State University, ProQuest Dissertations Publishing

* Potential and active functions in the gut microbiota of a healthy human cohort – Alessandro Tanca – Microbiome

[Letter to Editor] The necessity of gut microbiome characterization in diseases prevention and therapy – Sama Rezasoltani – Gastroenterology and Hepatology from Bed to Bench

[Review Article] The Intricate Interaction between Enteric Microbiota and Brain: Principles and Clinical Implications – Giovanni Gherardi – Journal of Digestive Diseases and Hepatology

Gut microbiota dysbiosis associated with glucose metabolism disorders and the metabolic syndrome in older adults – K Lippert – Beneficial Microbes

Animal experiments

Western Diet–Induced Dysbiosis in Farnesoid X Receptor Knockout Mice Causes Persistent Hepatic Inflammation after Antibiotic Treatment – Prasant K – The American Journal of Pathology

Grape pomace improves performance, antioxidant status, fecal microbiota and meat quality of piglets – I. Kafantaris – Animal

Animal microbiome

Microorganisms of the Intestinal Microbiota of Oncorhynchus Mykiss Produce Antagonistic Substances Against Bacteria Contaminating Food and Causing Disease in Humans – Lobos O – Italian Journal of Food Safety

Population-Specific Responses to Interspecific Competition in the Gut Microbiota of Two Atlantic Salmon (Salmo salar) Populations – Xiaoping He – Microbial Ecology

Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change – Cheng-Yu Chen – PLoS One

Vertically and horizontally transmitted microbial symbionts shape the gut microbiota ontogenesis of a skin-mucus feeding discus fish progeny – François-Étienne Sylvain – Scientific Reports

Microbiome overview in swine lungs – Franciele Maboni Siqueira – PLoS One

Plant, root, and soil microbiome

Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops – Zhaojin Chen – Ecotoxicology and Environmental Safety

Dynamics of Soil Bacterial Communities Over a Vegetation Season Relate to Both Soil Nutrient Status and Plant Growth Phenology – Davide Francioli – Microbial Ecology

* Microbial Populations of Stony Meteorites: Substrate Controls on First Colonizers – Alastair W. Tait – Frontiers in Microbiology | Extreme Microbiology

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil – Mengting M. Yuan – Global Change Biology

[PrePrint] Conditionally rare taxa contribute but do not account for prokaryotic community changes in soils – Rachel Kaminsky – bioRxiv

Water and extremophile microbiome 

Performance and bacterial community structure of a 10-years old constructed mangrove wetland – Tingting Tian – Marine Pollution Bulletin

A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields – Hai-liang Wang – PLoS One

Microbial Composition and Diversity Patterns in Deep Hyperthermal Aquifers from the Western Plain of Romania – Cecilia M. Chiriac – Microbiology of Aquatic Systems

Built environment

Pilot study to determine if microbial contamination levels in hospital washrooms are associated with hand drying method – Mark H. Wilcox – Journal of Hospital Infection

Probiotics / prebiotics

Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis – Pan Zhuang – BBA

Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic – Rebeca Martin – Frontiers in Microbiology | Food Microbiology

Bioinformatics

* Abundance estimation and differential testing on strain level in metagenomics data – Martina Fischer – Bioinformatics

Techniques

Development and Use of a Real-Time Quantitative PCR Method for Detecting and Quantifying Equol-Producing Bacteria in Human Faecal Samples and Slurry Cultures – Lucía Vázquez – Frontiers in Microbiology | Food Microbiology

Next-generation Sequencing of the DNA Virome from Fecal Samples – Monaco CL – Bio-protocol

Synthetic multispecies microbial communities reveals shifts in secondary metabolism and facilitates cryptic natural product discovery – Yutong Shi – Environmental Microbiology

Whole-genome sequencing of eukaryotes: From sequencing of DNA fragments to a genome assembly – K. S. Zadesenets – Russian Journal of Genetics

Microbes on the market

Microbiome Sequencing Services Market: trends, analysis, Overview, forecast up to 2021

Ed’s non-microbiology picks

Heavy metal accumulation by Saccharomyces cerevisiae cells armed with metal binding hexapeptides targeted to the inner face of the plasma membrane – Lavinia Liliana Ruta –Applied Microbiology and Biotechnology

Fracking can contaminate rivers and lakes with radioactive material, study finds

Subacute normobaric oxygen and hyperbaric oxygen therapy in drowning, reversal of brain volume loss: a case report – Paul G Harch – Medical Gas Research

No Effect of Commercial Cognitive Training on Neural Activity During Decision-Making – Joseph W. Kable – Journal of Neuroscience

Health Insurance Expansion and Incidence of Out‐of‐Hospital Cardiac Arrest: A Pilot Study in a US Metropolitan Community – Eric C. Stecker – Journal of the American Heart Association

17, July 2017

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In today’s digest, we learn more about how cloud-based computing is making it easier to analyses big datasets, and stochastic bottlenecks control bacterial colonization in animal host.

General Microbiome and Microbiology

New perspectives on dandruff and seborrheic dermatitis: lessons we learned from bacterial and fungal skin microbiota.

Paulino LC. European journal of dermatology

Harnessing microbiome‐based biotechnologies for sustainable mitigation of nitrous oxide emissions

Hu HW.Microbial Biotechnology

Human gut microbiome

Comparisons of Gut Microbiota Among Healthy Control, Patients With Conventional Adenoma, Sessile Serrated Adenoma, and Colorectal Cancer. Yoon H. Journal of Cancer Prevention

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. Xiong W. Microbiome

Assessing the impact of protein extraction methods for human gut metaproteomics

Zhang  X.Journal of Proteomics

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls

Stewart CJ. Microbiome

Animal and insect microbiome

Host–Microbe Interactions: Winning the Colonization Lottery

Lazzaro BP and GM Fox. Current Biology

Strategies for managing rival bacterial communities: lessons from burying beetles.

Kilner RM. Journal of Animal Ecology

Changes in the Gut Microbial Communities Following Addition of Walnuts to the Diet. Byerley, LO. Journal of Nutritional Biochemistry

Microbiome modelling

The Microbiome and Big Data

Navas-Molina JA. Current Opinion in Systems Biology

Plant, soil, and air microbiome

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US.

Kaleita AL.PloS one

Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata

Zhao M. Applied Soil Ecology

Changes in microbial community composition following phytostabilization of an extremely acidic Cu mine tailings

Yang T. Soil Biology and Biochemistry

Effects of between‐site variation in soil microbial communities and plant‐soil feedbacks on the productivity and composition of plant communities.   Bauer JT.Journal of Applied Ecology

Response of soil microbial communities to elevated antimony and arsenic contamination indicates the relationship between the innate microbiota and contaminant fractions. Sun W. Environmental Science and Technology

Marine and inland waters

The contribution of microbial biotechnology to mitigating coral reef degradation Damjanovic. Microbial Biotechnology

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Slaby BM. The ISME Journal

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

He T.  mBio

Built Microbiome

Microbial communities on painted wet and dry external surfaces of a historic fortress in Niterói, Brazil. Ogawa A. Journal of International Biodeterioration & Biodegradation

Preprint

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.Gerth M.PeerJ

July 14, 2017

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Events and jobs

Postdoc, Lieberman Lab

General microbiome

Assembly of Microbial Communities in Replicate Nutrient-Cycling Model Ecosystems Follows Divergent Trajectories, Leading to Alternate Stable States – Eulyn Pagaling – Environmental Microbiology

Human respiratory microbiome

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome – Marion Engel – PLOS ONE

Human gut microbiome

Gut bacterial peptides with autoimmunity potential as environmental trigger for late onset complex diseases: In–silico study – Sapna Negi – PLOS ONE

Impact of environmental microbiota on human microbiota of workers in academic mouse research facilities: An observational study – Peggy S. Lai – PLOS ONE

Reduced Mass and Diversity of the Colonic Microbiome in Patients with Multiple Sclerosis and Their Improvement with Ketogenic Diet – Alexander Swidsinski – Frontiers in Microbiology

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls – Christopher J. Stewart – Microbiome

Other Human microbiome

The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries – Apoena Aguiar Ribeiro – PLOS ONE

The oral fungal mycobiome: characteristics and relation to periodontitis in a pilot study – Brandilyn A. Peters – BMC Microbiology

Animal experiments

Three distinct pneumotypes characterize the microbiome of the lung in BALB/cJ mice – Julia Scheiermann – PLOS ONE

Assessment of gut microbiota populations in lean and obese Zucker rats – Reza Hakkak – PLOS ONE

Preparing the Gut with Antibiotics Enhances Gut Microbiota Reprogramming Efficiency by Promoting Xenomicrobiota Colonization – Shou K. Ji – Frontiers in Microbiology

Animal microbiome

On the core bacterial flora of Ixodes persulcatus (Taiga tick) – Shuo Sui – PLOS ONE

Skin microbiota in frogs from the Brazilian Atlantic Forest: Species, forest type, and potential against pathogens – Ananda Brito de Assis – PLOS ONE

Brackish habitat dictates cultivable Actinobacterial diversity from marine sponges – Gregory A. Ellis – PLOS ONE

Effects of Kluyveromyces marxianus supplementation on immune responses, intestinal structure and microbiota in broiler chickens – Weiwei Wang – PLOS ONE

Dominance-function relationships in the amphibian skin microbiome – Jenifer B. Walke – Environmental Microbiology

Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine keratoconjunctivitis – J.N.Cullen – Veterinary Microbiology

Bacterial community composition in Adélie (Pygoscelis adeliae) and Chinstrap (Pygoscelis antarctica) Penguin stomach contents from Signy Island, South Orkney Islands – W. C. Yew – Polar Biology

Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows – Ilma Tapio – PLOS ONE

Honeybee (Apis mellifera)-associated bacterial community affected by American foulbrood: detection of Paenibacillus larvae via microbiome analysis – Tomas Erban – Scientific Reports

Plant, root, and soil microbiome

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium – Arthur Prudêncio de Araujo Pereira – PLOS ONE

Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth – Heather C. Manching – bioRxiv

Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface – Lily Momper – Environmental Microbiology Reports

Patterns of soil bacterial richness and composition tied to plant richness, soil nitrogen, and soil acidity in alpine tundra – Xia Yuan – Arctic, Antarctic, and Alpine Research

Water and extremophile microbiome

Unravelling riverine microbial communities under wastewater treatment plant effluent discharge in large urban areas – Yang Huo – Applied Microbiology and Biotechnology

Phages and viruses

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans – Felipe H. Coutinho – Nature Communications

Science, publishing, and career

Jonathan Eisen named Faculty Director of the UC Davis Microbiome Initiative

July 7, 2017

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Human Microbiome

Review: Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis – Liu et al. – Digestive and Liver Disease

Non-antibiotic Isotretinoin treatment differentially controls Propionibacterium acnes on skin of acne patients. – Ryan-Kewley et al. – Frontiers in Microbiology

Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy – Namasivayam et al. – Microbiome (BMC)

Research Highlights: Obesity: Gut microbiome and serum metabolome changes – Claire Greenhill – Nature Reviews Endocrinology

Research Highlights:  Gut microbiota: Link between the gut and adipose tissues – Alan Morris – Nature Reviews Endocrinology

Review: The gut microbiome and liver cancer: mechanisms and clinical translation – Yu & Schwabe – Nature Reviews Gastroenterology and Hepatology

 

Pathogens

Reactive Oxygen Species-Dependent Essential Genes in Salmonella Typhimurium – Karash and Min Kwon – BioRxiv

Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes – Wang et al – Scientific Reports (Nature)

Effects of different substrates/growth media on microbial community of saliva-derived biofilm – Li et al – FEMS Microbiology letters

 

Methods (including bioinformatics)

Selective imaging of Gram-negative and Gram-positive microbiotas in the mouse gut – Wang et al. – Biochemistry (ACS)

Methodology: VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data – Ren et al. – Microbiome (BMC)

Methodology: A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform – de Muinck et al. – Microbiome (BMC)

Completing bacterial genome assemblies with multiplex MinION sequencing – Wick et al. – BioRxiv

Axe: rapid, competitive sequence read demultiplexing using a trie – Murray & Borevitz – BioRxiv

 

Water microbiome

Unraveling the microbial interactions and metabolic potentials in pre- and post-treated sludge from a wastewater treatment plant using metagenomic studies – Sidhu et al. – Frontiers in Microbiology

Nutrient dynamics and stream order influence microbial community patterns along a 2914 km transect of the Mississippi River – Henson et al. – BioRxiv

 

Extremophiles

Oxidative weathering and microbial diversity of an inactive seafloor hydrothermal sulfide chimney – Li et al. – Frontiers in Microbiology

Hidden biofilms in a far northern lake and implications for the changing Arctic – Mohit et al. – npj Biofilms and Microbiomes

 

Probiotics – Fermented Food

Amplicon sequencing of the slpH locus permits culture-independent strain typing of Lactobacillus helveticus in dairy products – Moser et al. – Frontiers in Microbiology

Probiotic Enterococcus mundtii Isolate Protects the Model Insect Tribolium castaneum against Bacillus thuringiensis – Grau et al. – Frontiers in Microbiology

 

Animal Microbiome

Regulation of gut luminal serotonin by commensal microbiota in mice –  Hata et al. – PLoS ONE

 

News

News: How Gut Bacteria Tell Their Hosts What to Eat – Knvul Sheikh via Scientific American Mind (Nature)

News: Mind over Meal: Does Weight-Loss Surgery Rewire Gut-Brain Connections? – Bret Stetka via Scientific American Mind (Nature)

 

Fellowships

Post-Doctoral Research Fellow, Microbiome and Vaccine Induced Immunity – Seattle, WA, United States

Postdoctoral Fellow (Listeria monocytogenes research) – Dunedin, New Zealand

 

Other

The earth is flat (p > 0.05): significance thresholds and the crisis of unreplicable research – Amrhein et al. – PeerJ

 

July 6, 2017

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The microbiota of spotted hyenas, a review of potential interactions between olfactory sensation and the microbiome-gut-brain axis, phylogenetic analysis of host-microbe symbioses to examine the evolution of dependence over time.

General microbiome

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia – Sami Ben Said – Frontiers in Microbiology

The evolution of host-symbiont dependence – Roberta M Fisher – Nature Communications

Review: The microbiota revolution: Excitement and caution – Maria Rescigno – European Journal of Immunology

Review: The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure? – Souhaila Al Khodor – Frontiers in Pediatrics

Human oral microbiome

Suppression of αvβ6 Integrin Expression by Polymicrobial Oral Biofilms in Gingival Epithelial Cells – Jiarui Bi – Scientific Reports

Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus – Kai Bao – Scientific Reports

Human vaginal microbiome

Quantifying the human vaginal community state types (CSTs) with the species specificity index – Zhanshan Ma – PeerJ

Animal experiments

Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups – Erica E Alexeev – PLOS ONE

Review: Disruptive physiology: olfaction and the microbiome-gut-brain axis – John Bienenstock – Biological Reviews Cambridge Philosophical Society

Effects of melanin from Sepiella Maindroni ink (MSMI) on the intestinal Microbiome of mice – Hui Dong – BMC Microbiology

Animal microbiome

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition – Emanuel Heitlinger – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Perspective: The deep, hot biosphere: Twenty-five years of retrospection – Daniel R Colman – PNAS

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – Gabriel L Lozano – Genome Announcements

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland – Johanna Birgander – Global Change Biology

Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework – Briana K Whitaker – Ecology Letters

Water and extremophile microbiome

Size and composition of subseafloor microbial community in the Benguela upwelling area examined from intact membrane lipid and DNA analysis – Thomas W Evans – Organic Geochemistry

FurukawaMarine microbes as a valuable resource for brand new industrial biocatalysts – Azadeh Beygmoradi – Biocatalysts and Agricultural Biotechnology

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens) – M Fujimoto – Microbial Ecology

Probiotics/prebiotics

Effects of the probiotic Bifidobacterium animalis subsp. lactis on the non-surgical treatment of periodontitis. A histomorphometric, microtomographic and immunohistochemical study in rats – Milla S T Ricoldi – PLOS ONE

Phages and viruses

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics – Mohammad Moniruzzaman – Nature Communications

Occurrence of Bacillus thuringensis Bacteriophages in the Egyptian Arid Soil – Amel S M Abo-Senna – International Journal of Virology and Molecular Biology

Bioinformatics

A conceptual framework for quality assessment and management of biodiversity data – Allan Koch Veiga – PLOS ONE

Techniques

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures – Joost Willemse – bioRxiv

Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem – Arisa Tsuboi – bioRxiv

More microbes

Review: Metabolic engineering pathways for rare sugars biosynthesis, physiological functionalities, and applications – A review – Muhammad Bilal – Critical Reviews in Food Science and Nutrition

Microbes in the news

Microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman – Medical Xpress

What Cheese Can Tell Us About Antibiotic Resistance – Jason Tetro – Huffington Post Canada

Cases of recurrent Clostridium difficile infection are soaring – Medical Xpress

Helium ions reveal how viruses attack bacteria – ScienceDaily

July 5, 2017

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General microbiome

Letter to the editor: Introducing the sporobiota and sporobiome – George Tetz – Gut Pathogens

Human oral microbiome

Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease – Hai-Yue Liu – Frontiers in Microbiology

Human respiratory microbiome

Review: Respiratory microbiota and lower respiratory tract disease – Miguel Lanaspa – Expert Review of Anti-infective Therapy

Human gut microbiome

Review: Feeding the microbiota: transducer of nutrient signals for the host – Fergus Shanahan – Gut

Animal microbiome

Early Postnatal Diets Affect the Bioregional Small Intestine Microbiome and Ileal Metabolome in Neonatal Pigs – Brian D Piccolo – The Journal of Nutrition

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major) – Lucie Kropáčková – Plos One

Temperature variation, bacterial diversity, and fungal infection dynamics in the amphibian skin – Ana V. Longo – Molecular Ecology

Early-Life Diet Affects Host Microbiota and Later-Life Defenses Against Parasites in Frogs – Sarah A. Knutie – Integrative & Comparitive Biology

Animal experiments

Relative variations of gut microbiota in disordered cholesterol metabolism caused by high-cholesterol diet and host genetics – Tao Bo – Microbiology Open

Plant, root, and soil microbiome

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities – Kelly Gravuer – Frontiers in Microbiology

Long-term rock phosphate fertilization impacts the microbial communities of maize rhizosphere – Ubiana C. Silva – Frontiers in Microbiology

Global change and the soil microbiome: A human-health perspective – Raúl Ochoa-Hueso – Frontiers in Ecology and Evolution

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms – Adam Št’ovíček – Frontiers in Microbiology

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand – Jocelyn C. Griffith – Plos One

Water and extremophile microbiome

Bacterial diversity and population shifts driven by spotlight wastewater micropollutants in low-temperature highly nitrifying activated sludge – Antonina Kruglova – JScience of The Total Environment

Probiotics / prebiotics

The potential synergistic behaviour of inter- and intra-genus probiotic combinations in the pattern and rate of short chain fatty acids formation during fibre fermentation – Warnakulasuriya M. A. D. B. Fernando – International Journal of Food Sciences and Nutrition

Review: Structural features underlying prebiotic activity of conventional and potential prebiotic oligosaccharides in food and health – Subin R. C. K. Rajendran – Journal of Food Biochemistry

Phages and viruses

Case control comparison of enteric viromes in captive rhesus macaques with acute or idiopathic chronic diarrhea – Beatrix Kapusinszky – Journal of Virology

A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections – Samuele Bovo – Plos One

Bioinformatics

Does colorectal cancer significantly influence the assembly of gut microbial communities? – Lin Dai – PeerJ

Review: Using metagenomics to investigate human and environmental resistomes – Johan Bengtsson-Palme – Journal of Antimicrobial Chemotherapy

RRmix: A method for simultaneous batch effect correction and analysis of metabolomics data in the absence of internal standards – Stephen Salerno Jr – Plos One

Predicting the ecological quality status of marine environments from eDNA metabarcoding data using supervised machine learning – Tristan Cordier – Environmental Science and Technology

Anitha’s non-microbiology picks

AI is changing how we do science. Get a glimpse

Scientists explain ancient Rome’s long-lasting concrete

July 3, 2017

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Pregnancy and early life
Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission – Sabrina Duranti –  Microbiome

 
Mini Review: The microbiome and disorders of the central nervous system – Valeria D. Felice – Pharmacology Biochemistry and Behavior

 
Human respiratory microbiome

 
Short Report: The metabolic footprint of the airway bacterial community in cystic fibrosis – Vaishnavi Narayanamurthy – Microbiome

 
Human gut microbiome

 
Gut microbial transformation of the dietary imidazoquinoxaline mutagen MeIQx reduces its cytotoxic and mutagenic potency – Jianbo Zhang –  Toxicological Science

 
Review: Practical considerations for large-scale gut microbiome studies – Doris Vandeputte – FEMS Microbiology Reviews

 
Association of altered gut microbiota composition with chronic urticaria – Edris Nabizadeh – Annals of Allergy, Asthma & Immunology

 
Animal microbiome 

 
A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria – Nathan J. Winans –  Molecular Ecology

 
The Gut Bacterial Community Composition of Wild Cervus albirostris (White-Lipped Deer) Detected by the 16S Ribosomal RNA Gene Sequencing – Jun-gang Li –  Current Microbiology

 
Microbial influence on Drosophila biology – ME Martino – Current Opinion in Microbiology

 
Plant, root, and soil microbiome

 
Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain – Arvind Kumar –  Biotech

 

Water and extremophile microbiome

 
Spatiotemporal Dynamics of the Bacterial Microbiota on Lacustrine Cladophora glomerata (Chlorophyta) – Michael J. Braus –  bioRxiv

 
Quantity and quality of particulate organic matter controls bacterial production in the Columbia River estuary – Byron C. Crump – Limnology and Oceanography

 
Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa – Marta Cobo-Simón –  BMC Genomics

 
Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing – Natàlia Corcoll – FEMS Microbiology Letters

 
Food microbiology

 

Cleaning and disinfection of biofilms composed of Listeria monocytogenes and background microbiota from meat processing surfaces – Annette Fagerlund – Applied and Environmental Microbiology

 

Probiotics / prebiotics

 
A human gut commensal ferments cranberry carbohydrates to produce formate – Ezgi Özcan – Applied and Environmental Microbiology

 
Review: Lifestyles in transition: evolution and natural history of the genus Lactobacillus – Rebbeca M. Duar – FEMS Microbiology Reviews

 
Phages and viruses

 
Synergistic elimination of bacteria by phage and the innate immune system – Chung Yin (Joey) Leung – Journal of Theoretical Biology

 
Biotechnology

 
Effect of zinc oxide nanoparticles on nitrogen removal, microbial activity and microbial community of CANON process in a membrane bioreactor – Xiaojing Zhang – Bioresource Technology

 
Microbes in the news

 
A new approach to tackling drug-resistant bacteria

New technology to cool the body: make the clothes made of microorganisms

 
Microbes on the market (news about biotech companies)

 
New Belgian Biotech will use Microorganisms to Replace Pesticides and Fertilizers

July 1, 2017

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General microbiome

The microbiome in hematopoietic stem cell transplant recipients and cancer patients: Opportunities for clinical advances that reduce infection – AY Koh – PLoS Pathogens

Research Highlight: New insights into the BAT–liver–gut axis – A Morris – Nature Reviews

Biodiversity and ecosystem function: making sense of numerous species interactions in multi-species communities – C Brophy – Ecology

Obstruction of pilus retraction stimulates bacterial surface sensing – CK Ellison – bioRxiv

 

Human gut microbiome

Hospital association of the gut microbiota mobilome in preterm infants – A Ravi – Pediatric Research

 

Human respiratory microbiome

Maturation of the Infant Respiratory Microbiota, Environmental Drivers and Health Consequences: A Prospective Cohort Study – AATM Bosch – Am J Respir Crit Care Med.

Review: Perna canaliculus and the Intestinal Microbiome – ET Saltzman – Marine Drugs

 

 

Animal microbiome

Host-specific associations affect the microbiome of Philornis downsi, an introduced parasite to the Galápagos Islands – MY Ben – Molecular Ecology

Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus – JA Yang – Journal of Microbiology

 

Plant, root and soil microbiome

Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient – S Pierre – Ecology

Bacterial periphytic communities related to mercury methylation within aquatic plant roots from a temperate freshwater lake (South-Western France) – S Gentès – Environ Sci Pollut Res Int.

Consistently inconsistent drivers of microbial diversity and abundance at macroecological scales – JN Hendershot – Ecology

Living cover crops have immediate impacts on soil microbial community structure and function – DM Finney – Journal of Soil and Water Conservation

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – GL Lozano – Genome Announcements

Colonization and Maize Growth Promotion Induced by Phosphate Solubilizing Bacterial Isolates – Y Li – International Journal of Molecular Sciences

Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils – S Jiao – Molecular Ecology

 

Water microbiome and extremophiles

Organohalide respiration with chlorinated ethenes under low pH conditions – Y Yang – Environmental Science & Technology

 

Microbes in news

These Cleaning Bots Can Zap Bacteria Out of Your Water Supply in Minutes – D Nield – Science Alert

Four strains of bacteria work together to produce pigment for food and cosmetics industry – ML Martialay – Phys.org

Texas: Fecal bacteria levels at Gulf beaches ahead of Fourth of July holiday weekend – K Bradshaw – mySA

Gut microbiome’s link to the brain – S Downing – Nine.com

Breast Milk Bacteria are Important for Establishing Infant Gut Microbiome – S Parmar – Medical News Bulletin

Fig Enzyme could Help to fight Infection and Heal Wounds – DN Gameiro – Labiotech.eu

Gut Health: The Next Mega-Trend in Health and Wellness – H Schieber – Researchci

I spent three days as a hunter-gatherer to see if it would improve my gut health – T Spector – Medical Xpress

Altering gut bacteria pathways may stimulate fat tissue to prevent obesity – Medical Xpress

The broiler chicken intestine – an apt target for proteomic studies – E O’Reilly – BMC Blog Network

June 30, 2017

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A few gut microbiome reviews, apparently a simple bacterial community in bullet ants, circadian rhythm of rhizosphere bacterial communities, and you might want to think twice before you step into the ocean for a swim this summer.

General microbiology

Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities – Tahir Yusufaly & James Q. Boedicker – ePub in Physical Biology, first in arXiv

Cheating fosters species co-existence in well-mixed bacterial communities – Anne Leinweber, R Fredrik Inglis and Rolf Kümmerli – ISME Journal

One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas – Rosaria Campilongo et al. – PLoS Genetics

PrePrint: Statistics and simulation of growth of single bacterial cells: illustrations with B. subtilis and E. coli – Johan H. van Heerden et al. – bioRxiv

Performance of electro-spun carbon nanofiber electrodes with conductive poly(3,4-ethylenedioxythiophene) coatings in bioelectrochemical systems – Juan J.L. Guzmana & Meryem O. Pehlivaner Kara et al. – Journal of Power Sources

Press: Bacteria-coated nanofiber electrodes digest pollutants – Blaine Friedlander – Phys.org

Human skin microbiome

Review: Keratinocytes as sensors and central players in the immune defense against Staphylococcus aureus in the skin – Katharina Bitschar et al. – Journal of Dermatological Science

Human gut microbiome

Review: The nutrition-gut microbiome-physiology axis and allergic diseases – Craig McKenzie – Immunological Reviews

16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease – Ashton JJ et al. – Medicine (Baltimore)

Review: The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology – Nathan T. Porter and Eric C. Martens – Annual Reviews of Microbiology

Review: Gut Microbiota as a Target for Preventive and Therapeutic Intervention against Food Allergy – Rosita Aitoro et al. – Nutrients

Two distinct metacommunities characterize the gut microbiota in Crohn’s disease patients – Qing He & Yuan Gao et al. – GigaScience

Animal experiments

PrePrint: Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut microbiomes – Matthew L Jenior et al. – bioRxiv

Animal microbiome

PrePrint: Bacterial community profiles and Vibrio parahaemolyticus abundance in individual oysters and their association with estuarine ecology – Ashley L. Marcinkiewicz et al. – bioRxiv

Diversity and Persistence of the Gut Microbiome of the Giant Neotropical Bullet Ant – Corrie S. Moreau & Benjamin E. R. Rubin – Integrative and Comparative Biology

PrePrint: Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens – Yin Wang & Daniel Rozen – bioRxiv

Plant, root and soil microbiome

Effects of habitat constraints on soil microbial community function – Naoise Nunan et al. – Scientific Reports

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism – Christopher Staley et al. – Microbiome

Biological control of Pythium, Rhizoctonia and Sclerotinia in lettuce: the plant protective activity of the bacterium Paenibacillus alvei K165 is associated with the induction of systemic resistance – G. Fatouros et al. – Plant Pathology

Water and extremophile microbiome

Membrane biofilm communities in full-scale membrane bioreactors are not randomly assembled and consist of a core microbiome – Gerald K. Matar & Samik Bagchi et al. – Water Research

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica – Hyunmin Koo et al. – Journal of Microbiological Methods

Built environment

Hospital Building and Healthcare Associated Infections (HAIs) in terms of total contamination data and cases grouped by department/areas – Shadha M. Abbas Al Asadi – Scientific Journal of Medical Research

Microbes in the news

The Bugs That Keep Us Safe – Maria-Luisa Alegre – American Journal of Transplantation

Study on human skin microbiome finds archaea abundance associated with age – Phys.org

The Dust Storm Microbiome – Weismann Institute of Science – Laboratory Equipment

Starbucks’ iced coffee may have fecal bacteria in it — so do all these other things – Donovan Harrell – Miami Herald (BBC investigation)

Bacteria change a liquid’s properties and escape entrapment – Gail Mccormick – Phys.org

Only association: Gut feelings are real: Some people have stomach bacteria that makes them more anxious and stressed, study shows – DailyMail

Elevated bacteria counts found at 4 Island beaches – Rick Kelley – Valley Morning Star

Plasmids: traffickers of antibiotic resistance – Modernising Medical Microbiology – University of Oxford

Microbes on the market

Diabetes: J&J and Seventure Partners launch investment – tg – European Biotechnology

Global Microbiome Drugs Market 2017- Pfizer, Second Genome , Seres Therapeutics, MaaT Pharma, Enterome Bioscience – Nakul Shirke – Daily Hover

June 28, 2017

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Human vaginal microbiome

Vaginal seeding or vaginal microbial transfer from the mother to the cesarean born neonate: a commentary regarding clinical management – Thor Haahr – BJOG

Human gut microbiome

*Review: The resilience of the intestinal microbiota influences health and disease – Felix Sommer – Nature Reviews Microbiology

Other human microbiome

Urinary catheter-associated microbiota change in accordance with treatment and infection status – Laetitia Bossa – PLOS ONE

Dynamics of the Oral Microbiota as a Tool to Estimate Time Since Death – Joe Adserias Garriga – Molecular Oral Microbiology

Animal experiments

Tuftsin-Phosphorylcholine maintains normal gut microbiota in collagen induced arthritic mice – Hila Ben-Amram – Frontiers in Microbiology

Animal microbiome

The Diet and Gut Microbial Communities of Two Closely Related Combtooth Blennies, Chasmodes saburrae and Scartella cristata – Peter J. Hundt – Copeia

Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom” – Alistair R. Legione – bioRxiv

Plant, root, and soil microbiome

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome – Luhua Yang – Frontiers in Plant Science

Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing – Honghong Guo – Ecotoxicology and Environmental Safety

Root Hair Mutations Displace the Barley Rhizosphere Microbiota – Senga Robertson-Albertyn – Frontiers in Plant Science

*Review: Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere – Franciska T. de Vries – Journal of Ecology

Rhizosphere microorganisms affected by soil solarization and cover cropping in Capsicum annuum and Phaseolus lunatus agroecosystems – Nancy Kokalis-Burelle – Applied Soil Ecology

Bacterial community dynamics in the rhizosphere of a long-lived, leguminous shrub across a 40-year age sequence – Xiaofan Na – Journal of Soils and Sediments

Microbial populations of stony meteorites: Substrate controls on first colonisers – Alastair W. Tait – Frontiers in Microbiology

Water and extremophile microbiome

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage – Wenkai Teng – Minerals

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer – Donald Pan – Frontiers in Microbiology

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat – Jackson Z Lee – bioRxiv

Bioinformatics

Mixed Effect Dirichlet-Tree Multinomial for Longitudinal Microbiome Data and Weight Prediction – Yunfan Tang – arXiv

Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project – James B. Pettengill – PeerJ

Techniques

Assembly and Tracking of Microbial Community Development within a Microwell Array Platform – Andrea C. Timm – JOVE